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@Article{ijms252212430,
AUTHOR = {Akhtar, Parveen and van Stokkum, Ivo H. M. and Lambrev, Petar H.},
TITLE = {The Quenching of Long-Wavelength Fluorescence by the Closed Reaction Center in Photosystem I in Thermostichus vulcanus at 77 K},
JOURNAL = {International Journal of Molecular Sciences},
VOLUME = {25},
YEAR = {2024},
NUMBER = {22},
ARTICLE-NUMBER = {12430},
URL = {https://www.mdpi.com/1422-0067/25/22/12430},
PubMedID = {39596495},
ISSN = {1422-0067},
ABSTRACT = {Photosystem I in most organisms contains long-wavelength or “Red” chlorophylls (Chls) absorbing light beyond 700 nm. At cryogenic temperatures, the Red Chls become quasi-traps for excitations as uphill energy transfer is blocked. One pathway for de-excitation of the Red Chls is via transfer to the oxidized RC (P700+), which has broad absorption in the near-infrared region. This study investigates the excitation dynamics of Red Chls in Photosystem I from the cyanobacterium Thermostichus vulcanus at cryogenic temperatures (77 K) and examines the role of the oxidized RC in modulating their fluorescence kinetics. Using time-resolved fluorescence spectroscopy, the kinetics of Red Chls were recorded for samples with open (neutral P700) and closed (P700+) RCs. We found that emission lifetimes in the range of 710–720 nm remained unaffected by the RC state, while more red-shifted emissions (>730 nm) decayed significantly faster when the RC was closed. A kinetic model describing the quenching by the oxidized RC was constructed based on simultaneous fitting to the recorded fluorescence emission in Photosystem I with open and closed RCs. The analysis resolved multiple Red Chl forms and variable quenching efficiencies correlated with their spectral properties. Only the most red-shifted Chls, with emission beyond 730 nm, are efficiently quenched by P700+, with rate constants of up to 6 ns−1. The modeling results support the notion that structural and energetic disorder in Photosystem I can have a comparable or larger effect on the excitation dynamics than the geometric arrangement of Chls.},
DOI = {10.3390/ijms252212430}
}
@article{doi:10.1021/jacs.4c06695,
author = {Liguori, Nicoletta and van Stokkum, Ivo H.M. and Muzzopappa, Fernando and Kennis, John T. M. and Kirilovsky, Diana and Croce, Roberta},
title = {The Orange Carotenoid Protein Triggers Cyanobacterial Photoprotection by Quenching Bilins via a Structural Switch of Its Carotenoid},
journal = {Journal of the American Chemical Society},
volume = {146},
number = {31},
pages = {21913-21921},
year = {2024},
doi = {10.1021/jacs.4c06695},
note ={PMID: 39058977},
URL = {
https://doi.org/10.1021/jacs.4c06695
},
eprint = {
https://doi.org/10.1021/jacs.4c06695
}
}
@article{https://doi.org/10.1111/ppl.14306,
author = {Nanda, Sanchali and Shutova, Tatyana and Cainzos, Maximiliano and Hu, Chen and Sasbrink, Bart and Bag, Pushan and
Blanken, Tristan den and Buijs, Ronald and Gracht, Lex van der and Hendriks, Frans and Lambrev, Petar and Limburg, Rob and Mascoli, Vincenzo and Nawrocki, Wojciech J and Reus, Michael and Parmessar, Ramon and Singerling, Björn and
Stokkum, Ivo H M and Jansson, Stefan and Holzwarth, Alfred R.},
title = {A new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection},
journal = {Physiologia Plantarum},
volume = {176},
number = {2},
pages = {e14306},
doi = {https://doi.org/10.1111/ppl.14306},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14306},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14306},
abstract = {Abstract Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.},
year = {2024}
}
@article{doi:10.1021/acs.jpclett.4c01555,
author = {van Stokkum, Ivo H.M. and Snellenburg, Joris J. and Chrupkov{\'{a}}, Petra and Dostal, Jakub and Weigand, Sebastian and Wei{\ss}enborn, J{\"o}rn and Kennis, John T.M. and Kloz, Miroslav},
title = {Target Analysis Resolves the Ground and Excited State Properties from Femtosecond Stimulated Raman Spectra},
journal = {The Journal of Physical Chemistry Letters},
volume = {15},
number = {0},
pages = {9397-9404},
year = {2024},
doi = {10.1021/acs.jpclett.4c01555},
note ={PMID: 39241188},
URL = { https://doi.org/10.1021/acs.jpclett.4c01555},
eprint = { https://doi.org/10.1021/acs.jpclett.4c01555}
}
@article{CHRUPKOVA2024168625,
title = {Raman Vibrational Signatures of Excited States of Echinenone in the Orange Carotenoid Protein (OCP) and Implications for its Photoactivation Mechanism},
journal = {Journal of Molecular Biology},
volume = {436},
number = {16},
pages = {168625},
year = {2024},
issn = {0022-2836},
doi = {https://doi.org/10.1016/j.jmb.2024.168625},
url = {https://www.sciencedirect.com/science/article/pii/S0022283624002201},
author = {Petra Chrupkov{\'{a}} and Ivo H.M. {van Stokkum} and Thomas Friedrich and Marcus Moldenhauer and Nediljko Budisa and Hsueh-Wei Tseng and Tom{\'{a}}s Pol{\'{i}}vka and
Dmitry A. Cherepanov and Eugene G. Maksimov and Miroslav Kloz},
keywords = {OCP, Raman, spectroscopy, ultrafast, echinenone},
abstract = {In this study, the vibrational characteristics of optically excited echinenone in various solvents and the Orange Carotenoid Protein (OCP) in red and orange states are systematically investigated through steady-state and time-resolved spectroscopy techniques. Time-resolved experiments, employing both Transient Absorption (TA) and Femtosecond Stimulated Raman Spectroscopy (FSRS), reveal different states in the OCP photoactivation process. The time-resolved studies indicate vibrational signatures of exited states positioned above the S1 state during the initial 140 fs of carotenoid evolution in OCP, an absence of a vibrational signature for the relaxed S1 state of echinenone in OCP, and more robust signatures of a highly excited ground state (GS) in OCP. Differences in S1 state vibration population signatures between OCP and solvents are attributed to distinct conformations of echinenone in OCP and hydrogen bonds at the keto group forming a short-lived intramolecular charge transfer (ICT) state. The vibrational dynamics of the hot GS in OCP show a more pronounced red shift of ground state CC vibration compared to echinenone in solvents, thus suggesting an unusually hot form of GS. The study proposes a hypothesis for the photoactivation mechanism of OCP, emphasizing the high level of vibrational excitation in longitudinal stretching modes as a driving force. In conclusion, the comparison of vibrational signatures reveals unique dynamics of energy dissipation in OCP, providing insights into the photoactivation mechanism and highlighting the impact of the protein environment on carotenoid behavior. The study underscores the importance of vibrational analysis in understanding the intricate processes involved in early phase OCP photoactivation.}
}
@Article{ijms25074125,
AUTHOR = {van Stokkum, Ivo H. M. and M{\"u}ller, Marc G. and Holzwarth, Alfred R.},
TITLE = {Energy Transfer and Radical-Pair Dynamics in Photosystem I with Different Red Chlorophyll a Pigments},
JOURNAL = {International Journal of Molecular Sciences},
VOLUME = {25},
YEAR = {2024},
NUMBER = {7},
ARTICLE-NUMBER = {4125},
URL = {https://www.mdpi.com/1422-0067/25/7/4125},
PubMedID = {38612934},
ISSN = {1422-0067},
ABSTRACT = {We establish a general kinetic scheme for the energy transfer and radical-pair dynamics in photosystem I (PSI) of Chlamydomonas reinhardtii, Synechocystis PCC6803, Thermosynechococcus elongatus and Spirulina platensis grown under white-light conditions. With the help of simultaneous target analysis of transient-absorption data sets measured with two selective excitations, we resolved the spectral and kinetic properties of the different species present in PSI. WL-PSI can be described as a Bulk Chl a in equilibrium with a higher-energy Chl a, one or two Red Chl a and a reaction-center compartment (WL-RC). Three radical pairs (RPs) have been resolved with very similar properties in the four model organisms. The charge separation is virtually irreversible with a rate of ≈900 ns−1. The second rate, of RP1 → RP2, ranges from 70–90 ns−1 and the third rate, of RP2 → RP3, is ≈30 ns−1. Since RP1 and the Red Chl a are simultaneously present, resolving the RP1 properties is challenging. In Chlamydomonas reinhardtii, the excited WL-RC and Bulk Chl a compartments equilibrate with a lifetime of ≈0.28 ps, whereas the Red and the Bulk Chl a compartments equilibrate with a lifetime of ≈2.65 ps. We present a description of the thermodynamic properties of the model organisms at room temperature.},
DOI = {10.3390/ijms25074125}
}
@article{
doi:10.1073/pnas.2318996121,
author = {Spyridon Kaziannis and Matthias Broser and Ivo H. M. van Stokkum and Jakub Dostal and Wayne Busse and Arno Munhoven and Cesar Bernardo and Miroslav Kloz and Peter Hegemann and John T. M. Kennis },
title = {Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction},
journal = {Proceedings of the National Academy of Sciences},
volume = {121},
number = {12},
pages = {e2318996121},
year = {2024},
doi = {10.1073/pnas.2318996121},
URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2318996121},
eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2318996121},
abstract = {The far-red absorbing rhodopsin modules (λmax = 661 nm) of bestrhodopsin are of high interest for a principle understanding of the photophysics and photochemistry of unusually far-red absorbing rhodopsins and optogenetic application in tissues that are more transparent to red light in comparison to blue or green light. Moreover, the identified light-induced isomeric switching processes on the ground state potential energy surface disclose a multi-isomerization activation mechanism that has so far remained unknown for rhodopsin. Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.}}
@ARTICLE{10.3389/fpls.2023.1300532,
AUTHOR={Biswas, Avratanu and Akhtar, Parveen and Lambrev, Petar H. and van Stokkum, Ivo H.M. },
TITLE={Energy transfer from phycobilisomes to photosystem I at room temperature},
JOURNAL={Frontiers in Plant Science},
VOLUME={14},
YEAR={2024},
URL={https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1300532},
DOI={10.3389/fpls.2023.1300532},
ISSN={1664-462X},
ABSTRACT={The phycobilisomes function as the primary light-harvesting antennae in cyanobacteria and red algae, effectively harvesting and transferring excitation energy to both photosystems. Here we investigate the direct energy transfer route from the phycobilisomes to photosystem I at room temperature in a mutant of the cyanobacterium Synechocystis sp. PCC 6803 that lacks photosystem II. The excitation dynamics are studied by picosecond time-resolved fluorescence measurements in combination with global and target analysis. Global analysis revealed several fast equilibration time scales and a decay of the equilibrated system with a time constant of ≈220 ps. From simultaneous target analysis of measurements with two different excitations of 400 nm (chlorophyll a) and 580 nm (phycobilisomes) a transfer rate of 42 ns-1 from the terminal emitter of the phycobilisome to photosystem I was estimated.
}}
@ARTICLE{10.3389/fpls.2023.1293813,
AUTHOR={van Stokkum, Ivo H. M. and Akhtar, Parveen and Biswas, Avratanu and Lambrev, Petar H. },
TITLE={Energy transfer from phycobilisomes to photosystem I at 77 K},
JOURNAL={Frontiers in Plant Science},
VOLUME={14},
YEAR={2023},
URL={https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1293813},
DOI={10.3389/fpls.2023.1293813},
ISSN={1664-462X},
ABSTRACT={Phycobilisomes serve as a light-harvesting antenna of both photosystem I (PSI) and II (PSII) in cyanobacteria, yet direct energy transfer from phycobilisomes to PSI is not well documented. Here we recorded picosecond time-resolved fluorescence at wavelengths of 605–760 nm in isolated photosystem I (PSI), phycobilisomes and intact cells of a PSII-deficient mutant of Synechocystis sp. PCC 6803 at 77 K to study excitation energy transfer and trapping. By means of a simultaneous target analysis of the kinetics of isolated complexes and whole cells, the pathways and dynamics of energy transfer in vitro and in vivo were established. We establish that the timescale of the slowest equilibration between different terminal emitters in the phycobilisome is ≈800 ps. It was estimated that the terminal emitter in about 40% of the phycobilisomes transfers its energy with a rate constant of 42 ns−1 to PSI. This energy transfer rate is higher than the rates of equilibration within the phycobilisome – between the rods and the core or between the core cylinders – and is evidence for the existence of specific phycobilisome-PSI interactions. The rest of the phycobilisomes remain unconnected or slowly transferring energy to PSI.
}}
@article{VANSTOKKUM2023107650,
title = {Energy transfer and trapping in photosystem {I} with and without chlorophyll-f},
journal = {iScience},
volume = {26},
number = {9},
pages = {107650},
year = {2023},
issn = {2589-0042},
doi = {https://doi.org/10.1016/j.isci.2023.107650},
url = {https://www.sciencedirect.com/science/article/pii/S2589004223017273},
author = {Ivo H.M. {van Stokkum} and Marc G. M{\"u}ller and J{\"o}rn Wei{\ss}enborn and Sebastian Weigand and Joris J. Snellenburg and Alfred R. Holzwarth},
keywords = {Chemistry, Biochemistry, Theoretical chemistry, Theoretical photochemistry, Biophysics},
abstract = {Summary
We establish a general kinetic scheme for energy transfer and trapping in the photosystem I (PSI) of cyanobacteria grown under white light (WL) or far-red light (FRL) conditions. With the help of simultaneous target analysis of all emission and transient absorption datasets measured in five cyanobacterial strains, we resolved the spectral and kinetic properties of the different species present in PSI. WL-PSI can be described by Bulk Chl a, two Red Chl a, and a reaction center compartment (WL-RC). The FRL-PSI contains two additional Chl f compartments. The lowest excited state of the FRL-RC is downshifted by{\approx} 29 nm. The rate of charge separation drops from{\approx}900 ns{\textsuperscript{-1}} in WL-RC to{\approx}300 ns{\textsuperscript{-1}} in FRL-RC. The delayed trapping in the FRL-PSI ({\approx}130 ps) is explained by uphill energy transfer from the Chl f compartments with Gibbs free energies of {\approx}kBT below that of the FRL-RC.}
}
@article{VANSTOKKUM2023Pyglotaran,
title = {Pyglotaran: a lego-like Python framework for global and target analysis of time resolved spectra},
journal = {Photochemical & Photobiological Sciences},
volume = {},
number = {},
pages = {},
year = {2023},
issn = {2589-0042},
doi = {https://doi.org/10.1007/s43630-023-00460-y},
author = {Ivo H.M. {van Stokkum} and J{\"o}rn Wei{\ss}enborn and Sebastian Weigand and Joris J. Snellenburg}
}
@article{doi:10.1021/acs.jpclett.2c03110,
author = {van Stokkum, Ivo H.M. and Hontani, Yusaku and Vierock, Johannes and Krause, Benjamin S. and Hegemann, Peter and Kennis, John T.M.},
title = {Reaction Dynamics in the Chrimson Channelrhodopsin: Observation of Product-State Evolution and Slow Diffusive Protein Motions},
journal = {The Journal of Physical Chemistry Letters},
volume = {14},
number = {6},
pages = {1485-1493},
year = {2023},
doi = {10.1021/acs.jpclett.2c03110},
note ={PMID: 36745035},
URL = {
https://doi.org/10.1021/acs.jpclett.2c03110
},
eprint = {
https://doi.org/10.1021/acs.jpclett.2c03110
}
}
@article{10.1093/plphys/kiac175,
author = {Arshad, Rameez and Saccon, Francesco and Bag, Pushan and Biswas, Avratanu and Calvaruso, Claudio and Bhatti, Ahmad Farhan and Grebe, Steffen and Mascoli, Vincenzo and
Mahbub, Moontaha and Muzzopappa, Fernando and Polyzois, Alexandros and Schiphorst, Christo and Sorrentino, Mirella and Streckait{\'{e}}, Simona and van Amerongen, Herbert and Aro, Eva-Mari and Bassi, Roberto and Boekema, Egbert J and Croce, Roberta and Dekker, Jan and van Grondelle, Rienk and Jansson, Stefan and Kirilovsky, Diana and Kou{{\v{r}}}il, Roman and Michel, Sylvie and Mullineaux, Conrad W and Panzarov{\'{a}}, Kl{\'{a}}ra and Robert, Bruno and Ruban, Alexander V and van Stokkum, Ivo and Wientjes, Emilie and B{\"u}chel, Claudia},
title = "{A kaleidoscope of photosynthetic antenna proteins and their emerging roles}",
journal = {Plant Physiology},
volume = {189},
number = {3},
pages = {1204-1219},
year = {2022},
month = {04},
abstract = "{Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.}",
issn = {0032-0889},
doi = {10.1093/plphys/kiac175},
url = {https://doi.org/10.1093/plphys/kiac175},
eprint = {https://academic.oup.com/plphys/article-pdf/189/3/1204/44267427/kiac175.pdf},
}
@article{VANSTOKKUM2022100154,
title = {Energy transfer in supramolecular calix[4]arene-Perylene bisimide dye light harvesting building blocks: Resolving loss processes with simultaneous target analysis},
journal = {Journal of Photochemistry and Photobiology},
volume = {12},
pages = {100154},
year = {2022},
issn = {2666-4690},
doi = {https://doi.org/10.1016/j.jpap.2022.100154},
url = {https://www.sciencedirect.com/science/article/pii/S2666469022000471},
author = {Ivo H.M. {van Stokkum} and Catharina Wohlmuth and Frank W{\"u}rthner and Ren{\'{e}} M. Williams},
keywords = {Transient absorption spectroscopy, Fluorescence resonance energy transfer, Photoinduced electron transfer, Species associated difference spectrum, Excitonic interaction},
abstract = {By the application of simultaneous target analysis of multiple femtosecond transient absorption data sets we have identified two loss channels within multi-chromophoric light harvesting arrays. Perylene bisimide-calix[4]arene arrays composed of up to three different types of perylene bisimide (PBI) chromophores, orange (o), red (r), and green (g) PBIs (named after their colors as solids), have previously been studied by transient absorption spectroscopy (Hippius et al., J. Phys. Chem C 112:2476, 2008) and here we present a simultaneous target analysis of those data matrices. A covalent system containing the red chromophore (r) and calix[4]arene (c), the rc system, shows extensive spectral evolution that can be described with four excited states (r1*→r2*→r3*→r4*→ground state). In the Perylene Orange calix[4]arene system (oc), a radical pair (ocRP) can be formed by photoinduced electron transfer (Hippius et al., J. Phys. Chem C 111:13988, 2007). In a simultaneous target analysis of the multichromophoric systems ocr, rcocr and ocrco the properties of rc and oc are integrated, and excitation energy transfer (EET) from o* to r* occurs. In addition, we demonstrate that the final Species Associated Difference Spectrum (SADS) also contains o bleach features that indicate an excitonic interaction, for ocr, rcocr and ocrco. In a simultaneous target analysis of rcg and gcrcg the properties of rc are integrated, and next to EET to g* we can resolve the formation of a new rcgRP that is formed from r1* or r2*, and represents a loss of 7 and 12%, respectively. In a simultaneous target analysis of ocrcg the properties of ocr and rcg are integrated, arriving at a consistent picture with an energy transfer quantum yield of formation of the excited state of the green PBI (g*) of 80%.}
}
@Article{D2CP02073D,
author ="Teles-Ferreira, Danielle Cristina and van Stokkum, Ivo HM and Conti, Irene and Ganzer, Lucia and Manzoni, Cristian and Garavelli, Marco and Cerullo, Giulio and Nenov, Artur and Borrego-Varillas, Roc{\'i}o and de Paula, Ana Maria",
title ="Coherent vibrational modes promote the ultrafast internal conversion and intersystem crossing in thiobases",
journal ="Phys. Chem. Chem. Phys.",
year ="2022",
volume ="24",
issue ="36",
pages ="21750-21758",
publisher ="The Royal Society of Chemistry",
doi ="10.1039/D2CP02073D",
url ="http://dx.doi.org/10.1039/D2CP02073D",
abstract ="Thionated nucleobases are obtained by replacing oxygen with sulphur atoms in the canonical nucleobases. They absorb light efficiently in the near-ultraviolet{,} populating singlet states which undergo intersystem crossing to the triplet manifold on an ultrashort time scale with a high quantum yield. Nonetheless there are still important open questions about the primary mechanisms responsible for this ultrafast transition. Here we track both the electronic and the vibrational ultrafast excited-state dynamics towards the triplet state for solvated 4-thiothymidine (4TT) and 4-thiouracil (4TU) with sub-30 fs broadband transient absorption spectroscopy in the ultraviolet. A global and target analysis allows us to simultaneously resolve the contributions of the different electronically and vibrationally excited states to the whole data set. Our experimental results{,} combined with state-of-the-art quantum mechanics/molecular mechanics simulations and Damped Oscillation Associated Spectra (DOAS) and target analysis{,} support that the relaxation to the triplet state is mediated by conical intersections promoted by vibrational coherences through the population of an intermediate singlet state. In addition{,} the analysis of the coherent vibrational dynamics reveals that{,} despite sharing the same relaxation mechanism and similar chemical structures{,} 4TT and 4TU exhibit rather different geometrical deformations{,} characterized by the conservation of planarity in 4TU and its partial rupture in 4TT."}
@article{Mooij_2022,
doi = {10.1088/2040-8986/ac6207},
url = {https://doi.org/10.1088/2040-8986/ac6207},
year = 2022,
volume = {24},
number = {6},
pages = {064007},
month = {mar},
publisher = {{IOP} Publishing},
author = {Bram J. A. Mooij and Ivo H. M. van Stokkum and Gareth R. Davies and Freek Ariese},
title = {Distinguishing bacteria from minerals in a layered sample using time-resolved Raman spectroscopy and global analysis},
journal = {Journal of Optics},
abstract = {Mars is one of the prime candidates in the search for extraterrestrial life. At the most comparable terrestrial Martian analogue sites, life often occurs in endolithic form; i.e. hiding below the surface. To detect biomarkers of endolithic life, the two most promising options are drilling or measuring through the surface, the latter being less invasive and preferable. Raman spectroscopy is an established chemical identification method, and advanced Raman modes have been developed for sub-surface analysis. Time-resolved Raman spectroscopy (TRRS), based on picosecond pulsed excitation and a gated intensified charge-coupled device (ICCD) detector, adds the capability of fluorescence suppression and depth selection. This paper focuses on the separation of layers with time differences that are much smaller than the full width at half-maximum gating time of the detector. As an analogue for endolithic life on Mars, Deinococcus radiodurans bacteria were measured through a and top layer of translucent calcite. TRRS spectra were recorded in a backscattering geometry, while stepwise increasing the detector delay in steps. Through both of these layers, the Raman spectrum of the bacteria�s carotenoids could be detected. Global analysis was used to model a complete time-resolved spectrum of the sample. Using this analysis, the signals could be separated into three components: mineral Raman, bacterial Raman and bacterial fluorescence. The model also corrects for gating differences across the horizontal axis of the ICCD camera. With this approach well-separated Raman spectra were obtained even for the calcite layer despite the temporal separation of approximately , which is much shorter than the detector gating time. TRRS could be a suitable approach for non-invasive detection of extraterrestrial subsurface biomarkers.}
}
@article{JCP2021,
author = {van Stokkum,Ivo H. M. and Kloz,Miroslav and Polli,Dario and Viola,Daniele and Wei{\ss}enborn,J{\"{o}}rn and Peerbooms,Ebo and Cerullo,Giulio and Kennis,John T. M. },
title = {Vibronic dynamics resolved by global and target analysis of ultrafast transient absorption spectra},
journal = {The Journal of Chemical Physics},
volume = {155},
number = {11},
pages = {114113},
year = {2021},
doi = {10.1063/5.0060672},
URL = {
https://doi.org/10.1063/5.0060672
},
eprint = {
https://doi.org/10.1063/5.0060672
}
}
@article{Boehme2021,
author = {Boehme, Simon Christian and Tchamba Yimga, Nadine and Frick, Achidi and Gunst, Susann and Untenecker, Harald and Kennis, John T. M. and van Stokkum, Ivo H. M. and Kirsch, Peer and von Hauff, Elizabeth},
title = {Correlating Ultrafast Dynamics, Liquid Crystalline Phases, and Ambipolar Transport in Fluorinated Benzothiadiazole Dyes},
journal = {Advanced Electronic Materials},
volume = {7},
number = {8},
pages = {2100186},
keywords = {ambipolar, dye, liquid crystal, organic electronics, ultrafast},
doi = {https://doi.org/10.1002/aelm.202100186},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aelm.202100186},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/aelm.202100186},
abstract = {Abstract A key challenge in the field of organic electronics is predicting how chemical structure at the molecular scale determines nature and dynamics of excited states, as well as the macroscopic optoelectronic properties in thin film. Here, the donor–acceptor dyes 4,7-bis[5-[4-(3-ethylheptyl)-2,3-difluorophenyl]-2-thienyl]-2,1,3-benzothiadiazole (2,3-FFPTB) and 4,7-bis[5-[4-(3-ethylheptyl)-2,6-difluorophenyl]-2-thienyl]-2,1,3-benzothiadiazole (2,6-FFPTB) are synthesized, which only differ in the position of one fluorine substitution. It is observed that this variation in chemical structure does not influence the energetic position of the molecular frontier orbitals or the ultrafast dynamics on the FFPTB backbone. However, it does result in differences at the macroscale, specifically regarding structural and electrical properties of the FFPTB films. Both FFPTB molecules form crystalline films at room temperature, whereas 2,3-FFPTB has two ordered smectic phases at elevated temperatures, and 2,6-FFPTB does not display any liquid crystalline phases. It is demonstrated that the altered location of the fluorine substitution allows to control the electrostatic potential along the molecular backbone without impacting molecular energetics or ultrafast dynamics. Such a design strategy succeeds in controlling molecular interactions in liquid crystalline phase, and it is shown that the associated molecular order, or rather disorder, can be exploited to achieve ambipolar transport in FFPTB films.},
year = {2021}
}
@article{TROS2020148206,
title = {Harvesting far-red light: Functional integration of chlorophyll f into Photosystem I complexes of Synechococcus sp. PCC 7002},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
volume = {1861},
number = {8},
pages = {148206},
year = {2020},
issn = {0005-2728},
doi = {https://doi.org/10.1016/j.bbabio.2020.148206},
url = {https://www.sciencedirect.com/science/article/pii/S0005272820300566},
author = {Martijn Tros and Luca Bersanini and Gaozhong Shen and Ming-Yang Ho and Ivo H.M. {van Stokkum} and Donald A. Bryant and Roberta Croce},
keywords = {Photosynthesis, Light harvesting, Pigments, Time-resolved fluorescence, Excitation energy transfer},
abstract = {The heterologous expression of the far-red absorbing chlorophyll (Chl) f in organisms that do not synthesize this pigment has been suggested as a viable solution to expand the solar spectrum that drives oxygenic photosynthesis. In this study, we investigate the functional binding of Chl f to the Photosystem I (PSI) of the cyanobacterium Synechococcus 7002, which has been engineered to express the Chl f synthase gene. By optimizing growth light conditions, one-to-four Chl f pigments were found in the complexes. By using a range of spectroscopic techniques, isolated PSI trimeric complexes were investigated to determine how the insertion of Chl f affects excitation energy transfer and trapping efficiency. The results show that the Chls f are functionally connected to the reaction center of the PSI complex and their presence does not change the overall pigment organization of the complex. Chl f substitutes Chl a (but not the Chl a red forms) while maintaining efficient energy transfer within the PSI complex. At the same time, the introduction of Chl f extends the photosynthetically active radiation of the new hybrid PSI complexes up to 750 nm, which is advantageous in far-red light enriched environments. These conclusions provide insights to engineer the photosynthetic machinery of crops to include Chl f and therefore increase the light-harvesting capability of photosynthesis.}
}
@article{JCP2020,
author = {van Stokkum,Ivo H. M. and Jumper,Chanelle C. and Lee,Tia S. and Myahkostupov,Mykhaylo and Castellano,Felix N. and Scholes,Gregory D. },
title = {Vibronic and excitonic dynamics in perylenediimide dimers and tetramer},
journal = {The Journal of Chemical Physics},
volume = {153},
number = {22},
pages = {224101},
year = {2020},
doi = {10.1063/5.0024530},
URL = {
https://doi.org/10.1063/5.0024530
},
eprint = {
https://doi.org/10.1063/5.0024530
}
}
@article{RN1677,
author = {Biswas, Avratanu and Huang, Xinpeng and Lambrev, Petar H. and van Stokkum, Ivo H. M.},
title = {Modelling excitation energy transfer and trapping in the filamentous cyanobacterium Anabaena variabilis PCC 7120},
journal = {Photosynthesis Research},
volume = {144},
number = {2},
pages = {261-272},
ISSN = {1573-5079},
DOI = {10.1007/s11120-020-00723-0},
url = {https://doi.org/10.1007/s11120-020-00723-0},
year = {2020},
type = {Journal Article}
}
@article{RN1676,
author = {Akhtar, Parveen and Biswas, Avratanu and Petrova, Nia and Zakar, Tomas and van Stokkum, Ivo H. M. and Lambrev, Petar H.},
title = {Time-resolved fluorescence study of excitation energy transfer in the cyanobacterium Anabaena PCC 7120},
journal = {Photosynthesis Research},
volume = {144},
number = {2},
pages = {247-259},
ISSN = {1573-5079},
DOI = {10.1007/s11120-020-00719-w},
url = {https://doi.org/10.1007/s11120-020-00719-w},
year = {2020},
type = {Journal Article}
}
@article{RN1674,
author = {Teles-Ferreira, Danielle Cristina and Conti, Irene and Borrego-Varillas, Rocio and Nenov, Artur and Stokkum, Ivo H. M. Van and Ganzer, Lucia and Manzoni, Cristian and Paula, Ana Maria and Cerullo, Giulio and Garavelli, Marco},
title = {A Unified Experimental/Theoretical Description of the Ultrafast Photophysics of Single and Double Thionated Uracils},
journal = {Chemistry - A European Journal},
volume = {26},
number = {1},
pages = {336-343},
ISSN = {0947-6539},
DOI = {10.1002/chem.201904541},
url = {https://doi.org/10.1002/chem.201904541},
year = {2020},
type = {Journal Article}
}
@article{MASCOLI20192900,
title = "Capturing the Quenching Mechanism of Light-Harvesting Complexes of Plants by Zooming in on the Ensemble",
journal = "Chem",
volume = "5",
number = "11",
pages = "2900 - 2912",
year = "2019",
issn = "2451-9294",
doi = "https://doi.org/10.1016/j.chempr.2019.08.002",
url = "http://www.sciencedirect.com/science/article/pii/S2451929419303699",
author = "Vincenzo Mascoli and Nicoletta Liguori and Pengqi Xu and Laura M. Roy and Ivo H.M. van Stokkum and Roberta Croce",
keywords = "SDG7: Affordable and clean energy, SDG15: Life on land, photosynthesis, light harvesting, photoprotection, antenna quenching, energy transfer, time-resolved electronic spectroscopy, mutational analysis, target kinetic modeling, carotenoids",
abstract = "Summary
The light-harvesting complexes (LHCs) of plants can regulate the energy flux to the reaction centers in response to fluctuating light by virtue of their vast conformational landscape. They do so by switching from a light-harvesting state to a quenched state, dissipating the excess absorbed energy as heat. However, isolated LHCs are prevalently in their light-harvesting state, which makes the identification of their photoprotective mechanism extremely challenging. Here, ensemble time-resolved fluorescence experiments show that monomeric CP29, a minor LHC of plants, exists in various emissive states with identical spectra but different lifetimes. The photoprotective mechanism active in a subpopulation of strongly quenched complexes is further investigated via ultrafast transient absorption spectroscopy, kinetic modeling, and mutational analysis. We demonstrate that the observed quenching is due to excitation energy transfer from chlorophylls to a dark state of the centrally bound lutein."
}
@article {Tian8320,
author = {Tian, Lijin and Nawrocki, Wojciech J. and Liu, Xin and Polukhina, Iryna and van Stokkum, Ivo H. M. and Croce, Roberta},
title = {p{H} dependence, kinetics and light-harvesting regulation of nonphotochemical quenching in {C}hlamydomonas},
volume = {116},
number = {17},
pages = {8320--8325},
year = {2019},
doi = {10.1073/pnas.1817796116},
publisher = {National Academy of Sciences},
abstract = {Photosynthetic organisms utilize sunlight as a form of energy. Under low light, they maximize their capacity to harvest photons; however, under excess light, they dissipate part of the harvested energy to prevent photodamage, at the expense of light-use efficiency. Optimally balancing light harvesting and energy dissipation in natural (fluctuating light) conditions is considered a target for improving the productivity of both algae and plants. Here we have studied the energy dissipation process in the green alga Chlamydomonas reinhardtii in vivo. We found that it is remarkably different from that of higher plants, highlighting the need of developing tailor-made strategies to optimize the light harvesting{\textendash}energy dissipation balance in different organisms.Sunlight drives photosynthesis but can also cause photodamage. To protect themselves, photosynthetic organisms dissipate the excess absorbed energy as heat, in a process known as nonphotochemical quenching (NPQ). In green algae, diatoms, and mosses, NPQ depends on the light-harvesting complex stress-related (LHCSR) proteins. Here we investigated NPQ in Chlamydomonas reinhardtii using an approach that maintains the cells in a stable quenched state. We show that in the presence of LHCSR3, all of the photosystem (PS) II complexes are quenched and the LHCs are the site of quenching, which occurs at a rate of \~{}150 ps-1 and is not induced by LHCII aggregation. The effective light-harvesting capacity of PSII decreases upon NPQ, and the NPQ rate is independent of the redox state of the reaction center. Finally, we could measure the pH dependence of NPQ, showing that the luminal pH is always above 5.5 in vivo and highlighting the role of LHCSR3 as an ultrasensitive pH sensor.},
issn = {0027-8424},
URL = {https://www.pnas.org/content/116/17/8320},
eprint = {https://www.pnas.org/content/116/17/8320.full.pdf},
journal = {Proceedings of the National Academy of Sciences}
}
@article{RN1673,
author = {Konold, Patrick E. and van Stokkum, Ivo H. M. and Muzzopappa, Fernando and Wilson, Adj{\'e}l{\'e} and Groot, Marie-Louise and Kirilovsky, Diana and Kennis, John T. M.},
title = {Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein},
journal = {Journal of the American Chemical Society},
volume = {141},
number = {1},
pages = {520-530},
ISSN = {0002-7863},
DOI = {10.1021/jacs.8b11373},
url = {https://doi.org/10.1021/jacs.8b11373},
year = {2019},
type = {Journal Article}
}
@article{RN1626,
author = {Wlodarczyk, Lucyna M. and Snellenburg, Joris J. and Dekker, Jan P. and Stokkum, Ivo H. M.},
title = {Development of fluorescence quenching in {C}hlamydomonas reinhardtii upon prolonged illumination at 77{K}},
journal = {Photosynthesis Research},
volume = {137},
number = {3},
pages = {503-513},
ISSN = {1573-5079},
DOI = {10.1007/s11120-018-0534-8},
url = {https://doi.org/10.1007/s11120-018-0534-8},
year = {2018},
type = {Journal Article}
}
@article{RN1627,
author = {Jumper, Chanelle C. and van Stokkum, Ivo H. M. and Mirkovic, Tihana and Scholes, Gregory D.},
title = {Vibronic Wavepackets and Energy Transfer in Cryptophyte Light-Harvesting Complexes},
journal = {The Journal of Physical Chemistry B},
volume = {122},
number = {24},
pages = {6328-6340},
ISSN = {1520-6106},
DOI = {10.1021/acs.jpcb.8b02629},
url = {https://doi.org/10.1021/acs.jpcb.8b02629},
year = {2018},
type = {Journal Article}
}
@article{RN1629,
author = {Acu{\~{n}}a, Alonso M. and van Alphen, Pascal and Branco dos Santos, Filipe and van Grondelle, Rienk and Hellingwerf, Klaas J. and van Stokkum, Ivo H. M.},
title = {Spectrally decomposed dark-to-light transitions in {S}ynechocystis sp. {PCC} 6803},
journal = {Photosynthesis Research},
volume = {137},
number = {2},
pages = {307-320},
ISSN = {1573-5079},
DOI = {10.1007/s11120-018-0505-0},
url = {https://doi.org/10.1007/s11120-018-0505-0},
year = {2018},
type = {Journal Article}
}
@article{RN1628,
author = {Mix, L. Tyler and Carroll, Elizabeth C. and Morozov, Dmitry and Pan, Jie and Gordon, Wendy Ryan and Philip, Andrew and Fuzell, Jack and Kumauchi, Masato and van Stokkum, Ivo and Groenhof, Gerrit and Hoff, Wouter D. and Larsen, Delmar S.},
title = {Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from {H}alorhodospira halophila},
journal = {Biochemistry},
volume = {57},
number = {11},
pages = {1733-1747},
ISSN = {0006-2960},
DOI = {10.1021/acs.biochem.7b01114},
url = {https://doi.org/10.1021/acs.biochem.7b01114},
year = {2018},
type = {Journal Article}
}
@article{RN1618,
author = {Acu{\~{n}}a, A. M. and Van Alphen, P. and Van Grondelle, R. and Van Stokkum, I. H. M.},
title = {The phycobilisome terminal emitter transfers its energy with a rate of (20 ps)-1 to photosystem {II}},
journal = {Photosynthetica},
volume = {56},
number = {1},
pages = {265-274},
ISSN = {1573-9058},
DOI = {10.1007/s11099-018-0779-7},
url = {https://doi.org/10.1007/s11099-018-0779-7},
year = {2018},
type = {Journal Article}
}
@inbook{RN1591,
author = {van Stokkum, Ivo},
title = {Systems biophysics: Global and target analysis of light harvesting and photochemical
quenching in vivo},
booktitle = {Light Harvesting in Photosynthesis},
editor = {Croce, Roberta and van Grondelle, Rienk and van Amerongen, Herbert and van Stokkum, Ivo},
publisher = {CRC Press},
address = {Boca Raton},
chapter = {20},
pages = {467-482},
year = {2018},
type = {Book Section}
}
@book{RN1589,
editor = {Croce, Roberta and van Grondelle, Rienk and van Amerongen, Herbert and van Stokkum, Ivo},
title = {Light Harvesting in Photosynthesis},
publisher = {CRC Press},
address = {Boca Raton},
series = {Foundations of biochemistry and biophysics},
pages = {625},
ISBN = {9781351242882},
year = {2018},
type = {Book}
}
@article{RN1588,
author = {Pandit, Anjali and van Stokkum, Ivo H. M. and van Amerongen, Herbert and Croce, Roberta},
title = {Introduction: light harvesting for photosynthesis},
journal = {Photosynthesis Research},
volume = {135},
number = {1},
pages = {1-2},
ISSN = {1573-5079},
DOI = {10.1007/s11120-017-0457-9},
url = {https://doi.org/10.1007/s11120-017-0457-9},
year = {2018},
type = {Journal Article}
}
@article{ACUNA201857,
title = "Spectrally decomposed dark-to-light transitions in a {PSI}-deficient mutant of {S}ynechocystis sp. {PCC} 6803",
journal = "Biochimica et Biophysica Acta (BBA) - Bioenergetics",
volume = "1859",
number = "2",
pages = "57 - 68",
year = "2018",
issn = "0005-2728",
doi = "https://doi.org/10.1016/j.bbabio.2017.11.002",
url = "http://www.sciencedirect.com/science/article/pii/S0005272817301615",
author = "Alonso M. Acu{\~{n}}a and Pascal van Alphen and Filipe Branco dos Santos and Rienk van Grondelle and Klaas J. Hellingwerf and Ivo H.M. van Stokkum",
keywords = "Cyanobacteria, Spectrally-resolved fluorometry, Singular Value Decomposition, Time-resolved spectroscopy"
}
@article{RN1576,
author = {Yamakawa, Hisanori and van Stokkum, Ivo H. M. and Heber, Ulrich and Itoh, Shigeru},
title = {Mechanisms of drought-induced dissipation of excitation energy in sun- and shade-adapted drought-tolerant mosses studied by fluorescence yield change and global and target analysis of fluorescence decay kinetics},
journal = {Photosynthesis Research},
volume = {135},
number = {1},
pages = {285-298},
ISSN = {1573-5079},
DOI = {10.1007/s11120-017-0465-9},
url = {https://doi.org/10.1007/s11120-017-0465-9},
year = {2018},
type = {Journal Article}
}
@Article{Acu�a2017,
author="Acu{\~{n}}a, Alonso M.
and Lemaire, Claire
and van Grondelle, Rienk
and Robert, Bruno
and van Stokkum, Ivo H. M.",
title={{Energy transfer and trapping in {S}ynechococcus {WH} 7803}},
journal="Photosynthesis Research",
volume = {135},
number = {1},
pages = {115-124},
ISSN = {1573-5079},
DOI = {10.1007/s11120-017-0451-2},
url = {https://doi.org/10.1007/s11120-017-0451-2},
year = {2018},
type = {Journal Article}
}
@article{RN1575,
author = {Liguori, Nicoletta and Xu, Pengqi and van Stokkum, Ivo H. M. and van Oort, Bart and Lu, Yinghong and Karcher, Daniel and Bock, Ralph and Croce, Roberta},
title = {Different carotenoid conformations have distinct functions in light-harvesting regulation in plants},
journal = {Nature Communications},
volume = {8},
number = {1},
pages = {1994},
ISSN = {2041-1723},
DOI = {10.1038/s41467-017-02239-z},
url = {https://doi.org/10.1038/s41467-017-02239-z},
year = {2017},
type = {Journal Article}
}
@article{RN1561,
author = {Hontani, Y. and Marazzi, M. and Stehfest, K. and Mathes, T. and van Stokkum, I. H. M. and Elstner, M. and Hegemann, P. and Kennis, J. T. M.},
title = {{Reaction dynamics of the chimeric channelrhodopsin C1C2}},
journal = {Sci Rep},
volume = {7},
DOI = {10.1038/s41598-017-07363-w},
year = {2017},
type = {Journal Article}
}
@Article{vanStokkum2017,
author="van Stokkum, Ivo H. M.
and Gwizdala, Michal
and Tian, Lijin
and Snellenburg, Joris J.
and van Grondelle, Rienk
and van Amerongen, Herbert
and Berera, Rudi",
title={{A functional compartmental model of the Synechocystis PCC 6803 phycobilisome}},
journal="Photosynthesis Research",
abstract="In the light-harvesting antenna of the Synechocystis PCC 6803 phycobilisome (PB), the core consists of three cylinders, each composed of four disks, whereas each of the six rods consists of up to three hexamers (Arteni et al., Biochim Biophys Acta 1787(4):272--279, 2009). The rods and core contain phycocyanin and allophycocyanin pigments, respectively. Together these pigments absorb light between 400 and 650�nm. Time-resolved difference absorption spectra from wild-type PB and rod mutants have been measured in different quenching and annihilation conditions. Based upon a global analysis of these data and of published time-resolved emission spectra, a functional compartmental model of the phycobilisome is proposed. The model describes all experiments with a common set of parameters. Three annihilation time constants are estimated, 3, 25, and 147�ps, which represent, respectively, intradisk, interdisk/intracylinder, and intercylinder annihilation. The species-associated difference absorption and emission spectra of two phycocyanin and two allophycocyanin pigments are consistently estimated, as well as all the excitation energy transfer rates. Thus, the wild-type PB containing 396 pigments can be described by a functional compartmental model of 22 compartments. When the interhexamer equilibration within a rod is not taken into account, this can be further simplified to ten compartments, which is the minimal model. In this model, the slowest excitation energy transfer rates are between the core cylinders (time constants 115--145�ps), and between the rods and the core (time constants 68--115�ps).",
volume = {135},
number = {1},
pages = {87-102},
ISSN = {1573-5079},
DOI = {10.1007/s11120-017-0424-5},
url = {https://doi.org/10.1007/s11120-017-0424-5},
year = {2018},
type = {Journal Article}
}
@article{SNELLENBURG2017854,
title = {{A four state parametric model for the kinetics of the non-photochemical quenching in Photosystem II}},
journal = "Biochimica et Biophysica Acta (BBA) - Bioenergetics",
volume = "1858",
number = "10",
pages = "854 - 864",
year = "2017",
issn = "0005-2728",
doi = "https://doi.org/10.1016/j.bbabio.2017.08.004",
url = "http://www.sciencedirect.com/science/article/pii/S0005272817301172",
author = "Joris J. Snellenburg and Matthew P. Johnson and Alexander V. Ruban and Rienk van Grondelle and Ivo H.M. van Stokkum",
keywords = "Fluorescence quenching analysis",
keywords = "Non-photochemical quenching",
keywords = "Parameter estimation",
keywords = "Time-resolved fluorescence spectroscopy"
}
@article{Snellenburg201764,
title = {{A model for the 77 K excited state dynamics in Chlamydomonas reinhardtii in state 1 and state 2}},
journal = "Biochimica et Biophysica Acta (BBA) - Bioenergetics ",
volume = "1858",
number = "1",
pages = "64-72",
year = "2017",
note = "",
issn = "0005-2728",
doi = "http://dx.doi.org/10.1016/j.bbabio.2016.10.001",
url = "http://www.sciencedirect.com/science/article/pii/S0005272816306302",
author = "Joris J. Snellenburg and Lucyna M. Wlodarczyk and Jan P. Dekker and Rienk van Grondelle and Ivo H.M. van Stokkum",
keywords = "Chlamydomonas reinhardtii",
keywords = "time-resolved fluorescence",
keywords = "target analysis",
keywords = "77 K "
}
@article{vanStokkum2016b,
author = {Ivo H. M. van Stokkum and Chanelle C. Jumper and Joris J. Snellenburg and Gregory D. Scholes and Rienk van Grondelle and Pavel Mal{\'{y}}},
title = {Estimation of damped oscillation associated spectra from ultrafast transient absorption spectra},
journal = {The Journal of Chemical Physics},
volume = {145},
number = {17},
pages = {174201},
year = {2016},
doi = {10.1063/1.4966196},
URL = {http://dx.doi.org/10.1063/1.4966196},
eprint = {
http://dx.doi.org/10.1063/1.4966196
}
}
@Article{Acuna2016b,
author="Acu{\~{n}}a, Alonso M.
and Ka{\v{n}}a, Radek
and Gwizdala, Michal
and Snellenburg, Joris J.
and van Alphen, Pascal
and van Oort, Bart
and Kirilovsky, Diana
and van Grondelle, Rienk
and van Stokkum, Ivo H. M.",
title={{A method to decompose spectral changes in Synechocystis PCC 6803 during light-induced state transitions}},
journal="Photosynthesis Research",
year="2016",
volume="130",
number="1",
pages="237--249",
abstract="Cyanobacteria have developed responses to maintain the balance between the energy absorbed and the energy used in different pigment-protein complexes. One of the relatively rapid (a few minutes) responses is activated when the cells are exposed to high light intensities. This mechanism thermally dissipates excitation energy at the level of the phycobilisome (PB) antenna before it reaches the reaction center. When exposed to low intensities of light that modify the redox state of the plastoquinone pool, the so-called state transitions redistribute energy between photosystem I and II. Experimental techniques to investigate the underlying mechanisms of these responses, such as pulse-amplitude modulated fluorometry, are based on spectrally integrated signals. Previously, a spectrally resolved fluorometry method has been introduced to preserve spectral information. The analysis method introduced in this work allows to interpret SRF data in terms of species-associated spectra of open/closed reaction centers (RCs), (un)quenched PB and state 1 versus state 2. Thus, spectral differences in the time-dependent fluorescence signature of photosynthetic organisms under varying light conditions can be traced and assigned to functional emitting species leading to a number of interpretations of their molecular origins. In particular, we present evidence that state 1 and state 2 correspond to different states of the PB-PSII-PSI megacomplex.",
issn="1573-5079",
doi="10.1007/s11120-016-0248-8",
url="http://dx.doi.org/10.1007/s11120-016-0248-8"
}
@incollection{vanStokkum2016,
editor = "Bruno Robert",
booktitle = "Artificial Photosynthesis",
publisher = "Academic Press",
year = "2016",
volume = "79",
pages = "169 - 192",
series = "Advances in Botanical Research ",
issn = "0065-2296",
doi = "http://dx.doi.org/10.1016/bs.abr.2016.04.003",
keywords = "Electron transfer, Excited state absorption, Excited state energy transfer, Global analysis, Kinetic modelling, Target analysis, Transient absorption spectroscopy",
author = "{van Stokkum}, {I. H. M.} and J. Ravensbergen and Snellenburg, {J. J.} and {van Grondelle}, R. and S. Pillai and Moore, {T. A.} and D. Gust and Moore, {A. L.} and Kennis, {J. T. M.}",
title = "Resolving Energy and Electron Transfer Processes in Dyads With the Help of Global and Target Analysis",
}
@article{2016Alonso,
author = {Acuna, A. M. and Snellenburg, J. J. and Gwizdala, M. and Kirilovsky, D. and van Grondelle, R. and van Stokkum, I. H. M.},
title = {{Resolving the contribution of the uncoupled phycobilisomes to cyanobacterial pulse-amplitude modulated (PAM) fluorometry signals}},
journal = {Photosynthesis Research},
volume = {127},
number = {1},
pages = {91-102},
ISSN = {0166-8595},
DOI = {10.1007/s11120-015-0141-x},
url = {://WOS:000366156400011},
year = {2016},
type = {Journal Article}
}
@article{LeQuiniou2015JBC,
author = {Le Quiniou, C. and van Oort, B. and Drop, B. and van Stokkum, I. H. M. and Croce, R.},
title = {{The High Efficiency of Photosystem I in the Green Alga Chlamydomonas reinhardtii Is Maintained after the Antenna Size Is Substantially Increased by the Association of Light-harvesting Complexes II}},
journal = {Journal of Biological Chemistry},
volume = {290},
number = {51},
pages = {30587-30595},
abstract = {Photosystems (PS) I and II activities depend on their light-harvesting capacity and trapping efficiency, which vary in different environmental conditions. For optimal functioning, these activities need to be balanced. This is achieved by redistribution of excitation energy between the two photosystems via the association and disassociation of light-harvesting complexes (LHC) II, in a process known as state transitions. Here we study the effect of {LHCII} binding to PSI on its absorption properties and trapping efficiency by comparing time-resolved fluorescence kinetics of PSI-LHCI and PSI-LHCI-{LHCII} complexes of Chlamydomonas reinhardtii. PSI-LHCI-{LHCII} of C. reinhardtii is the largest PSI supercomplex isolated so far and contains seven Lhcbs, in addition to the PSI core and the nine Lhcas that compose PSI-LHCI, together binding similar to 320 chlorophylls. The average decay time for PSI-LHCI-{LHCII} is similar to 65 ps upon 400 nm excitation (15 ps slower than PSI-LHCI) and similar to 78 ps upon 475 nm excitation (27 ps slower). The transfer of excitation energy from {LHCII} to PSI-LHCI occurs in similar to 60 ps. This relatively slow transfer, as compared with that from LHCI to the PSI core, suggests loose connectivity between {LHCII} and PSI-LHCI. Despite the relatively slow transfer, the overall decay time of PSI-LHCI-{LHCII} remains fast enough to assure a 96% trapping efficiency, which is only 1.4% lower than that of PSI-LHCI, concomitant with an increase of the absorption cross section of 47%. This indicates that, at variance with PSII, the design of PSI allows for a large increase of its light-harvesting capacities.},
ISSN = {0021-9258},
DOI = {10.1074/jbc.M115.687970},
url = {://WOS:000366738200033},
year = {2015},
type = {Journal Article}
}
@article{LeQuiniou2015458,
title = "{PSI-LHCI of Chlamydomonas reinhardtii: Increasing the absorption cross section without losing efficiency} ",
journal = "Biochimica et Biophysica Acta (BBA) - Bioenergetics ",
volume = "1847",
number = "4-5",
pages = "458 - 467",
year = "2015",
note = "",
issn = "0005-2728",
doi = "http://dx.doi.org/10.1016/j.bbabio.2015.02.001",
url = "http://www.sciencedirect.com/science/article/pii/S0005272815000250",
author = "Clotilde Le Quiniou and Lijin Tian and Bartlomiej Drop and Emilie Wientjes and Ivo H.M. van Stokkum and Bart van Oort and Roberta Croce",
}
@article{Bart2015,
author = {van Oort, B. and van Grondelle, R. and van Stokkum, I. H. M.},
title = {{A Hidden State in Light-Harvesting Complex II Revealed By Multipulse Spectroscopy}},
journal = {Journal of Physical Chemistry B},
volume = {119},
number = {16},
pages = {5184-5193},
abstract = {Light-harvesting complex II ({{LHCII}}) is pivotal both for collecting solar radiation for photosynthesis, and for protection against photodamage under high light intensities (via a process called nonphotochemical quenching, NPQ). Aggregation of {LHCII} is associated with fluorescence quenching, and is used as an in vitro model system of NPQ. However, there is no agreement on the nature of the quencher and on the validity of aggregation as a model system. Here, we use ultrafast multipulse spectroscopy to populate a quenched state in unquenched (unaggregated) {LHCII}. The state shows characteristic features of lutein and chlorophyll, suggesting that it is an excitonically coupled state between these two compounds. This state decays in approximately 10 ps, making it a strong competitor for photodamage and photochemical quenching. It is observed in trimeric and monomeric {LHCII}, upon re-excitation with pulses of different wavelengths and duration. We propose that this state is always present, but is scarcely populated under low light intensities. Under high light intensities it may become more accessible, e.g. by conformational changes, and then form a quenching channel. The same state may be the cause of fluorescence blinking observed in single-molecule spectroscopy of {LHCII} trimers, where a small subpopulation is in an energetically higher state where the pathway to the quencher opens up.},
ISSN = {1520-6106},
DOI = {10.1021/acs.jpcb.5b01335},
url = {://WOS:000353604800009},
year = {2015},
type = {Journal Article}
}
@article{doi:10.1021/jp506785q,
author = {Zhu, Jingyi and Vreede, Jocelyne and Hospes, Marijke and Arents, Jos and Kennis, John T. M. and van Stokkum, Ivo H. M. and Hellingwerf, Klaas J. and Groot, Marie Louise},
title = {Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield},
journal = {The Journal of Physical Chemistry B},
volume = {119},
number = {6},
pages = {2372-2383},
year = {2015},
doi = {10.1021/jp506785q},
URL = {
http://dx.doi.org/10.1021/jp506785q
},
eprint = {
http://dx.doi.org/10.1021/jp506785q
}
}
@article{Wlodarczyk2015261,
title = "Functional Rearrangement of the Light-Harvesting Antenna upon State Transitions in a Green Alga ",
journal = "Biophysical Journal ",
volume = "108",
number = "2",
pages = "261 - 271",
year = "2015",
note = "",
issn = "0006-3495",
doi = "http://dx.doi.org/10.1016/j.bpj.2014.11.3470",
url = "http://www.sciencedirect.com/science/article/pii/S0006349514046839",
author = "Lucyna M. Wlodarczyk and Joris J. Snellenburg and Janne A. Ihalainen and Rienk van Grondelle and Ivo H.M. van Stokkum and Jan P. Dekker",
abstract = "Abstract State transitions in the green alga Chlamydomonas reinhardtii serve to balance excitation energy transfer to photosystem I (PSI) and to photosystem \{II\} (PSII) and possibly play a role as a photoprotective mechanism. Thus, light-harvesting complex \{II\} ({LHCII}) can switch between the photosystems consequently transferring more excitation energy to \{PSII\} (state 1) or to \{PSI\} (state 2) or can end up in {LHCII}-only domains. In this study, low-temperature (77 K) steady-state and time-resolved fluorescence measured on intact cells of Chlamydomonas reinhardtii shows that independently of the state excitation energy transfer from \{{LHCII}\} to \{PSI\} or to \{PSII\} occurs on two main timescales of <15� ps and ∼100 ps. Moreover, in state 1 almost all \{{LHCII}s\} are functionally connected to PSII, whereas the transition from state 1 to a state 2 chemically locked by 0.1� M sodium fluoride leads to an almost complete functional release of \{{LHCII}s\} from PSII. About 2/3 of the released \{{LHCII}s\} transfer energy to \{PSI\} and ∼1/3 of the released \{{LHCII}s\} form a component designated X-685 peaking at 685� nm that decays with time constants of 0.28 and 5.8� ns and does not transfer energy to \{PSI\} or to PSII. A less complete state 2 was obtained in cells incubated under anaerobic conditions without chemical locking. In this state about half of all \{{LHCII}s\} remained functionally connected to PSII, whereas the remaining half became functionally connected to \{PSI\} or formed X-685 in similar amounts as with chemical locking. We demonstrate that X-685 originates from \{{LHCII}\} domains not connected to a photosystem and that its presence introduces a change in the interpretation of 77 K steady-state fluorescence emission measured upon state transitions in Chalamydomonas reinhardtii. "
}
@article{Ramanan20141507,
title = "Exploring the mechanism(s) of energy dissipation in the light harvesting complex of the photosynthetic algae Cyclotella meneghiniana ",
journal = "Biochimica et Biophysica Acta (BBA) - Bioenergetics ",
volume = "1837",
number = "9",
pages = "1507 - 1513",
year = "2014",
issn = "0005-2728",
doi = "http://dx.doi.org/10.1016/j.bbabio.2014.02.016",
url = "http://www.sciencedirect.com/science/article/pii/S0005272814000632",
author = "Charusheela Ramanan and Rudi Berera and Kathi Gundermann and Ivo van Stokkum and Claudia B{\"{u}}chel and Rienk van Grondelle",
keywords = "Photosynthesis",
keywords = "Photoprotection",
keywords = "Non-photochemical quenching",
keywords = "Light-harvesting",
keywords = "Diatoms",
keywords = "Transient absorption ",
abstract = "Abstract Photosynthetic organisms have developed vital strategies which allow them to switch from a light-harvesting to an energy dissipative state at the level of the antenna system in order to survive the detrimental effects of excess light illumination. These mechanisms are particularly relevant in diatoms, which grow in highly fluctuating light environments and thus require fast and strong response to changing light conditions. We performed transient absorption spectroscopy on FCPa, the main light-harvesting antenna from the diatom Cyclotella meneghiniana, in the unquenched and quenched state. Our results show that in quenched \{FCPa\} two quenching channels are active and are characterized by differing rate constants and distinct spectroscopic signatures. One channel is associated with a faster quenching rate (16 ns− 1) and virtually no difference in spectral shape compared to the bulk unquenched chlorophylls, while a second channel is associated with a slower quenching rate (2.7 ns− 1) and exhibits an increased population of red-emitting states. We discuss the origin of the two processes in the context of the models proposed for the regulation of photosynthetic light-harvesting. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy. "
}
@incollection{Mathes2014,
year={2014},
isbn={978-1-4939-0451-8},
booktitle={Flavins and Flavoproteins},
volume={1146},
series={Methods in Molecular Biology},
editor={Weber, Stefan and Schleicher, Erik},
doi={10.1007/978-1-4939-0452-5_16},
title={Photoactivation Mechanisms of Flavin-Binding Photoreceptors Revealed Through Ultrafast Spectroscopy and Global Analysis Methods},
url={http://dx.doi.org/10.1007/978-1-4939-0452-5_16},
publisher={Springer New York},
keywords={BLUF; LOV; Photoreceptor; Ultrafast spectroscopy; Global analysis},
author={Mathes, Tilo and van Stokkum, Ivo H.M. and Kennis, John T.M.},
pages={401-442},
language={English}
}
@incollection{QuantSpectAnal,
year={2014},
isbn={978-1-62703-648-1},
booktitle={Fluorescence Spectroscopy and Microscopy},
volume={1076},
series={Methods in Molecular Biology},
editor={Engelborghs, Yves and Visser, Antonie J.W.G.},
doi={10.1007/978-1-62703-649-8_3},
title={Quantitative Fluorescence Spectral Analysis of Protein Denaturation},
url={http://dx.doi.org/10.1007/978-1-62703-649-8_3},
publisher={Humana Press},
keywords={Global analysis; Protein denaturation; Singular value decomposition; Steady-state fluorescence},
author={Stokkum, Ivo H.M. and Laptenok, Sergey P.},
pages={43-51},
language={English}
}
@article{ ISI:000327557700002,
Author = {Maiuri, M. and Snellenburg, J. J. and van Stokkum, I. H. M. and Pillai,
S. and Carter, K. Wong and Gust, D. and Moore, T. A. and Moore, A. L.
and van Grondelle, R. and Cerullo, G. and Polli, D.},
Title = {{Ultrafast Energy Transfer and Excited State Coupling in an Artificial
Photosynthetic Antenna}},
Journal = {The Journal of Physical Chemistry B},
Year = {2013},
Volume = {{117}},
Number = {{46}},
Pages = {{14183-14190}},
Abstract = {{We have studied the energy transfer dynamics in an artificial
lightharvesting dyad composed of a phthalocyanine (Pc) covalently linked
to a carotenoid (Car). The combination of high temporal resolution
transient absorption spectroscopy with global and target analysis
allowed us to quantify the efficiency of the energy transfer from the
S-2 excited state of the Car to the Pc at 37\%, close to values observed
in some natural light-harvesting complexes. In addition, following
selective excitation of the Pc, we have identified the spectral
signatures of the S-1, excited state of the Car which appear within the
approximate to 30 fs time resolution of our measurement. This strongly
indicates excited state coupling between the S, state of Car and the
Q(x) state of Pc, with important implications for the regulation of
photosynthetic activity.}},
DOI = {{10.1021/JP401073wl}},
ISSN = {{1520-6106}},
Unique-ID = {{ISI:000327557700002}},
}
@article{doi:10.1021/jp4020977,
author = {Lambrev, Petar H. and Miloslavina, Yuliya and van Stokkum, Ivo H. M. and Stahl, Andreas D. and Michalik, Maciej and Susz, Anna and Tworzydlo, Jedrzej and Fiedor, Joanna and Huhn, Gabriella and
Groot, Marie-Louise and van Grondelle, Rienk and Garab, Gy{\"{o}}z{\"{o}} and Fiedor, Leszek},
title = {Excitation Energy Trapping and Dissipation by {Ni}-Substituted Bacteriochlorophyll a in Reconstituted {LH1} Complexes from {Rhodospirillum rubrum}},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11260-11271},
year = {2013},
doi = {10.1021/jp4020977},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp4020977},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp4020977}
}
@article{doi:10.1021/jp401364a,
author = {van Stokkum, Ivo H.M. and Desquilbet, Thibaut E. and van der Weij-de Wit, Chantal D. and Snellenburg, Joris J. and van Grondelle, Rienk and Thomas, Jean-Claude and Dekker, Jan P. and Robert, Bruno},
title = {Energy Transfer and Trapping in Red-Chlorophyll-Free {Photosystem I} from {Synechococcus WH} 7803},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11176-11183},
year = {2013},
doi = {10.1021/jp401364a},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp401364a},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp401364a}
}
@article{doi:10.1021/jp402086p,
author = {Williams, Ren{\'{e}} M. and Van Anh, Nguyen and van Stokkum, Ivo H. M.},
title = {Triplet Formation by Charge Recombination in Thin Film Blends of Perylene Red and Pyrene: Developing a Target Model for the Photophysics of Organic Photovoltaic Materials},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11239-11248},
year = {2013},
doi = {10.1021/jp402086p},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp402086p},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp402086p}
}
@article{doi:10.1021/jp401114e,
author = {Kennis, John T. M. and van Stokkum, Ivo H. M. and Peterson, Dayna S. and Pandit, Anjali and Wachter, Rebekka M.},
title = {Ultrafast Proton Shuttling in {Psammocora Cyan Fluorescent Protein}},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11134-11143},
year = {2013},
doi = {10.1021/jp401114e},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp401114e},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp401114e}
}
@article{doi:10.1021/jp311906f,
author = {Zhu, Jingyi and Paparelli, Laura and Hospes, Marijke and Arents, Jos and Kennis, John T. M. and van Stokkum, Ivo H. M. and Hellingwerf, Klaas J. and Groot, Marie Louise},
title = {Photoionization and Electron Radical Recombination Dynamics in {Photoactive Yellow Protein} Investigated by Ultrafast Spectroscopy in the Visible and Near-Infrared Spectral Region},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11042-11048},
year = {2013},
doi = {10.1021/jp311906f},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp311906f},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp311906f}
}
@article{doi:10.1021/jp309570u,
author = {Tian, Lijin and van Stokkum, Ivo H. M. and Koehorst, Rob B. M. and van Amerongen, Herbert},
title = {Light Harvesting and Blue-Green Light Induced Non-Photochemical Quenching in Two Different {C-Phycocyanin} Mutants of {Synechocystis PCC 6803}},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11000-11006},
year = {2013},
doi = {10.1021/jp309570u},
URL = {http://pubs.acs.org/doi/abs/10.1021/jp309570u},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp309570u}
}
@article{Berera2013,
author = {Berera, R. and Gwizdala, M. and van Stokkum, I. H. M. and Kirilovsky, D. and van Grondelle, R.},
title = {Excited States of the Inactive and Active Forms of the {Orange Carotenoid Protein}},
journal = {Journal of Physical Chemistry B},
volume = {117},
number = {31},
pages = {9121-9128},
DOI = {10.1021/jp307420p},
year = {2013}
}
@article{ Joris2013,
author = {Snellenburg, Joris J. and Dekker, Jan P. and van Grondelle, Rienk and van Stokkum, Ivo H. M.},
title = {Functional Compartmental Modeling of the Photosystems in the Thylakoid Membrane at 77 {K}},
journal = {The Journal of Physical Chemistry B},
volume = {117},
number = {38},
pages = {11363-11371},
DOI = {10.1021/jp4031283},
year = {2013}
}
@article{ZhuBJ2013,
author = {Zhu, J. Y. and van Stokkum, I. H. M. and Paparelli, L. and Jones, M. R. and Groot, M. L.},
title = {Early Bacteriopheophytin Reduction in Charge Separation in Reaction Centers of Rhodobacter sphaeroides},
journal = {Biophysical Journal},
volume = {104},
number = {11},
pages = {2493-2502},
DOI = {10.1016/j.bpj.2013.04.026},
year = {2013}
}
@article{Mathes2012b,
author = {Mathes, T. and van Stokkum, I. H. M. and Stierl, M. and Kennis, J. T. M.},
title = {Redox Modulation of Flavin and Tyrosine Determines Photoinduced Proton-coupled Electron Transfer and Photoactivation of {BLUF} Photoreceptors},
journal = {Journal of Biological Chemistry},
volume = {287},
number = {38},
pages = {31725-31738},
ISSN = {0021-9258},
DOI = {10.1074/jbc.M112.391896},
year = {2012},
type = {Journal Article}
}
@article{Snellenburg2012,
author = {Snellenburg, Joris J. and Laptenok, Sergey P. and Seger, Ralf and Mullen, Katharine M. and van Stokkum, Ivo H. M.},
file = {:home/jsg210/scratch/References/Snellenburg et al/Snellenburg et al. - Journal of Statistical Software - 2012.pdf:pdf},
journal = {Journal of Statistical Software},
keywords = {global analysis,glotaran,java,target analysis,time-resolved spectroscopy,timp},
number = {3},
pages = {1--22},
title = {{Glotaran: a Java-based Graphical User Interface for the R-package TIMP}},
url = {http://www.jstatsoft.org/v49/i03},
volume = {49},
year = {2012}
}
@article{vanOort2012,
author = {van Oort, B. and ter Veer, M. J. T. and Groot, M. L. and van Stokkum, I. H. M.},
title = {Excited state proton transfer in strongly enhanced {GFP} (s{GFP2})},
journal = {Physical Chemistry Chemical Physics},
volume = {14},
number = {25},
pages = {8852-8858},
ISSN = {1463-9076},
DOI = {10.1039/c2cp40694b},
year = {2012},
type = {Journal Article}
}
@ARTICLE{Laptenok2012a, author = {Laptenok, S. P. and van Stokkum, I. H. M. and Borst, J. W. and van Oort, B. and Visser, A. J. W. G. and van Amerongen, H.},
title = {Disentangling Picosecond Events That Complicate the Quantitative Use of the Calcium Sensor {YC3.60}},
journal = {The Journal of Physical Chemistry B},
volume = {116},
number = {9},
pages = {3013-3020},
DOI = { 10.1021/jp211830e},
year = {2012}
}
@ARTICLE{Berera2012a, author = {Berera, Rudi and van Stokkum, Ivo H. M. and Gwizdala, Michal and Wilson, Adj{\'e}l{\'e} and Kirilovsky, Diana and van Grondelle, Rienk},
title = {The Photophysics of the {Orange Carotenoid Protein}, a Light-Powered Molecular Switch},
journal = {The Journal of Physical Chemistry B},
volume = {116},
number = {8},
pages = {2568-2574},
DOI = { 10.1021/jp2108329},
year = {2012}
}
@ARTICLE{Marin2012a, author = {Marin, A. and van Stokkum, I. H. M. and Novoderezhkin, V. I. and van Grondelle, R.},
title = {Excitation-induced polarization decay in the plant light-harvesting complex {{LHCII}}},
journal = {Journal of Photochemistry and Photobiology A-Chemistry},
volume = {234},
pages = {91-99},
abstract = {The energy migration dynamics of the major light-harvesting antenna ({LHCII}) of plants was experimentally studied in the chlorophyll Q(y) region (630-700 nm). Using polarized transient absorption (TA) spectroscopy at 77 K we obtain information unaccessible to conventional isotropic TA on the energy transfer dynamics between isoenergetic Chlorophylls (Chls). The data are simultaneously analyzed with a target analysis and interpreted in the context of the exciton model for {LHCII}. The transients at 652 and 662 nm excitation show that the memory of polarization is completely lost with a (3.3-5.0 ps)(-1) rate over the whole Q(y) range, which is attributed to equilibration within monomers and between the three subunits of the {LHCII} trimer. (c) 2012 Elsevier B.V. All rights reserved.},
year = {2012}
}
@ARTICLE{Tian2012a, author = {Tian, L. J. and Gwizdala, M. and van Stokkum, I. H. M. and Koehorst, R. B. M. and Kirilovsky, D. and van Amerongen, H.},
title = {Picosecond Kinetics of Light Harvesting and Photoprotective Quenching in Wild-Type and Mutant Phycobilisomes Isolated from the Cyanobacterium Synechocystis {PCC} 6803},
journal = {Biophysical Journal},
volume = {102},
number = {7},
pages = {1692-1700},
abstract = {In high light conditions, cyanobacteria dissipate excess absorbed energy as heat in the light-harvesting phycobilisomes (PBs) to protect the photosynthetic system against photodamage. This process requires the binding of the red active form of the Orange Carotenoid Protein (OCPr), which can effectively quench the excited state of one of the allophycocyanin bilins. Recently, an in vitro reconstitution system was developed using isolated OCP and isolated PBs from Synechocystis PCC 6803. Here we have used spectrally resolved picosecond fluorescence to study wild-type and two mutated PBs. The results demonstrate that the quenching for all types of PBs takes place on an allophycocyanin bilin emitting at 660 nm (APC(Q)(660)) with a molecular quenching rate that is faster than (1 ps)(-1). Moreover, it is concluded that both the mechanism and the site of quenching are the same in vitro and in vivo. Thus, utilization of the in vitro system should make it possible in the future to elucidate whether the quenching is caused by charge transfer between APC(Q)(660) and OCP or by excitation energy transfer from APC(Q)(660) to the S-1 state of the carotenoid-a distinction that is very hard, if not impossible, to make in vivo.},
year = {2012}
}
@ARTICLE{Mathes2012a,
author = {Mathes, T. and Zhu, J. Y. and van Stokkum, I. H. M. and Groot, M. L. and Hegemann, P. and Kennis, J. T. M.},
title = {Hydrogen Bond Switching among Flavin and Amino Acids Determines the Nature of Proton-Coupled Electron Transfer in BLUF Photoreceptors},
journal = {Journal of Physical Chemistry Letters},
volume = {3},
number = {2},
pages = {203-208},
year = {2012}
}
@ARTICLE{Stahl2012,
author = {Stahl, A. D. and Crouch, L. I. and Jones, M. R. and Stokkum, I. and Van Grondelle, R. and Groot, M. L.},
title = {Role of PufX in Photochemical Charge Separation in the {RC-LH1} Complex from Rhodobacter sphaeroides: An Ultrafast Mid-IR Pump-Probe Investigation},
journal = {Journal of Physical Chemistry B},
volume = {116},
number = {1},
pages = {434-444},
year = {2012}
}
@ARTICLE{Sytina2012,
author = {Sytina, O. A. and van Stokkum, I. H. M. and Heyes, D. J. and Hunter, C. N. and Groot, M. L.},
title = {Spectroscopic characterization of the first ultrafast catalytic intermediate in protochlorophyllide oxidoreductase},
journal = {Physical Chemistry Chemical Physics},
volume = {14},
number = {2},
pages = {616-625},
year = {2012}
}
@ARTICLE{Abbott1997,
author = {Abbott, Geoffrey W. and Bloemendal, Michael and Van Stokkum, Ivo
H. M. and Mercer, Eric A. J. and Miller, Rob T. and Sewing, Sabine
and Wolters, Mark and Pongs, Olaf and Srai, Surjit K. S.},
title = {Secondary structure, stability and tetramerisation of recombinant
{KV1.1} potassium channel cytoplasmic {N}-terminal fragment},
journal = {Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular
Enzymology},
year = {1997},
volume = {1341},
pages = {71--78},
month = {Aug},
day = {15},
issue = {1},
keywords = {Fourier transform infrared spectroscopy},
url = {http://www.sciencedirect.com/science/article/B6T21-3TGKN3C-7/2/eb9c9b15b22407e5419bd9fa97abb357}
}
@ARTICLE{MaximeAlexandre09152007,
author = {Alexandre, Maxime T. A. and L{\"{u}}hrs, Daniel C. and van Stokkum,
Ivo H. M. and Hiller, Roger and Groot, Marie-Louise and Kennis, John
T. M. and van Grondelle, Rienk},
title = {{Triplet State Dynamics in Peridinin-Chlorophyll-a-Protein: A New
Pathway of Photoprotection in LHCs?}},
journal = {Biophys. J.},
year = {2007},
volume = {93},
pages = {2118-2128},
number = {6},
abstract = {This work investigates the interaction of carotenoid and chlorophyll
triplet states in the peridinin-chlorophyll-a-protein (PCP) of Amphidinium
carterae using step-scan Fourier transform infrared spectroscopy.
We identify two carotenoid triplet state lifetimes of [~]13 and [~]42
{micro}s in the spectral region between 1800 and 1100 cm1 after excitation
of the blue' and red' peridinin (Per) conformers and the Qy of chlorophyll-a
(Chl-a). The fast and slow decaying triplets exhibit different spectral
signatures in the carbonyl region. The fast component generated at
all excitation wavelengths is from a major conformer with a lactone
stretching mode bleach at 1745 cm1. One (1720 cm1) and two (1720
cm1 and 1741 cm1) different Per conformers are observed for the slow
component upon 670- and 530480-nm excitation, respectively. The above
result implies that 3Per triplets are formed via two different pathways,
corroborating and complementing visible triplet-singlet (T-S) spectra
(Kleima et al., Biochemistry (2000), 39, 5184). Surprisingly, all
difference spectra show that Per and Chl-a modes are simultaneously
present during the 3Per decay, implying significant involvement of
3Chl-a in the 3Per state. We suggest that this Per-Chl-a interaction
via a delocalized triplet state lowers the 3Per energy and thus provides
a general, photoprotection mechanism for light-harvesting antenna
complexes. },
doi = {10.1529/biophysj.107.106674},
eprint = {http://www.biophysj.org/cgi/reprint/93/6/2118.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/93/6/2118}
}
@ARTICLE{BaffreauJ._jp066415+,
author = {Baffreau, J. and Leroy-Lhez, S. and Hudhomme, P. and Groeneveld,
M.M. and van Stokkum, I. H. M. and Williams, R.M.},
title = {Superabsorbing Fullerenes: Spectral and Kinetic Characterization
of Photoinduced Interactions in Perylenediimide-Fullerene-{$C_{60}$}
Dyads},
journal = {Journal of Physical Chemistry A},
year = {2006},
volume = {110},
pages = {13123-13125},
number = {49},
issn = {1089-5639},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp066415+}
}
@ARTICLE{BalkowskiG._jp050404j,
author = {Balkowski, G. and Szemik-Hojniak, A. and van Stokkum, I. H. M. and
Zhang, H. and Buma, W.J.},
title = {Femtosecond Excited State Studies of the Two-Center Three-Electron
Bond Driven Twisted Internal Charge Transfer Dynamics in 1,8-Bis(dimethylamino)naphthalene},
journal = {Journal of Physical Chemistry A},
year = {2005},
volume = {109},
pages = {3535-3541},
number = {16},
issn = {1089-5639},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp050404j}
}
@ARTICLE{Baltuska1997,
author = {Baltu{\v{s}}ka, A. and van Stokkum, I. H. M. and Kroon, A. and Monshouwer,
R. and Hellingwerf, K. J. and van Grondelle, R.},
title = {The primary events in the photoactivation of yellow protein},
journal = {Chemical Physics Letters},
year = {1997},
volume = {270},
pages = {263--266},
month = {May},
day = {23},
issue = {3-4},
url = {http://www.sciencedirect.com/science/article/B6TFN-3S9T08S-W/2/c08618cc95af10869ee68e2651bfddb0}
}
@ARTICLE{BeekmanL.M.P._jp963447w,
author = {Beekman, L.M.P. and Frese, R.N. and Fowler, G.J.S. and Picorel, R.
and Cogdell, R.J. and van Stokkum, I. H. M. and Hunter, C.N. and
van Grondelle, R.},
title = {Characterization of the Light-Harvesting Antennas of Photosynthetic
Purple Bacteria by Stark Spectroscopy. 2. {LH2} Complexes: Influence
of the Protein Environment},
journal = {Journal of Physical Chemistry B},
year = {1997},
volume = {101},
pages = {7293-7301},
number = {37},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp963447w}
}
@INPROCEEDINGS{beekc,
author = {Beekman, L.M.P. and Jones, M.R. and Van Stokkum, I. H. M. and Van
Grondelle, R.},
title = {Wavelength dependence of the stimulated emission decay of membrane
bound {Rb.} sphaeroides reaction centers and observation of a {BChl-a}
anion involved in electron transfer},
booktitle = {Photosynthesis: from Light to Biosphere},
year = {1995},
editor = {P. Mathis},
volume = {1},
pages = {495-498},
publisher = {Dordrecht, Kluwer}
}
@ARTICLE{BeekmanL.M.P._jp963445b,
author = {Beekman, L.M.P. and Steffen, M. and van Stokkum, I. H. M. and Olsen,
J.D. and Hunter, C.N. and Boxer, S.G. and van Grondelle, R.},
title = {Characterization of the Light-Harvesting Antennas of Photosynthetic
Purple Bacteria by Stark Spectroscopy. 1. LH1 Antenna Complex and
the B820 Subunit from Rhodospirillum rubrum},
journal = {Journal of Physical Chemistry B},
year = {1997},
volume = {101},
pages = {7284-7292},
number = {37},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp963445b}
}
@ARTICLE{BeekmanL.M.P._jp953054h,
author = {Beekman, L.M.P. and van Stokkum, I. H. M. and Monshouwer, R. and
Rijnders, A.J. and McGlynn, P. and Visschers, R.W. and Jones, M.R.
and van Grondelle, R.},
title = {Primary Electron Transfer in Membrane-Bound Reaction Centers with
Mutations at the {M210} Position},
journal = {Journal of Physical Chemistry},
year = {1996},
volume = {100},
pages = {7256-7268},
number = {17},
issn = {0022-3654},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp953054h}
}
@ARTICLE{BeekmanL.M.P._bi00045a012,
author = {Beekman, L. M. P. and Visschers, R. W. and Monshouwer, R. and Heer-Dawson,
M. and Mattioli, T. A. and McGlynn, P. and Hunter, C. N. and Robert,
B. and van Stokkum, I. H. M.},
title = {Time-resolved and steady-state spectroscopic analysis of membrane-bound
reaction centers from Rhodobacter sphaeroides: Comparisons with detergent-solubilized
complexes},
journal = {Biochemistry},
year = {1995},
volume = {34},
pages = {14712-14721},
number = {45},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi00045a012}
}
@ARTICLE{RudiBerera04042006,
author = {Berera, Rudi and Herrero, Christian and van Stokkum, Ivo H. M. and
Vengris, Mikas and Kodis, Gerdenis and Palacios, Rodrigo E. and van
Amerongen, Herbert and van Grondelle, Rienk and Gust, Devens and
Moore, Thomas A. and Moore, Ana L. and Kennis, John T. M.},
title = {{A simple artificial light-harvesting dyad as a model for excess
energy dissipation in oxygenic photosynthesis}},
journal = {PNAS},
year = {2006},
volume = {103},
pages = {5343-5348},
number = {14},
doi = {10.1073/pnas.0508530103},
file = {5343.pdf:http\://www.pnas.org/cgi/reprint/103/14/5343.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/103/14/5343}
}
@ARTICLE{RudiBerera2006PPS,
author = {Berera, Rudi and Moore, Gary F. and van Stokkum, Ivo H. M. and Kodis,
Gerdenis and Liddell, Paul A. and Gervaldo, Miguel and van Grondelle,
Rienk and Kennis, John T. M. and Gust, Devens and Moore, Thomas A.
and Moore, Ana L. },
title = {{Charge separation and energy transfer in a caroteno-C{$_{60}$} dyad:
photoinduced electron transfer from the carotenoid excited states}},
journal = {Photochem. Photobiol. Sci.},
year = {2006},
volume = {5},
pages = {1142-1149}
}
@ARTICLE{BereraBJ2009,
author = {Berera, Rudi and van Stokkum, Ivo H. M. and d{'}Haene, Sandrine and
Kennis, John T. M. and van Grondelle, Rienk and Dekker, Jan P.},
title = {A Mechanism of Energy Dissipation in Cyanobacteria},
journal = {Biophysical Journal},
year = {2009},
volume = {96},
pages = {2261-2267},
number = {6},
url = {http://www.cell.com/biophysj/abstract/S0006-3495(09)00329-4}
}
@ARTICLE{Berera2010,
author = {Rudi Berera and Ivo H. M. van Stokkum and John T.M. Kennis and Rienk
van Grondelle and Jan P. Dekker},
title = {The light-harvesting function of carotenoids in the cyanobacterial
stress-inducible {IsiA} complex},
journal = {Chemical Physics},
year = {2010},
volume = {373},
pages = {65-70},
number = {1-2},
abstract = {We present a spectroscopic investigation of the light-harvesting role
of carotenoids in aggregates of the IsiA pigment-protein complex
of the cyanobacterium Synechocystis PCC 6803. The results show that
carotenoids in IsiA transfer energy on the sub-100 fs timescale from
the S-2 state to chlorophyll to about the same extent as in the related
pigment-protein complexes CP43 and CP47. Selective excitation at
the red edge of the S-2 absorption of the carotenoids shows that
echinenone is more efficient in energy transfer to chlorophyll (37%)
when compared to the other carotenoid species in the system (22%).
(C) 2010 Elsevier B. V. All rights reserved.},
doi = {DOI: 10.1016/j.chemphys.2010.01.011},
issn = {0301-0104},
keywords = {Carotenoids},
url = {http://www.sciencedirect.com/science/article/B6TFM-4Y7P71C-1/2/d6a1fdc6d96d3554c3f99f646eadca3c}
}
@ARTICLE{BereraR_jp071010q,
author = {Berera, R. and van Stokkum, I. H. M. and Kodis, G. and Keirstead,
A.E. and Pillai, S. and Herrero, C. and Palacios, R.E. and Vengris,
M. and van Grondelle, R. and Gust, D. and Moore, T.A. and Moore,
A.L. and Kennis, J.T.M.},
title = {Energy Transfer, Excited-State Deactivation, and Exciplex Formation
in Artificial Caroteno-Phthalocyanine Light-Harvesting Antennas},
journal = {Journal of Physical Chemistry B},
year = {2007},
volume = {111},
pages = {6868-6877},
number = {24},
affiliation = {Department of Biophysics, Division of Physics and Astronomy, Faculty
of Sciences, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands,
and Department of Chemistry and Biochemistry and the Center for the
Study of Early Events in Photosynthesis, Arizona State University,
Tempe, Arizona 85287-1604},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp071010q}
}
@ARTICLE{Binsl:Mullen:vanStokkum:Heringa:vanBeek:2007:JSSOBK:v18i07,
author = {Thomas W. Binsl and Katharine M. Mullen and Ivo H. M. van Stokkum
and Jaap Heringa and Johannes H. G. M. van Beek},
title = {{FluxSimulator}: An {R} Package to Simulate Isotopomer Distributions
in Metabolic Networks},
journal = {Journal of Statistical Software},
year = {2007},
volume = {18},
number = {7},
accepted = {2007-01-10},
bibdate = {2007-01-10},
coden = {JSSOBK},
issn = {1548-7660},
submitted = {2006-09-28},
url = {http://www.jstatsoft.org/v18/i07}
}
@INCOLLECTION{ivo91,
author = {Bloemendal, M. and Van Stokkum, I. H. M. and Van Grondelle, R.},
title = {A new approach for the estimation of protein secondary structure
from circular dichroism spectroscopy},
booktitle = {Spectroscopy of biological molecules},
publisher = {Royal Society of Chemistry, Cambridge},
year = {1991},
editor = {Hester, R.E. and Girling, R.B.},
pages = {33-34}
}
@ARTICLE{Bonetti2010,
author = {Bonetti, C. and Alexandre, M. T. A. and van Stokkum, I. H. M. and
Hiller, R. G. and Groot, M. L. and van Grondelle, R. and Kennis,
J. T. M.},
title = {Identification of excited-state energy transfer and relaxation pathways
in the peridinin-chlorophyll complex: an ultrafast mid-infrared study},
journal = {Physical Chemistry Chemical Physics},
year = {2010},
volume = {12},
pages = {9256-9266},
number = {32},
abstract = {The peridinin chlorophyll-a protein (PCP) is a water-soluble, trimeric
light harvesting complex found in marine dinoflagellates that binds
peridinin and Chl-a in an unusual stoichiometric ratio of 4 : 1.
In this paper, the pathways of excited-state energy transfer and
relaxation in PCP were identified by means of femtosecond visible-pump,
mid-infrared probe spectroscopy. In addition, excited-state relaxation
of peridinin dissolved in organic solvent (CHCl3 and MeOH) was investigated.
For peridinin in solution, the transient IR signatures of the low-lying
S-1 and intramolecular charge transfer (ICT) states were similar,
in line with a previous ultrafast IR study. In PCP, excitation of
the optically allowed S-2 state of peridinin results in ultrafast
energy transfer to Chl-a, in competition with internal conversion
to low-lying optically forbidden states of peridinin. After vibrational
relaxation of the peridinin hot S-1 state in 150 fs, two separate
low-lying peridinin singlet excited states are distinguished, assigned
to an ICT state and to a slowly transferring, vibrationally relaxed
S-1 state. These states exhibit different lactone bleaches, indicating
that the ICT and S-1 states localize on distinct peridinins. Energy
transfer from the peridinin ICT state to Chl-a constitutes the dominant
energy transfer channel and occurs with a time constant of 2 ps.
The peridinin S-1 state mainly decays to the ground state through
internal conversion, in competition with slow energy transfer to
Chl-a. The singlet excited state of Chl-a undergoes intersystem crossing
(ISC) to the triplet state on the nanosecond timescale, followed
by rapid triplet excitation energy transfer (TEET) from Chl-a to
peridinin, whereby no Chl-a triplet is observed but rather a direct
rise of the peridinin triplet. The latter contains some Chl-a features
due to excitonic coupling of the pigments. The peridinin triplet
state shows a lactone bleach mode at 1748 cm(-1), while that of the
peridinin ICT state is located at 1745 cm(-1), indicating that the
main channels of singlet and triplet energy transfer in PCP proceed
through distinct peridinins. Our results are consistent with an energy
transfer scheme where the ICT state mainly localizes on Per621/611
and Per623/613, the S1 state on Per622/612 and the triplet state
on Per624/614.}
}
@ARTICLE{biophysj.108.139246,
author = {Cosimo Bonetti and Tilo Mathes and Ivo H. M. van Stokkum and Katharine
M. Mullen and Marie{-}Louise Groot and Rienk van Grondelle and Peter
Hegemann and John T.M. Kennis},
title = {Hydrogen bond switching among flavin and amino acid side chains in
the {BLUF} photoreceptor observed by ultrafast infrared spectroscopy},
journal = {Biophysical Journal},
year = {2008},
volume = {95},
pages = {4790-4802},
url = {http://www.biophysj.org/cgi/content/abstract/95/10/4790}
}
@ARTICLE{cosimoB09,
author = {Bonetti, Cosimo and Stierl, Manuela and Mathes, Tilo and van Stokkum,
Ivo H. M. and Mullen, Katharine M. and Cohen-Stuart, Thomas A. and
van Grondelle, Rienk and Hegemann, Peter and Kennis, John T. M.},
title = {The Role of Key Amino Acids in the Photoactivation Pathway of the
Synechocystis Slr1694 BLUF Domain},
journal = {Biochemistry},
year = {2009},
volume = {48},
pages = {11458-11469},
number = {48},
doi = {10.1021/bi901196x}
}
@ARTICLE{i96,
author = {van Brederode, ME and Hoff, WD and van Stokkum, I. H. M. and Groot,
ML and Hellingwerf, KJ},
title = {Protein folding thermodynamics applied to the photocycle of photoactive
yellow protein},
journal = {Biophysical Journal},
year = {1996},
volume = {71},
pages = {365-380}
}
@ARTICLE{vanBrederodeM.E._bi9829128,
author = {van Brederode, M.E. and van Stokkum, I. H. M. and Katilius, E. and
van Mourik, F. and Jones, M.R. and van Grondelle, R.},
title = {Primary Charge Separation Routes in the {BChl:BPhe} Heterodimer Reaction
Centers of Rhodobacter sphaeroides},
journal = {Biochemistry},
year = {1999},
volume = {38},
pages = {7545-7555},
number = {23},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9829128}
}
@ARTICLE{vanBrederodeM.E._bi9950793,
author = {van Brederode, M.E. and van Stokkum, I. H. M. and Katilius, E. and
van Mourik, F. and Jones, M.R. and van Grondelle, R.},
title = {Primary Charge Separation Routes in the {BChl:BPhe} Heterodimer Reaction
Centers of Rhodobacter sphaeroides},
journal = {Biochemistry},
year = {1999},
volume = {38},
pages = {9556-9556},
number = {29},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9950793}
}
@ARTICLE{MarionE.vanBrederode03021999,
author = {van Brederode, Marion E. and van Mourik, Frank and van Stokkum, Ivo
H. M. and Jones, Michael R. and van Grondelle, Rienk},
title = {{Multiple pathways for ultrafast transduction of light energy in
the photosynthetic reaction center of Rhodobacter sphaeroides}},
journal = {PNAS},
year = {1999},
volume = {96},
pages = {2054-2059},
number = {5},
doi = {10.1073/pnas.96.5.2054},
file = {2054.pdf:http\://www.pnas.org/cgi/reprint/96/5/2054.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/96/5/2054}
}
@ARTICLE{photo_98,
author = {Marion E. van Brederode and Justin P. Ridge and Ivo H. M. van Stokkum
and Frank van Mourik and Michael R. Jones and Rienk van Grondelle},
title = {On the efficiency of energy transfer and the different pathways of
electron transfer in mutant reaction centers of Rhodobacter sphaeroides},
journal = {Photosynthesis Research},
year = {1998},
volume = {55},
pages = {141--146},
number = {2},
url = {http://www.springerlink.com/content/v702557x62725142}
}
@ARTICLE{Carroll2010,
author = {Carroll, E. C. and Song, S. H. and Kumauchi, M. and van Stokkum,
I. H. M. and Jailaubekov, A. and Hoff, W. D. and Larsen, D. S.},
title = {Subpicosecond Excited-State Proton Transfer Preceding Isomerization
During the Photorecovery of Photoactive Yellow Protein},
journal = {Journal of Physical Chemistry Letters},
year = {2010},
volume = {1},
pages = {2793-2799},
number = {19},
abstract = {The ultrafast excited-state dynamics underlying the receptor state
photorecovery is resolved in the M100A mutant of the photoactive
yellow protein (PYP) from Halorhodospira halophila. The M100A PYP
mutant, with its distinctly slower photocycle than wt PYP, allows
isolation of the pB signaling state for study of the photodynamics
of the protonated chromophore cis-p-coumaric acid. Transient absorption
signals indicate a subpicosecond excited-state proton-transfer reaction
in the pB state that results in chromophore deprotonation prior to
the cis-trans isomerization required in the photorecovery dynamics
of the pG state. Two terminal photoproducts are observed, a blue-absorbing
species presumed to be deprotonated trans-p-coumaric acid and an
ultraviolet-ansorbing protonated photoproduct. These two photoproducts
are hypothesized to originated from an equilibrium of open and closed
folded forms of the signaling state, I-2 and I-2'.}
}
@ARTICLE{doi:10.1021/jp107935f,
author = {Chen, Xiyi and Larsen, Delmar S. and Bradforth, Stephen E. and van
Stokkum, Ivo H. M.},
title = {Broadband Spectral Probing Revealing Ultrafast Photochemical Branching
after Ultraviolet Excitation of the Aqueous Phenolate Anion},
journal = {The Journal of Physical Chemistry A},
year = {2011},
volume = {{115}},
pages = {{3807-3819}},
number = {{16}},
month = {{Apr 28}},
doi = {10.1021/jp107935f},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp107935f},
url = {http://pubs.acs.org/doi/abs/10.1021/jp107935f}
}
@ARTICLE{Cofino2005,
author = {Cofino, Wim P. and van Stokkum, Ivo H. M. and van Steenwijk, Jaap
and Wells, David E.},
title = {A new model for the inference of population characteristics from
experimental data using uncertainties: Part {II}. Application to
censored datasets},
journal = {Analytica Chimica Acta},
year = {2005},
volume = {533},
pages = {31--39},
month = {Mar},
day = {21},
issue = {1},
keywords = {Censored data},
url = {http://www.sciencedirect.com/science/article/B6TF4-4F1J8PY-5/2/29f748e8695962cdce5f8f8738329ec3}
}
@ARTICLE{Cofino2000,
author = {Cofino, Wim P. and van Stokkum, Ivo H. M. and Wells, David E. and
Ariese, Freek and Wegener, Jan-Willem M. and Peerboom, Renee A. L.},
title = {A new model for the inference of population characteristics from
experimental data using uncertainties. Application to interlaboratory
studies},
journal = {Chemometrics and Intelligent Laboratory Systems},
year = {2000},
volume = {53},
pages = {37--55},
month = {Nov},
day = {13},
issue = {1-2},
keywords = {Population characteristics},
url = {http://www.sciencedirect.com/science/article/B6TFP-41H9NH7-3/2/70ba5522c9ed18193d3c054836259e5a}
}
@ARTICLE{doi:10.1021/bi101565w,
author = {Di Donato, Mariangela and Stahl, Andreas D. and van Stokkum, Ivo
H. M. and van Grondelle, Rienk and Groot, Marie-Louise},
title = {Cofactors Involved in Light-Driven Charge Separation in Photosystem
{I} Identified by Subpicosecond Infrared Spectroscopy},
journal = {Biochemistry},
year = {2011},
volume = {50},
pages = {480-490},
number = {4},
doi = {10.1021/bi101565w},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi101565w},
url = {http://pubs.acs.org/doi/abs/10.1021/bi101565w}
}
@ARTICLE{DiDonatoM_jp068315,
author = {DiDonato, M. and van Grondelle, R. and van Stokkum, I. H. M. and
Groot, M.L.},
title = {Excitation Energy Transfer in the Photosystem {II} Core Antenna Complex
CP43 Studied by Femtosecond Visible/Visible and Visible/Mid-Infrared
Pump Probe Spectroscopy},
journal = {Journal of Physical Chemistry B},
year = {2007},
volume = {111},
pages = {7345-7352},
number = {25},
affiliation = {Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit,
1081 HV Amsterdam, The Netherlands},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp068315+}
}
@ARTICLE{DoustA.B._jp051173j,
author = {Doust, A.B. and van Stokkum, I. H. M. and Larsen, D.S. and Wilk,
K.E. and Curmi, P.M.G. and van Grondelle, R. and Scholes, G.D.},
title = {Mediation of Ultrafast Light-Harvesting by a Central Dimer in Phycoerythrin
545 Studied by Transient Absorption and Global Analysis},
journal = {Journal of Physical Chemistry B},
year = {2005},
volume = {109},
pages = {14219-14226},
number = {29},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp051173j}
}
@ARTICLE{FreseR.N._bi0273516,
author = {Frese, R.N. and Germano, M. and de Weerd, F.L. and van Stokkum, I.
H. M. and Shkuropatov, A.Ya. and Shuvalov, V.A. and van Gorkom, H.J.
and van Grondelle, R. and Dekker, J.P.},
title = {Electric Field Effects on the Chlorophylls, Pheophytins, and {$\beta$}-Carotenes
in the Reaction Center of Photosystem {II}},
journal = {Biochemistry},
year = {2003},
volume = {42},
pages = {9205-9213},
number = {30},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi0273516}
}
@INPROCEEDINGS{i98b,
author = {Frese, RN and Gobets, B and van Stokkum, I. H. M. and van Grondelle,
R and van Mourik, F},
title = {Dielectric relaxation on a picosecond time-scale at 77 {K}: a fluorescence
study on the {LH2 B800-820} complex of {R}ps. acidophila},
booktitle = {Photosynthesis: Mechanisms and Effects},
year = {1998},
editor = {Garab, G},
pages = {41-44},
publisher = {Kluwer Academic Publishers, Dordrecht}
}
@ARTICLE{photo_05,
author = {Raoul Frese and Uwe Oberheide and Ivo van Stokkum and Rienk van Grondelle
and Markus Foidl and J{\"u}rgen Oelze and Herbert van Amerongen},
title = {The organization of bacteriochlorophyll c in chlorosomes from Chloroflexus
aurantiacus and the structural role of carotenoids and protein},
journal = {Photosynthesis Research},
year = {1997},
volume = {54},
pages = {115--126},
issue = {2},
url = {http://www.springerlink.com/content/l04663t5qj575152}
}
@ARTICLE{Frese2002,
author = {Frese, Raoul N. and Palacios, Miguel A. and Azzizi, Aissa and van
Stokkum, Ivo H. M. and Kruip, Jochen and Rogner, Matthias and Karapetyan,
Navassard V. and Schlodder, Eberhard and van Grondelle, Rienk and
Dekker, Jan P.},
title = {Electric field effects on red chlorophylls, {$\beta$}-carotenes and
{P700} in cyanobacterial Photosystem {I} complexes},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {2002},
volume = {1554},
pages = {180--191},
month = {Jul},
day = {01},
issue = {3},
keywords = {Synechocystis PCC 6803},
url = {http://www.sciencedirect.com/science/article/B6T1S-4639K94-2/2/f35393c5825b6bf4795ee14986204c99}
}
@INPROCEEDINGS{m04,
author = {M. Gauden and S. Crosson and I. H. M. van Stokkum and R.van Grondelle
and K. Moffat and J.T.M. Kennis},
title = {Low-temperature and time-resolved spectroscopic characterization
of the {LOV2} domain of Avena sativa phototropin},
booktitle = {Volume 5463 - Femtosecond Laser Applications in Biology},
year = {2004},
pages = {97-104},
publisher = {Proceedings of SPIE},
editors = {S. Avrillier and J.M. Tualle}
}
@ARTICLE{GaudenM_bi7006433,
author = {Gauden, M. and Grinstead, J.S. and Laan, W. and van Stokkum, I. H.
M. and Avila-Perez, M. and Toh, K.C. and Boelens, R. and Kaptein,
R. and van Grondelle, R. and Hellingwerf, K.J. and Kennis, J.T.M.},
title = {On the Role of Aromatic Side Chains in the Photoactivation of BLUF
Domains},
journal = {Biochemistry},
year = {2007},
volume = {46},
pages = {7405-7415},
number = {25},
affiliation = {Biophysics Group, Department of Physics and Astronomy, Faculty of
Sciences, Vrije Universiteit, De Boelelaan 1081, 1081HV Amsterdam,
The Netherlands, Department of NMR spectroscopy, Bijvoet Center for
Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands, and Swammerdam Institute for Life Science, University
of Amsterdam, Nieuwe Achtergracht 166, 1018 WY Amsterdam, The Netherlands},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi7006433}
}
@ARTICLE{MagdalenaGauden07182006,
author = {Gauden, Magdalena and van Stokkum, Ivo H. M. and Key, Jason M. and
L{\"{u}}hrs, Daniel Ch. and van Grondelle, Rienk and Hegemann, Peter
and Kennis, John T. M.},
title = {{Hydrogen-bond switching through a radical pair mechanism in a flavin-binding
photoreceptor}},
journal = {PNAS},
year = {2006},
volume = {103},
pages = {10895-10900},
number = {29},
doi = {10.1073/pnas.0600720103},
file = {10895.pdf:http\://www.pnas.org/cgi/reprint/103/29/10895.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/103/29/10895}
}
@ARTICLE{GaudenM._bi047359a,
author = {Gauden, M. and Yeremenko, S. and Laan, W. and van Stokkum, I. H.
M. and Ihalainen, J.A. and van Grondelle, R. and Hellingwerf, K.J.
and Kennis, J.T.M.},
title = {Photocycle of the Flavin-Binding Photoreceptor AppA, a Bacterial
Transcriptional Antirepressor of Photosynthesis Genes},
journal = {Biochemistry},
year = {2005},
volume = {44},
pages = {3653-3662},
number = {10},
affiliation = {Department of Biophysics, Faculty of Sciences, Vrije Universiteit,
De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, and Swammerdam
Institute for Life Sciences, University of Amsterdam, Nieuwe Achtergracht
166, 1018 WY Amsterdam, The Netherlands},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi047359a}
}
@ARTICLE{Gensch2002,
author = {Gensch, T. and Gradinaru, C. C. and van Stokkum, I. H. M. and Hendriks,
J. and Hellingwerf, K. J. and van Grondelle, R.},
title = {The primary photoreaction of photoactive yellow protein ({PYP}):
anisotropy changes and excitation wavelength dependence},
journal = {Chemical Physics Letters},
year = {2002},
volume = {356},
pages = {347--354},
month = {Apr},
day = {22},
issue = {3-4},
url = {http://www.sciencedirect.com/science/article/B6TFN-45F9235-B/2/0149a895b50bb6debf89a672c79a1f18}
}
@ARTICLE{M.Germano03012004,
author = {Germano, M. and Gradinaru, C. C. and Shkuropatov, A. Ya. and van
Stokkum, I. H. M. and Shuvalov, V. A. and Dekker, J. P. and Grondelle,
R. van and van Gorkom, H. J.},
title = {{Energy and Electron Transfer in Photosystem {II} Reaction Centers
with Modified Pheophytin Composition}},
journal = {Biophysical Journal},
year = {2004},
volume = {86},
pages = {1664-1672},
number = {3},
file = {1664.pdf:http\://www.biophysj.org/cgi/reprint/86/3/1664.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/86/3/1664}
}
@ARTICLE{K.Gibasiewicz03012005,
author = {Gibasiewicz, K. and Croce, R. and Morosinotto, T. and Ihalainen,
J. A. and van Stokkum, I. H. M. and Dekker, J. P. and Bassi, R. and
van Grondelle, R.},
title = {{Excitation Energy Transfer Pathways in {Lhca}4}},
journal = {Biophysical Journal},
year = {2005},
volume = {88},
pages = {1959-1969},
number = {3},
doi = {10.1529/biophysj.104.049916},
file = {1959.pdf:http\://www.biophysj.org/cgi/reprint/88/3/1959.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/88/3/1959}
}
@ARTICLE{Giera2010106,
author = {Wojciech Giera and V.M. Ramesh and Andrew N. Webber and Ivo van Stokkum
and Rienk van Grondelle and Krzysztof Gibasiewicz},
title = {Effect of the {P700} pre-oxidation and point mutations near {A0}
on the reversibility of the primary charge separation in Photosystem
{I} from {Chlamydomonas reinhardtii}},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {2010},
volume = {1797},
pages = {106 - 112},
number = {1},
doi = {DOI: 10.1016/j.bbabio.2009.09.006},
issn = {0005-2728},
keywords = {Time-resolved fluorescence},
url = {http://www.sciencedirect.com/science/article/B6T1S-4X7GMJJ-3/2/94690520750a9e06b785410279d33c99}
}
@ARTICLE{GobetsB._jp011901c,
author = {Gobets, B. and Kennis, J.T.M. and Ihalainen, J.A. and Brazzoli, M.
and Croce, R. and van Stokkum, I. H. M. and Bassi, R. and Dekker,
J.P. and van Amerongen, H. and Fleming, G.R. and van Grondelle, R.},
title = {Excitation Energy Transfer in Dimeric Light Harvesting Complex {I}:
A Combined Streak-Camera/Fluorescence Upconversion Study},
journal = {Journal of Physical Chemistry B},
year = {2001},
volume = {105},
pages = {10132-10139},
number = {41},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp011901c}
}
@ARTICLE{BasGobets12012003,
author = {Gobets, Bas and van Stokkum, Ivo H. M. and van Mourik, Frank and
Dekker, Jan P. and van Grondelle, Rienk},
title = {{Excitation Wavelength Dependence of the Fluorescence Kinetics in
{Photosystem I} Particles from Synechocystis {PCC} 6803 and Synechococcus
elongatus}},
journal = {Biophysical Journal},
year = {2003},
volume = {85},
pages = {3883-3898},
number = {6},
file = {3883.pdf:http\://www.biophysj.org/cgi/reprint/85/6/3883.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/85/6/3883}
}
@INPROCEEDINGS{i98c,
author = {Gobets, B and van Stokkum, I. H. M. and van Mourik, F and R{\"o}gner,
M and Kruip, J and Dekker, JP and van Grondelle R},
title = {Time-resolved fluorescence measurements of photosystem 1 from Synechocystis
{PCC} 6803},
booktitle = {Photosynthesis: Mechanisms and Effects},
year = {1998},
editor = {Garab, G},
pages = {571-574},
publisher = {Kluwer Academic Publishers, Dordrecht}
}
@ARTICLE{BasGobets07012001,
author = {Gobets, Bas and van Stokkum, Ivo H. M. and Rogner, Matthias and Kruip,
Jochen and Schlodder, Eberhard and Karapetyan, Navassard V. and Dekker,
Jan P. and van Grondelle, Rienk},
title = {{Time-Resolved Fluorescence Emission Measurements of Photosystem
I Particles of Various Cyanobacteria: A Unified Compartmental Model}},
journal = {Biophysical Journal},
year = {2001},
volume = {81},
pages = {407-424},
number = {1},
file = {407.pdf:http\://www.biophysj.org/cgi/reprint/81/1/407.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/81/1/407}
}
@ARTICLE{i98a,
author = {Gradinaru, CC and {\"O}zdemir, S and G{\"u}len, D and van Stokkum,
I. H. M. and van Grondelle, R and van Amerongen, H},
title = {The flow of excitation in {LHC{II}} monomers: Implications for the
structural model of the major plant antenna},
journal = {Biophysical Journal},
year = {1998},
volume = {75},
pages = {3064-3077}
}
@INPROCEEDINGS{i98x,
author = {Gradinaru, CC and van Stokkum, I. H. M. and van Grondelle, R and
van Amerongen},
title = {Ultrafast absorption changes of the LHC{II} carotenoids upon selective
excitation of the chlorophylls},
booktitle = {Photosynthesis: Mechanisms and Effects},
year = {1998},
editor = {Garab, G},
pages = {277-281},
publisher = {Kluwer Academic Publishers, Dordrecht}
}
@ARTICLE{GradinaruC.C._jp001752i,
author = {Gradinaru, C.C. and van Stokkum, I. H. M. and Pascal, A.A. and van
Grondelle, R. and van Amerongen, H.},
title = {Identifying the Pathways of Energy Transfer between Carotenoids and
Chlorophylls in {{LHCII}} and {CP29}. A Multicolor, Femtosecond Pump-Probe
Study},
journal = {Journal of Physical Chemistry B},
year = {2000},
volume = {104},
pages = {9330-9342},
number = {39},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp001752i}
}
@ARTICLE{ClaudiuC.Gradinaru02272001,
author = {Gradinaru, Claudiu C. and Kennis, John T. M. and Papagiannakis, Emmanouil
and van Stokkum, Ivo H. M. and Cogdell, Richard J. and Fleming, Graham
R. and Niederman, Robert A. and van Grondelle, Rienk},
title = {{An unusual pathway of excitation energy deactivation in carotenoids:
Singlet-to-triplet conversion on an ultrafast timescale in a photosynthetic
antenna}},
journal = {PNAS},
year = {2001},
volume = {98},
pages = {2364-2369},
number = {5},
doi = {10.1073/pnas.051501298},
file = {2364.pdf:http\://www.pnas.org/cgi/reprint/98/5/2364.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/98/5/2364}
}
@ARTICLE{Groen1996,
author = {Groen, B. H. and Bloemendal, M. and Mulders, J. W. M. and Hadden,
J. M. and Chapman, D. and Van Stokkum, I. H. M. and Van Grondelle,
R.},
title = {Spectroscopic characterization of recombinant follicle stimulating
hormone},
journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy},
year = {1996},
volume = {52},
pages = {1331--1346},
month = {Sep},
issue = {10},
keywords = {FSH},
url = {http://www.sciencedirect.com/science/article/B6VNG-4G83X49-N/2/68a0fa60fcc70406221ed2946d55f896}
}
@ARTICLE{GrootM.L._bi034878p,
author = {Groot, M.L. and van Wilderen, L.J.G.W. and Larsen, D.S. and van der
Horst, M.A. and van Stokkum, I. H. M. and Hellingwerf, K.J. and van
Grondelle, R.},
title = {Initial Steps of Signal Generation in Photoactive Yellow Protein
Revealed with Femtosecond Mid-Infrared Spectroscopy},
journal = {Biochemistry},
year = {2003},
volume = {42},
pages = {10054-10059},
number = {34},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi034878p}
}
@ARTICLE{MarieLouiseGroot09132005,
author = {Groot, Marie Louise and Pawlowicz, Natalia P. and van Wilderen, Luuk
J. G. W. and Breton, Jacques and van Stokkum, Ivo H. M. and van Grondelle,
Rienk},
title = {{Initial electron donor and acceptor in isolated Photosystem {II}
reaction centers identified with femtosecond mid-{IR} spectroscopy}},
journal = {PNAS},
year = {2005},
volume = {102},
pages = {13087-13092},
number = {37},
doi = {10.1073/pnas.0503483102},
file = {13087.pdf:http\://www.pnas.org/cgi/reprint/102/37/13087.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/102/37/13087}
}
@ARTICLE{gr94,
author = {Groot, M. L. and Peterman, E. J. G. and van Kan, P. J. M. and van
Stokkum, I. H. M. and Dekker, JP and van Grondelle, R},
title = {Temperature dependent triplet and fluorescence quantum yields of
the photosystem {II} reaction center described in a thermodynamic
model},
journal = {Biophysical Journal},
year = {1994},
volume = {67},
pages = {318-330}
}
@ARTICLE{MLGroot01011995,
author = {Groot, M L and Peterman, E J G and van Stokkum, I H M and Dekker,
J P and van Grondelle, R},
title = {{Triplet and fluorescing states of the CP47 antenna complex of photosystem
II studied as a function of temperature.}},
journal = {Biophys. J.},
year = {1995},
volume = {68},
pages = {281-290},
number = {1},
abstract = {Fluorescence emission and triplet-minus-singlet (T-S) absorption difference
spectra of the CP47 core antenna complex of photosystem {II} were
measured as a function of temperature and compared to those of chlorophyll
a in Triton X-100. Two spectral species were found in the chlorophyll
T-S spectra of CP47, which may arise from a difference in ligation
of the pigments or from an additional hydrogen bond, similar to what
has been found for Chl molecules in a variety of solvents. The T-S
spectra show that the lowest lying state in CP47 is at approximately
685 nm and gives rise to fluorescence at 690 nm at 4 K. The fluorescence
quantum yield is 0.11 +/- 0.03 at 4 K, the chlorophyll triplet yield
is 0.16 +/- 0.03. Carotenoid triplets are formed efficiently at 4
K through triplet transfer from chlorophyll with a yield of 0.15
+/- 0.02. The major decay channel of the lowest excited state in
CP47 is internal conversion, with a quantum yield of about 0.58.
Increase of the temperature results in a broadening and blue shift
of the spectra due to the equilibration of the excitation over the
antenna pigments. Upon increasing the temperature, a decrease of
the fluorescence and triplet yields is observed to, at 270 K, a value
of about 55% of the low temperature value. This decrease is significantly
larger than of chlorophyll a in Triton X-100. Although the coupling
to low-frequency phonon or vibration modes of the pigments is probably
intermediate in CP47, the temperature dependence of the triplet and
fluorescence quantum yield can be modeled using the energy gap law
in the strong coupling limit of Englman and Jortner (1970. J. Mol.
Phys. 18:145-164) for non-radiative decays. This yields for CP47
an average frequency of the promoting/accepting modes of 350 cm-1
with an activation energy of 650 cm-1 for internal conversion and
activationless intersystem crossing to the triplet state through
a promoting mode with a frequency of 180 cm-1. For chlorophyll a
in Triton X-100 the average frequency of the promoting modes for
non-radiative decay is very similar, but the activation energy (300
cm-1) is significantly smaller. },
eprint = {http://www.biophysj.org/cgi/reprint/68/1/281.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/68/1/281}
}
@ARTICLE{i99a,
author = {Groot, M-L and Frese, RN and de Weerd, FL and Bromek, K and Pettersson
{\AA} and Peterman, EJG and van Stokkum, I. H. M. and van Grondelle,
R and Dekker, JP},
title = {Spectroscopic properties of the {CP43} core antenna protein of photosystem
{II}},
journal = {Biophysical Journal},
year = {1999},
volume = {77},
pages = {328-340}
}
@ARTICLE{Marie-LouiseGroot04291997,
author = {Groot, Marie-Louise and van Mourik, Frank and Eijckelhoff, Camiel
and van Stokkum, Ivo H. M. and Dekker, Jan P. and van Grondelle,
Rienk},
title = {{Charge separation in the reaction center of photosystem {II} studied
as a function oftemperature}},
journal = {PNAS},
year = {1997},
volume = {94},
pages = {4389-4394},
number = {9},
doi = {10.1073/pnas.94.9.4389},
file = {4389.pdf:http\://www.pnas.org/cgi/reprint/94/9/4389.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/94/9/4389}
}
@INPROCEEDINGS{gr1996,
author = {Groot, M-L and van Mourik, F and van Stokkum, I. H. M. and van Grondelle,
R.},
title = {Quantum beats in the reaction center of photosystem {II}},
booktitle = {Ultrafast Phenomena {X}, Springer Series in Chemical Physics},
year = {1996},
editor = {Barbara, PF and Fujimoto, JG and Knox, WH and Zinth, W},
volume = {1},
pages = {344-345},
publisher = {Springer-Verlag, Berlin}
}
@INPROCEEDINGS{g96,
author = {Groot, M-L and P{\aa}lsson, L-O and Pribi{\'{c}}, R and van Stokkum,
I. H. M. and Dekker, JP and van Grondelle, R.},
title = {Energetics and excited state dynamics of the radical pair formation
in isolated {CP47}- reaction center complex of Photosystem {II} at
various temperatures},
booktitle = {Fast Elementary Processes in Chemical and Biological Systems},
year = {1996},
editor = {Tramer, A},
pages = {288-292},
publisher = {AIP Press, New York}
}
@ARTICLE{Hadden1994,
author = {Hadden, Jonathan M. and Bloemendal, Michael and Haris, Parvez I.
and van Stokkum, Ivo H. M. and Chapman, Dennis and Srai, Surjit K.
S.},
title = {Structure and thermal stability of the extracellular fragment of
human transferrin receptor at extracellular and endosomal {pH}},
journal = {FEBS Letters},
year = {1994},
volume = {350},
pages = {235--239},
month = {Aug},
day = {22},
issue = {2-3},
keywords = {Fourier transform infrared spectroscopy},
url = {http://www.sciencedirect.com/science/article/B6T36-447N60H-KF/2/b701db71e778ecc07d8c756df641d0d5}
}
@ARTICLE{AndreaHaker02282003,
author = {Haker, Andrea and Hendriks, Johnny and van Stokkum, Ivo H. M. and
Heberle, Joachim and Hellingwerf, Klaas J. and Crielaard, Wim and
Gensch, Thomas},
title = {{The Two Photocycles of Photoactive Yellow Protein from Rhodobacter
sphaeroides}},
journal = {J. Biol. Chem.},
year = {2003},
volume = {278},
pages = {8442-8451},
number = {10},
doi = {10.1074/jbc.M209343200},
file = {8442.pdf:http\://www.jbc.org/cgi/reprint/278/10/8442.pdf:PDF},
url = {http://www.jbc.org/cgi/content/abstract/278/10/8442}
}
@ARTICLE{Hendriks1999,
author = {Hendriks, Johnny and van Stokkum, Ivo H. M. and Crielaard, Wim and
Hellingwerf, Klaas J.},
title = {Kinetics of and intermediates in a photocycle branching reaction
of the photoactive yellow protein from Ectothiorhodospira halophila},
journal = {FEBS Letters},
year = {1999},
volume = {458},
pages = {252--256},
month = {Sep},
day = {17},
issue = {2},
keywords = {Transient spectroscopy},
url = {http://www.sciencedirect.com/science/article/B6T36-3XCF7ST-17/2/0dc7786b9d3b7ff1281dec9d8fdda390}
}
@ARTICLE{JohnnyHendriks02012003,
author = {Hendriks, Johnny and van Stokkum, Ivo H. M. and Hellingwerf, Klaas
J.},
title = {{Deuterium Isotope Effects in the Photocycle Transitions of the Photoactive
Yellow Protein}},
journal = {Biophysical Journal},
year = {2003},
volume = {84},
pages = {1180-1191},
number = {2},
file = {1180.pdf:http\://www.biophysj.org/cgi/reprint/84/2/1180.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/84/2/1180}
}
@ARTICLE{nat,
author = {Derren J. Heyes and C. Neil Hunter and Ivo H. M. van Stokkum and
Rienk van Grondelle and Marie Louise Groot},
title = {Ultrafast enzymatic reaction dynamics in protochlorophyllide oxidoreductase},
journal = {Nature Structural Biology},
year = {2003},
volume = {10},
pages = {491 - 492}
}
@ARTICLE{HippiusC._jp711120v,
author = {Hippius, C. and van Stokkum, I. H. M. and Gs{\"a}nger, M. and Groeneveld,
M.M. and Williams, R.M. and W{\"u}rthner, F.},
title = {Sequential {FRET} Processes in Calix[4]arene-Linked Orange-Red-Green
Perylene Bisimide Dye Zigzag Arrays},
journal = {Journal of Physical Chemistry C},
year = {2008},
volume = {112},
pages = {2476-2486},
number = {7},
affiliation = {Institut f{\"u}r Organische Chemie and R{\"o}ntgen Research Center for Complex
Material Systems, Universit{\"a}t W{\"u}rzburg, Am Hubland, D-97074 W{\"u}rzburg,
Germany, Molecular Photonics Group, van't Hoff Institute for Molecular
Sciences (HIMS), Universiteit van Amsterdam, Nieuwe Achtergracht
129, 1018 WV Amsterdam, The Netherlands, and Department of Physics
and Astronomy, Vrije Universiteit, de Boelelaan 1081, 1081 HV Amsterdam,
The Netherlands},
issn = {1932-7447},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp711120v}
}
@ARTICLE{HippiusC._jp0733825,
author = {Hippius, C. and van Stokkum, I. H. M. and Zangrando, E. and Williams,
R.M. and W{\"u}rthner, F.},
title = {Excited State Interactions in Calix[4]arene-Perylene Bisimide Dye
Conjugates: Global and Target Analysis of Supramolecular Building
Blocks},
journal = {Journal of Physical Chemistry C},
year = {2007},
volume = {111},
pages = {13988-13996},
number = {37},
affiliation = {Universit{\"a}t W{\"u}rzburg, Institut f{\"u}r Organische Chemie and R{\"o}ntgen Research
Center for Complex Material Systems, Am Hubland, D-97074 W{\"u}rzburg,
Germany, Molecular Photonics Group, van't Hoff Institute for Molecular
Sciences (HIMS), Universiteit van Amsterdam, Nieuwe Achtergracht
129, WS 1018 Amsterdam, The Netherlands, Department of Physics and
Astronomy, Vrije Universiteit, de Boelelaan 1081, 1081 HV Amsterdam,
The Netherlands, and University of Trieste, Dipartimento di Scienze
Chimiche, Via Licio Giorgieri 1, 34127 Trieste, Italy},
issn = {1932-7447},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0733825}
}
@ARTICLE{HippiusCatharina_jp804068b,
author = {Hippius, Catharina and van Stokkum, Ivo H. M. and Zangrando, Ennio
and Williams, Ren{\'e} M. and Wykes, Michael and Beljonne, David and
W{\"u}rthner, Frank},
title = {Ground- and Excited-State Pinched Cone Equilibria in Calix[4]arenes
Bearing Two Perylene Bisimide Dyes},
journal = {Journal of Physical Chemistry C},
year = {2008},
volume = {112},
pages = {14626-14638},
number = {37},
affiliation = {Institut f{\"u}r Organische Chemie and R�ntgen Research Center for Complex
Material Systems, Universit{\"a}t W{\"u}rzburg, Am Hubland, D-97074 W{\"u}rzburg,
Germany, Department of Physics and Astronomy, Vrije Universiteit,
de Boelelaan 1081, 1081 HV Amsterdam, The Netherlands, Dipartimento
di Scienze Chimiche, University of Trieste, Via Licio Giorgieri 1,
34127 Trieste, Italy, Molecular Photonics Group, vant Hoff Institute
for Molecular Sciences (HIMS), Universiteit van Amsterdam, Nieuwe
Achtergracht 129, WS 1018 Amsterdam, The Netherlands, and Laboratory
for Chemistry of Novel Materials, Center for Research in Molecular
Electronics and Photonics, University of Mons-Hainaut, Place du Parc
20, 7000 Mons, Belgium},
issn = {1932-7447},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp804068b}
}
@ARTICLE{HoffW.D._bi980504y,
author = {Hoff, W.D. and Xie, A. and Van Stokkum, I. H. M. and Tang, X.-j.
and Gural, J. and Kroon, A.R. and Hellingwerf, K.J.},
title = {Global Conformational Changes upon Receptor Stimulation in Photoactive
Yellow Protein},
journal = {Biochemistry},
year = {1999},
volume = {38},
pages = {1009-1017},
number = {3},
affiliation = {Department of Biochemistry and Molecular Biology, The University of
Chicago, Chicago, Illinois 60637, Department of Physics, Oklahoma
State University, Stillwater, Oklahoma 74078, Faculty of Physics
and Astronomy, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands,
Wyeth-Ayherst Research, 401 North Middletown Road, Pearl River, New
York 10965, and Department of Microbiology, E. C. Slater Institute,
University of Amsterdam, 1018 WS Amsterdam, The Netherlands},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi980504y}
}
@ARTICLE{WD_Hoff10011994,
author = {Hoff, W D and van Stokkum, I H M and van Ramesdonk, H J and van Brederode,
M E and Brouwer, A M and Fitch, J C and Meyer, T E and van Grondelle,
R and Hellingwerf, K J},
title = {{Measurement and global analysis of the absorbance changes in the
photocycle of the photoactive yellow protein from Ectothiorhodospira
halophila.}},
journal = {Biophys. J.},
year = {1994},
volume = {67},
pages = {1691-1705},
number = {4},
abstract = {The photocycle of the photoactive yellow protein (PYP) from Ectothiorhodospira
halophila was examined by time-resolved difference absorption spectroscopy
in the wavelength range of 300-600 nm. Both time-gated spectra and
single wavelength traces were measured. Global analysis of the data
established that in the time domain between 5 ns and 2 s only two
intermediates are involved in the room temperature photocycle of
PYP, as has been proposed before (Meyer T.E., E. Yakali, M. A. Cusanovich,
and G. Tollin. 1987. Biochemistry. 26:418-423; Meyer, T. E., G. Tollin,
T. P. Causgrove, P. Cheng, and R. E. Blankenship. 1991. Biophys.
J. 59:988-991). The first, red-shifted intermediate decays biexponentially
(60% with tau = 0.25 ms and 40% with tau = 1.2 ms) to a blue-shifted
intermediate. The last step of the photocycle is the biexponential
(93% with tau = 0.15 s and 7% with tau = 2.0 s) recovery to the ground
state of the protein. Reconstruction of the absolute spectra of these
photointermediates yielded absorbance maxima of about 465 and 355
nm for the red- and blue-shifted intermediate with an epsilon max
at about 50% and 40% relative to the epsilon max of the ground state.
The quantitative analysis of the photocycle in PYP described here
paves the way to a detailed biophysical analysis of the processes
occurring in this photoreceptor molecule. },
eprint = {http://www.biophysj.org/cgi/reprint/67/4/1691.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/67/4/1691}
}
@ARTICLE{Hoff1997,
author = {Hoff, Wouter D. and Van Stokkum, Ivo H. M. and Gural, Jechiam and
Hellingwerf, Klaas J.},
title = {Comparison of acid denaturation and light activation in the eubacterial
blue-light receptor photoactive yellow protein},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {1997},
volume = {1322},
pages = {151--162},
month = {Dec},
day = {15},
issue = {2-3},
keywords = {Protein folding},
url = {http://www.sciencedirect.com/science/article/B6T1S-3SXDX2J-7/2/2fbd53f7485d78438af3ff2ee4241fbc}
}
@ARTICLE{vanderHorst2001,
author = {van der Horst, Michael A. and van Stokkum, Ivo H. and Crielaard,
Wim and Hellingwerf, Klaas J.},
title = {The role of the {N}-terminal domain of photoactive yellow protein
in the transient partial unfolding during signalling state formation},
journal = {FEBS Letters},
year = {2001},
volume = {497},
pages = {26--30},
month = {May},
day = {18},
issue = {1},
keywords = {Photocycle kinetics},
url = {http://www.sciencedirect.com/science/article/B6T36-43N8FNN-5/2/ea66f61cb831e7a207fe84a797239ff6}
}
@ARTICLE{vanderHorstM.A._bi050237d,
author = {van der Horst, M.A. and van Stokkum, I. H. M. and Dencher, N.A. and
Hellingwerf, K.J.},
title = {Controlled Reduction of the Humidity Induces a Shortcut Recovery
Reaction in the Photocycle of Photoactive Yellow Protein},
journal = {Biochemistry},
year = {2005},
volume = {44},
pages = {9160-9167},
number = {25},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi050237d}
}
@ARTICLE{JanneAIhalainen03272007,
author = {Ihalainen, Janne A. and Bredenbeck, Jens and Pfister, Rolf and Helbing,
Jan and Chi, Lei and van Stokkum, Ivo H. M. and Woolley, G. Andrew
and Hamm, Peter},
title = {{Folding and unfolding of a photoswitchable peptide from picoseconds
to microseconds}},
journal = {Proceedings of the National Academy of Sciences},
year = {2007},
volume = {104},
pages = {5383-5388},
number = {13},
abstract = {Using time-resolved IR spectroscopy, we monitored the kinetics of
folding and unfolding processes of a photoswitchable 16-residue alanine-based
{alpha}-helical peptide on a timescale from few picoseconds to almost
40 {micro}s and over a large temperature range (279-318 K). The folding
and unfolding processes were triggered by an ultrafast laser pulse
that isomerized the cross linker within a few picoseconds. The main
folding and unfolding times (700 ns and 150 ns, respectively, at
room temperature) are in line with previous T-jump experiments obtained
from similar peptides. However, both processes show complex, strongly
temperature-dependent spectral kinetics that deviate clearly from
a single-exponential behavior. Whereas in the unfolding experiment
the ensemble starts from a well defined folded state, the starting
ensemble in the folding experiment is more heterogeneous, which leads
to distinctly different kinetics of the experiments, because they
are sensitive to different regions of the energy surface. A qualitative
agreement with the experimental data-set can be obtained by a model
where the unfolded states act as a hub connected to several separated
"misfolded" states with a distribution of rates. We conclude that
a rather large spread of rates (k1 : kn {approx} 9) is needed to
explain the experimentally observed stretched exponential response
with stretching factor {$\beta$} = 0.8 at 279 K. },
doi = {10.1073/pnas.0607748104},
eprint = {http://www.pnas.org/cgi/reprint/104/13/5383.pdf},
url = {http://www.pnas.org/cgi/content/abstract/104/13/5383}
}
@ARTICLE{JanneA.Ihalainen10012002,
author = {Ihalainen, Janne A. and Jensen, Poul Erik and Haldrup, Anna and van
Stokkum, Ivo H. M. and van Grondelle, Rienk and Scheller, Henrik
Vibe and Dekker, Jan P.},
title = {{Pigment Organization and Energy Transfer Dynamics in Isolated Photosystem
I (PSI) Complexes from Arabidopsis thaliana Depleted of the PSI-G,
PSI-K, PSI-L, or PSI-N Subunit}},
journal = {Biophysical Journal},
year = {2002},
volume = {83},
pages = {2190-2201},
number = {4},
file = {2190.pdf:http\://www.biophysj.org/cgi/reprint/83/4/2190.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/83/4/2190}
}
@ARTICLE{Ihalainen2005,
author = {Ihalainen, Janne A. and Klimmek, Frank and Ganeteg, Ulrika and van
Stokkum, Ivo H. M. and van Grondelle, Rienk and Jansson, Stefan and
Dekker, Jan P.},
title = {Excitation energy trapping in photosystem {I} complexes depleted
in {Lhca}1 and {Lhca}4},
journal = {FEBS Letters},
year = {2005},
volume = {579},
pages = {4787--4791},
month = {Aug},
day = {29},
issue = {21},
keywords = {Photosynthesis},
url = {http://www.sciencedirect.com/science/article/B6T36-4GTWRWW-D/2/8dc2787303500a4bc1ec9f31cb2bbc89}
}
@ARTICLE{Ihalainen2005a,
author = {Ihalainen, Janne A. and van Stokkum, Ivo H. M. and Gibasiewicz, Krzysztof
and Germano, Marta and van Grondelle, Rienk and Dekker, Jan P.},
title = {Kinetics of excitation trapping in intact Photosystem {I} of {C}hlamydomonas
reinhardtii and {A}rabidopsis thaliana},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {2005},
volume = {1706},
pages = {267--275},
month = {Feb},
day = {17},
issue = {3},
keywords = {Photosystem I},
url = {http://www.sciencedirect.com/science/article/B6T1S-4F01KGF-1/2/32a548dbbad01cb8fe2d3809138ecc59}
}
@ARTICLE{IhalainenJ.A._jp0519316,
author = {Ihalainen, J.A. and Croce, R. and Morosinotto, T. and van Stokkum,
I. H. M. and Bassi, R. and Dekker, J.P. and van Grondelle, R.},
title = {Excitation Decay Pathways of {Lhca} Proteins: A Time-Resolved Fluorescence
Study},
journal = {Journal of Physical Chemistry B},
year = {2005},
volume = {109},
pages = {21150-21158},
number = {44},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0519316}
}
@ARTICLE{IhalainenJ.A._jp010921b,
author = {Ihalainen, J.A. and Linnanto, J. and Myllyperkio, P. and van Stokkum,
I. H. M. and Ucker, B. and Scheer, H. and Korppi-Tommola, J.E.I.},
title = {Energy Transfer in {LH2} of Rhodospirillum Molischianum, Studied
by Subpicosecond Spectroscopy and Configuration Interaction Exciton
Calculations},
journal = {Journal of Physical Chemistry B},
year = {2001},
volume = {105},
pages = {9849-9856},
number = {40},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp010921b}
}
@ARTICLE{KennisJ.T.M._bi034022k,
author = {Kennis, J.T.M. and Crosson, S. and Gauden, M. and van Stokkum, I.
H. M. and Moffat, K. and van Grondelle, R.},
title = {Primary Reactions of the {LOV2} Domain of Phototropin, a Plant Blue-Light
Photoreceptor},
journal = {Biochemistry},
year = {2003},
volume = {42},
pages = {3385-3392},
number = {12},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi034022k}
}
@ARTICLE{kenn,
author = {Kennis, JTM and Gobets, B and van Stokkum, I. H. M. and Dekker, JP
and van Grondelle R and Fleming GR},
title = {Light harvesting by chlorophylls and carotenoids in the photosystem
{I} core complex of Synechococcus elongatus: a fluorescence upconversion
study},
journal = {J. Phys. Chem. B},
year = {2001},
volume = {105},
pages = {4485-4494}
}
@ARTICLE{KennisJ.T.M._bi9712605,
author = {Kennis, J.T.M. and Shkuropatov, A.Ya. and van Stokkum, I. H. M. and
Gast, P. and Hoff, A.J. and Shuvalov, V.A. and Aartsma, T.J.},
title = {Formation of a Long-Lived {P+BA-} State in Plant Pheophytin-Exchanged
Reaction Centers of Rhodobacter sphaeroides {R26} at Low Temperature},
journal = {Biochemistry},
year = {1997},
volume = {36},
pages = {16231-16238},
number = {51},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9712605}
}
@ARTICLE{KennisJ.T.M._ja031840r,
author = {Kennis, J.T.M. and van Stokkum, I. H. M. and Crosson, S. and Gauden,
M. and Moffat, K. and van Grondelle, R.},
title = {The {LOV2} Domain of Phototropin: A Reversible Photochromic Switch},
journal = {Journal of the American Chemical Society},
year = {2004},
volume = {126},
pages = {4512-4513},
number = {14},
issn = {0002-7863},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja031840r}
}
@ARTICLE{JohnT.M.Kennis12282004,
author = {Kennis, John T. M. and Larsen, Delmar S. and van Stokkum, Ivo H.
M. and Vengris, Mikas and van Thor, Jasper J. and van Grondelle,
Rienk},
title = {{Uncovering the hidden ground state of green fluorescent protein}},
journal = {PNAS},
year = {2004},
volume = {101},
pages = {17988-17993},
number = {52},
doi = {10.1073/pnas.0404262102},
file = {17988.pdf:http\://www.pnas.org/cgi/reprint/101/52/17988.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/101/52/17988}
}
@ARTICLE{KleimaF.J._bi9716480,
author = {Kleima, F.J. and Gradinaru, C.C. and Calkoen, F. and van Stokkum,
I. H. M. and van Grondelle, R. and van Amerongen, H.},
title = {Energy Transfer in {{LHCII}} Monomers at {77K} Studied by Sub-Picosecond
Transient Absorption Spectroscopy},
journal = {Biochemistry},
year = {1997},
volume = {36},
pages = {15262-15268},
number = {49},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9716480}
}
@INPROCEEDINGS{i98y,
author = {Kleima, FJ and Hofmann, E and Gobets, B and van Stokkum, I. H. M.
and van Grondelle and van Amerongen, H},
title = {Peridinin chlorophyll protein: structure and dynamics related},
booktitle = {Photosynthesis: Mechanisms and Effects},
year = {1998},
editor = {Garab, G},
pages = {441-444},
publisher = {Kluwer Academic Publishers, Dordrecht}
}
@ARTICLE{FoskeJ.Kleima01012000,
author = {Kleima, Foske J. and Hofmann, Eckhard and Gobets, Bas and van Stokkum,
Ivo H. M. and van Grondelle, Rienk and Diederichs, Kay and van Amerongen,
Herbert},
title = {{F{\"o}rster Excitation Energy Transfer in Peridinin-Chlorophyll-a-Protein}},
journal = {Biophysical Journal},
year = {2000},
volume = {78},
pages = {344-353},
number = {1},
file = {344.pdf:http\://www.biophysj.org/cgi/reprint/78/1/344.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/78/1/344}
}
@ARTICLE{Klerk2010,
author = {Klerk, Joost de and van Stokkum, Ivo H. M. and Szemik-Hojniak, Anna
and Deperasinska, Irena and Gooijer, Cees and Zhang, Hong and Buma,
Wybren-Jan and Ariese, Freek},
title = {Excited State Processes of 2-Butylamino-6-methyl-4-nitropyridine
N-oxide in Nonpolar Solvents. A Transient Absorption Spectroscopy
Study},
journal = {The Journal of Physical Chemistry A},
year = {2010},
volume = {114},
pages = {4045-4050},
number = {12},
doi = {doi: 10.1021/jp909468h}
}
@ARTICLE{Koehorst2010,
author = {Koehorst, R. B. M. and Laptenok, S. and van Oort, B. and van Hoek,
A. and Spruijt, R. B. and van Stokkum, I. H. M. and van Amerongen,
H. and Hemminga, M. A.},
title = {Profiling of dynamics in protein-lipid-water systems: a time-resolved
fluorescence study of a model membrane protein with the label BADAN
at specific membrane depths},
journal = {European Biophysics Journal with Biophysics Letters},
year = {2010},
volume = {39},
pages = {647-656},
number = {4},
abstract = {Profiles of lipid-water bilayer dynamics were determined from picosecond
time-resolved fluorescence spectra of membrane-embedded BADAN-labeled
M13 coat protein. For this purpose, the protein was labeled at seven
key positions. This places the label at well-defined locations from
the water phase to the center of the hydrophobic acyl chain region
of a phospholipid model membrane, providing us with a nanoscale ruler
to map membranes. Analysis of the time-resolved fluorescence spectroscopic
data provides the characteristic time constant for the twisting motion
of the BADAN label, which is sensitive to the local flexibility of
the protein-lipid environment. In addition, we obtain information
about the mobility of water molecules at the membrane-water interface.
The results provide an unprecedented nanoscale profiling of the dynamics
and distribution of water in membrane systems. This information gives
clear evidence that the actual barrier of membranes for ions and
aqueous solvents is located at the region of carbonyl groups of the
acyl chains.}
}
@ARTICLE{RemcoKort07012005,
author = {Kort, Remco and O'Brien, Andrea C. and van Stokkum, Ivo H. M. and
Oomes, Suus J. C. M. and Crielaard, Wim and Hellingwerf, Klaas J.
and Brul, Stanley},
title = {{Assessment of Heat Resistance of Bacterial Spores from Food Product
Isolates by Fluorescence Monitoring of Dipicolinic Acid Release}},
journal = {Applied and Environmental Microbiology},
year = {2005},
volume = {71},
pages = {3556-3564},
number = {7},
file = {3556.pdf:http\://aem.asm.org/cgi/reprint/71/7/3556.pdf:PDF},
url = {http://aem.asm.org/cgi/content/abstract/71/7/3556}
}
@ARTICLE{BrentP.Krueger06012001,
author = {Krueger, Brent P. and Lampoura, Stefania S. and van Stokkum, Ivo
H. M. and Papagiannakis, Emmanouil and Salverda, Jante M. and Gradinaru,
Claudiu C. and Rutkauskas, Danielis and Hiller, Roger G. and van
Grondelle, Rienk},
title = {{Energy Transfer in the Peridinin Chlorophyll-a Protein of Amphidinium
carterae Studied by Polarized Transient Absorption and Target Analysis}},
journal = {Biophys. J.},
year = {2001},
volume = {80},
pages = {2843-2855},
number = {6},
file = {2843.pdf:http\://www.biophysj.org/cgi/reprint/80/6/2843.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/80/6/2843}
}
@ARTICLE{wout_2003,
author = {Wouter Laan and Michael A. van der Horst and Ivo H. van Stokkum and
Klaas J. Hellingwerf},
title = {Initial Characterization of the Primary Photochemistry of AppA, a
Blue-light-using Flavin Adenine Dinucleotide-domain Containing Transcriptional
Antirepressor Protein from Rhodobacter sphaeroides: A Key Role for
Reversible Intramolecular Proton Transfer from the Flavin Adenine
Dinucleotide Chromophore to a Conserved Tyrosine},
journal = {Photochemistry and Photobiology},
year = {2003},
volume = {78},
pages = {290-297},
number = {3},
file = {PhotochemPhotobiol2003_78_290Laan.pdf:http\://www.nat.vu.nl/~ivo/pub/2003/PhotochemPhotobiol2003_78_290Laan.pdf:PDF}
}
@ARTICLE{LampouraS.S._jp0021289,
author = {Lampoura, S.S. and van Grondelle, R. and van Stokkum, I. H. M. and
Cogdell, R.J. and Wiersma, D.A. and Duppen, K.},
title = {Exciton Dynamics in {LH1} and {LH2} of Rhodopseudomonas Acidophila
and Rhodobium Marinum Probed with Accumulated Photon Echo and Pump-Probe
Measurements},
journal = {Journal of Physical Chemistry B},
year = {2000},
volume = {104},
pages = {12072-12078},
number = {50},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0021289}
}
@ARTICLE{la,
author = {Lampoura, S.S. and B.P. Krueger and I. H. M. van Stokkum and J.M.
Salverda and C.C. Gradinaru and D. Rutkauskas and R.G. Hiller and
R. van Grondelle},
title = {Energy transfer in the peridinin chlorophyll: a protein of Amphidinium
carterae studied by polarized transient absorption Measurements},
journal = {Int. J. Mod. Phys. B},
year = {2001},
volume = {15},
pages = {3849-3852}
}
@ARTICLE{laptenok2010,
author = {Sergey Laptenok and Jan Willem Borst and Katharine M. Mullen and
Ivo H. M. van Stokkum and Antonie J. W. G. Visser and Herbert van
Amerongen},
title = {Global analysis of {F}{\"o}rster resonance energy transfer in live cells
measured by fluorescence lifetime imaging microscopy exploiting the
rise time of acceptor fluorescence},
journal = {Physical Chemistry Chemical Physics},
year = {2010},
volume = {12},
pages = {7593-7602}
}
@ARTICLE{laptenok,
author = {Sergey Laptenok and Katharine M. Mullen and Jan Willem Borst and
Ivo H. M. van Stokkum and Vladimir V. Apanasovich and Antonie J.
W. G. Visser},
title = {Fluorescence Lifetime Imaging Microscopy ({FLIM}) data analysis with
\pkg{TIMP}},
journal = {Journal of Statistical Software},
year = {2007},
volume = {18},
number = {8},
url = {http://www.jstatsoft.org/v18/i08/}
}
@ARTICLE{doi:10.1021/bi101965d,
author = {Laptenok, Sergey P. and Visser, Nina V. and Engel, Ruchira and Westphal,
Adrie H. and van Hoek, Arie and Van Mierlo, Carlo P. M. and van Stokkum,
Ivo H.M. and van Amerongen, Herbert and Visser, Antonie J. W. G.},
title = {A General Approach to Detect Folding Intermediates from Steady-State
and Time-Resolved Fluorescence of Single Tryptophan-Containing Proteins},
journal = {Biochemistry},
year = {2011},
volume = {{50}},
pages = {{3441-3450}},
number = {{17}},
month = {{May 3}},
doi = {10.1021/bi101965d},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi101965d},
url = {http://pubs.acs.org/doi/abs/10.1021/bi101965d}
}
@ARTICLE{Larsen2003c,
author = {Larsen, Delmar S. and Papagiannakis, Emmanouil and van Stokkum, Ivo
H. M. and Vengris, Mikas and Kennis, John T. M. and van Grondelle,
Rienk},
title = {Excited state dynamics of {$\beta$}-carotene explored with dispersed
multi-pulse transient absorption},
journal = {Chemical Physics Letters},
year = {2003},
volume = {381},
pages = {733--742},
month = {Nov},
day = {21},
issue = {5-6},
url = {http://www.sciencedirect.com/science/article/B6TFN-49XPV3C-4/2/17ec647f103b82d63a809bd92e29e372}
}
@ARTICLE{DelmarS.Larsen09012004,
author = {Larsen, Delmar S. and van Stokkum, Ivo H. M. and Vengris, Mikas and
van der Horst, Michael A. and de Weerd, Frank L. and Hellingwerf,
Klaas J. and van Grondelle, Rienk},
title = {{Incoherent Manipulation of the Photoactive Yellow Protein Photocycle
with Dispersed Pump-Dump-Probe Spectroscopy}},
journal = {Biophysical Journal},
year = {2004},
volume = {87},
pages = {1858-1872},
number = {3},
doi = {10.1529/biophysj.104.043794},
file = {1858.pdf:http\://www.biophysj.org/cgi/reprint/87/3/1858.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/87/3/1858}
}
@ARTICLE{Larsen2003b,
author = {Larsen, Delmar S. and Vengris, Mikas and van Stokkum, Ivo H. M. and
van der Horst, Michael A. and Cordfunke, Robert A. and Hellingwerf,
Klaas J. and van Grondelle, Rienk},
title = {Initial photo-induced dynamics of the photoactive yellow protein
chromophore in solution},
journal = {Chemical Physics Letters},
year = {2003},
volume = {369},
pages = {563--569},
month = {Feb},
day = {28},
issue = {5-6},
url = {http://www.sciencedirect.com/science/article/B6TFN-47T2P87-2/2/b697a1f805ce6672a0932c6ead538958}
}
@ARTICLE{DelmarS.Larsen04012004,
author = {Larsen, Delmar S. and Vengris, Mikas and van Stokkum, Ivo H. M. and
van der Horst, Michael A. and de Weerd, Frank L. and Hellingwerf,
Klaas J. and van Grondelle, Rienk},
title = {{Photoisomerization and Photoionization of the Photoactive Yellow
Protein Chromophore in Solution}},
journal = {Biophysical Journal},
year = {2004},
volume = {86},
pages = {2538-2550},
number = {4},
file = {2538.pdf:http\://www.biophysj.org/cgi/reprint/86/4/2538.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/86/4/2538}
}
@ARTICLE{LarsenO.F.A._jp021756i,
author = {Larsen, O.F.A. and van Stokkum, I. H. M. and Pandit, A. and van Grondelle,
R. and van Amerongen, H.},
title = {Ultrafast Polarized Fluorescence Measurements on Tryptophan and a
Tryptophan-Containing Peptide},
journal = {Journal of Physical Chemistry B},
year = {2003},
volume = {107},
pages = {3080-3085},
number = {13},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp021756i}
}
@ARTICLE{OlafF.A.Larsen08012001,
author = {Larsen, Olaf F. A. and van Stokkum, Ivo H. M. and Gobets, Bas and
van Grondelle, Rienk and van Amerongen, Herbert},
title = {{Probing the Structure and Dynamics of a DNA Hairpin by Ultrafast
Quenching and Fluorescence Depolarization}},
journal = {Biophysical Journal},
year = {2001},
volume = {81},
pages = {1115-1126},
number = {2},
file = {1115.pdf:http\://www.biophysj.org/cgi/reprint/81/2/1115.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/81/2/1115}
}
@ARTICLE{Larsen2003a,
author = {Larsen, Olaf F. A. and van Stokkum, Ivo H. M. and Groot, Marie-Louise
and Kennis, John T. M. and van Grondelle, Rienk and van Amerongen,
Herbert},
title = {Electronic states in 2-aminopurine revealed by ultrafast transient
absorption and target analysis},
journal = {Chemical Physics Letters},
year = {2003},
volume = {371},
pages = {157--163},
month = {Mar},
day = {28},
issue = {1-2},
url = {http://www.sciencedirect.com/science/article/B6TFN-483BWY0-2/2/137488826d0dae4caad04cd5e855cde1}
}
@ARTICLE{olaf_04,
author = {Olaf F. A. Larsen and Ivo H. M. van Stokkum and Frank L. de Weerd
and Mikas Vengris and Charuvila T. Aravindakumar and Rienk van Grondelle
and Nicholas E. Geacintov and Herbert van Amerongen},
title = {Ultrafast transient-absorption and steady-state fluorescence measurements
on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted
{DNA} duplexes},
journal = {Physical Chemistry Chemical Physics},
year = {2004},
volume = {6},
pages = {154 - 160}
}
@ARTICLE{LauteslagerX.Y._jp983595h,
author = {Lauteslager, X.Y. and van Stokkum, I. H. M. and van Ramesdonk, H.J.
and Brouwer, A.M. and Verhoeven, J.W.},
title = {Conformational Dynamics of Semiflexibly Bridged Donor-Acceptor Systems
Studied with a Streak Camera and Spectrotemporal Parametrization
of Fluorescence},
journal = {Journal of Physical Chemistry A},
year = {1999},
volume = {103},
pages = {653-659},
number = {6},
issn = {1089-5639},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp983595h}
}
@ARTICLE{i01s,
author = {Xavier Y. Lauteslager and Ivo H. M. van Stokkum and H. John van Ramesdonk
and Dick Bebelaar and Jan Fraanje and Kees Goubitz and Henk Schenk
and Albert M. Brouwer and Jan W. Verhoeven},
title = {Conformational Dynamics of Charge-Transfer States in Donor-Bridge-Acceptor
Systems},
journal = {European Journal of Organic Chemistry},
year = {2001},
volume = {16},
pages = {3105-3118}
}
@ARTICLE{ISI:000291571100033,
author = {Marin, Alessandro and Passarini, Francesca and van Stokkum, Ivo H.
M. and van Grondelle, Rienk and Croce, Roberta},
title = {{Minor Complexes at Work: Light-Harvesting by Carotenoids in the
{Photosystem II} Antenna Complexes CP24 and CP26}},
journal = {Biophysical Journal},
year = {2011},
volume = {{100}},
pages = {{2829-2838}},
number = {{11}},
month = {{Jun 8}},
address = {{600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA}},
affiliation = {{Croce, R (Reprint Author), Univ Groningen, Dept Biophys Chem, Groningen
Biomol Sci \& Biotechnol Inst, Groningen, Netherlands. Passarini,
F; Croce, R, Univ Groningen, Dept Biophys Chem, Groningen Biomol
Sci \& Biotechnol Inst, Groningen, Netherlands. Marin, A; van Stokkum,
IHM; van Grondelle, R, Vrije Univ Amsterdam, Fac Sci, Amsterdam,
Netherlands.}},
author-email = {{r.croce@vu.nl}},
doc-delivery-number = {{776WQ}},
doi = {{10.1016/j.bpj.2011.04.029}},
funding-acknowledgement = {{Netherlands Organization for Scientific Research-Chemical Sciences;
Earth and Life Science (ALW)}},
funding-text = {{This work was supported by the Netherlands Organization for Scientific
Research-Chemical Sciences through a TOP grant to R.v.G. and Earth
and Life Science (ALW) through a Vidi grant to R.C.}},
issn = {{0006-3495}},
journal-iso = {{Biophys. J.}},
keywords-plus = {{FEMTOSECOND TRANSIENT ABSORPTION; CHLOROPHYLL ENERGY-TRANSFER; HIGHER-PLANTS;
BINDING-SITES; GREEN PLANTS; EXCITED-STATE; S-1 STATE; FUNCTIONAL
ARCHITECTURE; TRANSFER PATHWAYS; LOW-TEMPERATURE}},
language = {{English}},
number-of-cited-references = {{63}},
publisher = {{CELL PRESS}},
subject-category = {{Biophysics}},
times-cited = {{0}},
type = {{Article}},
unique-id = {{ISI:000291571100033}}
}
@ARTICLE{ISI000291709500028,
author = {Mathes, Tilo and van Stokkum, Ivo H. M. and Bonetti, Cosimo and Hegemann,
Peter and Kennis, John T. M.},
title = {{The Hydrogen-Bond Switch Reaction of the Blrb Bluf Domain of Rhodobacter
sphaeroides}},
journal = {Journal of Physical Chemistry B},
year = {2011},
volume = {{115}},
pages = {{7963-7971}},
number = {{24}},
month = {{Jun 23}},
address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
affiliation = {{Mathes, T (Reprint Author), Humboldt Univ, Inst Biol Expt Biophys,
Invalidenstr 42, D-10115 Berlin, Germany. Mathes, T; Hegemann, P,
Humboldt Univ, Inst Biol Expt Biophys, D-10115 Berlin, Germany. van
Stokkum, IHM; Bonetti, C; Kennis, JTM, Vrije Univ Amsterdam, Fac
Sci, Dept Phys \& Astron, Biophys Grp, NL-1081 HV Amsterdam, Netherlands.}},
author-email = {{tilo.mathes.1@biologie.hu-berlin.de}},
doi = {{10.1021/jp201296m}},
issn = {{1520-6106}},
keywords-plus = {{ULTRAFAST INFRARED-SPECTROSCOPY; FLAVIN-BINDING PHOTORECEPTOR; MEDIATED
SIGNAL-TRANSDUCTION; LIGHT PHOTORECEPTOR; ENERGY-TRANSFER; ADENINE-DINUCLEOTIDE;
ELECTRONIC-STRUCTURE; CRYSTAL-STRUCTURES; ESCHERICHIA-COLI; AQUEOUS-SOLUTION}},
language = {{English}},
publisher = {{AMER CHEMICAL SOC}},
subject-category = {{Chemistry}},
type = {{Article}}
}
@INPROCEEDINGS{bred,
author = {Van Brederode ME and van Stokkum I. H. M. and Jones MR, Van Grondelle
R},
title = {Wavelength and temperature dependence of the {P+QA} recombination
reaction in the {M210W} reaction centre only mutant of Rhodobacter
sphaeroides},
booktitle = {Photosynthesis: from Light to Biosphere},
year = {1995},
editor = {P. Mathis},
volume = {1},
pages = {907-910},
publisher = {Dordrecht, Kluwer}
}
@INCOLLECTION{ivo88a,
author = {Melssen, W.J. and Van Stokkum, I. H. M.},
title = {Selectivity for interaural time-difference and amplitude-modulation
frequency in the auditory midbrain of the grassfrog},
booktitle = {Basic Issues in Hearing},
publisher = {Academic Press, London},
year = {1988},
editor = {H. Duifhuis and J.W. Horst and H.P. Wit},
pages = {279-284}
}
@ARTICLE{Melssen1990,
author = {Melssen, Willem J. and Epping, Willem J. M. and van Stokkum, Ivo
H. M.},
title = {Sensitivity for interaural time and intensity difference of auditory
midbrain neurons in the grassfrog},
journal = {Hearing Research},
year = {1990},
volume = {47},
pages = {235--256},
month = {Aug},
day = {15},
issue = {3},
keywords = {Amplitude modulation},
url = {http://www.sciencedirect.com/science/article/B6T73-485GF8D-B9/2/ada19ef668b1f657dc28e80f594f8ac5}
}
@INCOLLECTION{pereyra2010,
author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
title = {Exponential models for time-resolved spectroscopy data},
booktitle = {Exponential Data Fitting and its Applications},
publisher = {Bentham},
year = {2010},
editor = {Victor Pereyra and Godela Scherer},
pages = {110-127}
}
@ARTICLE{numalg,
author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
title = {The variable projection algorithm in time-resolved spectroscopy,
microscopy and mass spectrometry applications},
journal = {Numerical Algorithms},
year = {2009},
volume = {51},
pages = {319-340},
issue = {3}
}
@ARTICLE{intro,
author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
title = {An Introduction to the Special Volume ``{S}pectroscopy and {C}hemometrics
in {R}''},
journal = {Journal of Statistical Software},
year = {2007},
volume = {18},
number = {1},
url = {http://www.jstatsoft.org/v18/i01/}
}
@ARTICLE{TIMP,
author = {Katharine M. Mullen and Ivo H. M. van Stokkum},
title = {{TIMP}: an {R} package for modeling multi-way spectroscopic measurements},
journal = {Journal of Statistical Software},
year = {2007},
volume = {18},
number = {3},
url = {http://www.jstatsoft.org/v18/i03/}
}
@INPROCEEDINGS{go05,
author = {Katharine M. Mullen and Mikas Vengris and Ivo H. M. van Stokkum},
title = {Separable nonlinear models for time-resolved spectra},
booktitle = {Proceedings of the International Workshop on Global Optimization},
year = {2005},
editor = {I. Garc\'{i}a and L. G. Casado and E.M.T. Hendrix and B. T\'{o}th},
pages = {183-188},
month = {September},
author1_email = {kate@nat.vu.nl},
author2_email = {ivo@nat.vu.nl}
}
@ARTICLE{jgo,
author = {Katharine M. Mullen and Mikas Vengris and Ivo H. M. van Stokkum},
title = {Algorithms for Separable Nonlinear Least Squares with Application
to Modelling Time-resolved Spectra},
journal = {Journal of Global Optimization},
year = {2007},
volume = {38},
pages = {201-213}
}
@ARTICLE{iv01,
author = {Naus, H. and van Stokkum, I. H. M. and Ubachs, W and Hogervorst,
W.},
title = {Quantitative analysis of decay transients applied to a multi-mode
pulsed cavity ring-down experiment},
journal = {Applied Optics},
year = {2001},
volume = {40},
pages = {4416-4426}
}
@ARTICLE{Palacios2003,
author = {Palacios, Miguel A. and Frese, Raoul N. and Gradinaru, Claudiu C.
and van Stokkum, I. H. M. and Premvardhan, Lavanya L. and Horton,
Peter and Ruban, Alexander V. and van Grondelle, Rienk and van Amerongen,
Herbert},
title = {Stark spectroscopy of the light-harvesting complex {II} in different
oligomerisation states},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {2003},
volume = {1605},
pages = {83--95},
month = {Aug},
day = {18},
issue = {1-3},
keywords = {{LHCII}},
url = {http://www.sciencedirect.com/science/article/B6T1S-490H910-1/2/0ee0ab00e8580fc343a19b188392c30d}
}
@ARTICLE{photo_2006,
author = {Miguel A. Palacios and Joerg Standfuss and Mikas Vengris and and
Bart F. van Oort and Ivo H. M. van Stokkum and Werner K{\"{u}}hlbrandt
and Herbert van Amerongen and Rienk van Grondelle},
title = {A comparison of the three isoforms of the light-harvesting complex
{II} using transient absorption and time-resolved fluorescence measurements},
journal = {Photosynthesis Research},
year = {2006},
volume = {88},
pages = {269--285},
number = {3},
url = {http://www.springerlink.com/content/yp125x44j1r28688}
}
@ARTICLE{PanditA._jp021757a,
author = {Pandit, A. and Larsen, O.F.A. and van Stokkum, I. H. M. and van Grondelle,
R. and Kraayenhof, R. and van Amerongen, H.},
title = {Ultrafast Polarized Fluorescence Measurements on Monomeric and Self-Associated
Melittin},
journal = {Journal of Physical Chemistry B},
year = {2003},
volume = {107},
pages = {3086-3090},
number = {13},
affiliation = {Department of Structural Biology, Faculty of Earth and Life Sciences,
Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam,
The Netherlands, Division of Physics and Astronomy, Faculty of Sciences,
Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam,
The Netherlands, and Laboratory of Biophysics, Department of Agrotechnology
and Food Sciences, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp021757a}
}
@ARTICLE{PanditA._bi0269005,
author = {Pandit, A. and Ma, H. and van Stokkum, I. H. M. and Gruebele, M.
and van Grondelle, R.},
title = {Time-Resolved Dissociation of the Light-Harvesting 1 Complex of Rhodospirillum
rubrum, Studied by Infrared Laser Temperature Jump},
journal = {Biochemistry},
year = {2002},
volume = {41},
pages = {15115-15120},
number = {51},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi0269005}
}
@ARTICLE{photo_2003,
author = {Anjali Pandit and Ivo H. M. van Stokkum and Sofia Georgakopoulou
and Gert van der Zwan and Rienk van Grondelle},
title = {Investigations of intermediates appearing in the reassociation of
the light-harvesting 1 complex of Rhodospirillum rubrum},
journal = {Photosynthesis Research},
year = {2003},
volume = {75},
pages = {235--248},
number = {3},
url = {http://www.springerlink.com/content/gl27263k40g62490}
}
@ARTICLE{pan,
author = {Pandit, A and Visschers, RW and van Stokkum, I. H. M. and Kraayenhof,
R and van Grondelle, R},
title = {Oligomerization of light-harvesting {I} antenna peptides of Rhodospirillum
rubrum},
journal = {Biochemistry},
year = {2001},
volume = {40},
pages = {12913-12924}
}
@ARTICLE{PapagiannakisE._jp027174i,
author = {Papagiannakis, E. and Das, S.K. and Gall, A. and van Stokkum, I.
H. M. and Robert, B. and van Grondelle, R. and Frank, H.A. and Kennis,
J.T.M.},
title = {Light Harvesting by Carotenoids Incorporated into the {B850} Light-Harvesting
Complex from Rhodobacteris phaeroides {R-26.1}: Excited-State Relaxation,
Ultrafast Triplet Formation, and Energy Transfer to Bacteriochlorophyll},
journal = {Journal of Physical Chemistry B},
year = {2003},
volume = {107},
pages = {5642-5649},
number = {23},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp027174i}
}
@ARTICLE{EmmanouilPapagiannakis04302002,
author = {Papagiannakis, Emmanouil and Kennis, John T. M. and van Stokkum,
Ivo H. M. and Cogdell, Richard J. and van Grondelle, Rienk},
title = {{An alternative carotenoid-to-bacteriochlorophyll energy transfer
pathway in photosynthetic light harvesting}},
journal = {PNAS},
year = {2002},
volume = {99},
pages = {6017-6022},
number = {9},
doi = {10.1073/pnas.092626599},
file = {6017.pdf:http\://www.pnas.org/cgi/reprint/99/9/6017.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/99/9/6017}
}
@ARTICLE{PapagiannakisE._bi047977r,
author = {Papagiannakis, E. and Larsen, D.S. and van Stokkum, I. H. M. and
Vengris, M. and Hiller, R.G. and van Grondelle, R.},
title = {Resolving the Excited State Equilibrium of Peridinin in Solution},
journal = {Biochemistry},
year = {2004},
volume = {43},
pages = {15303-15309},
number = {49},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi047977r}
}
@INCOLLECTION{bookpulse1,
author = {Emmanouil Papagiannakis and Delmar Larsen and Mikas Vengris and Ivo
van Stokkum and Rienk van Grondelle},
title = {Multi-Pulse Transient Absorption and Carotenoid Excited-State Dynamics:
{$\beta$}-Carotene},
booktitle = {Ultrafast Phenomena XIV},
year = {2005},
pages = {592--594},
url = {http://www.springerlink.com/content/m1506825m25288u7}
}
@ARTICLE{photo1_05,
author = {Emmanouil Papagiannakis and Ivo H. M. van Stokkum and Holger Fey
and Claudia B{\"{u}}chel and Rienk van Grondelle},
title = {Spectroscopic Characterization of the Excitation Energy Transfer
in the Fucoxanthin-Chlorophyll Protein of Diatoms},
journal = {Photosynthesis Research},
year = {2005},
volume = {86},
pages = {241--250},
issue = {1},
url = {http://www.springerlink.com/content/t25612216t0xp288}
}
@ARTICLE{PapagiannakisE._jp034931j,
author = {Papagiannakis, E. and van Stokkum, I. H. M. and van Grondelle, R.
and Niederman, R.A. and Zigmantas, D. and Sundstrom, V. and Polivka,
T.},
title = {A Near-Infrared Transient Absorption Study of the Excited-State Dynamics
of the Carotenoid Spirilloxanthin in Solution and in the LH1 Complex
of {R}hodospirillum rubrum},
journal = {Journal of Physical Chemistry B},
year = {2003},
volume = {107},
pages = {11216-11223},
number = {40},
affiliation = {Department of Chemical Physics, Lund University, P.O. Box 124, 22100
Lund, Sweden},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp034931j}
}
@ARTICLE{PapagiannakisE._jp054633h,
author = {Papagiannakis, E. and van Stokkum, I. H. M. and Vengris, M. and Cogdell,
R.J. and van Grondelle, R. and Larsen, D.S.},
title = {Excited-State Dynamics of Carotenoids in Light-Harvesting Complexes.
1. Exploring the Relationship between the {S$_1$} and {S*} States},
journal = {Journal of Physical Chemistry B},
year = {2006},
volume = {110},
pages = {5727-5736},
number = {11},
affiliation = {Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081,
1081 HV Amsterdam, The Netherlands, Institute of Biomedical & Life
Sciences, University of Glasgow, Glasgow, United Kingdom, Department
of Chemistry, University of California, Davis, One Shields Avenue,
Davis, California 95616, and Faculty of Physics, Vilnius University,
Sauletekio Avenue 9, Block 3, Vilnius, Lithuania},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp054633h}
}
@ARTICLE{PapagiannakisE._jp053094d,
author = {Papagiannakis, E. and Vengris, M. and Larsen, D.S. and van Stokkum,
I. H. M. and Hiller, R.G. and van Grondelle, R.},
title = {Use of Ultrafast Dispersed Pump-Dump-Probe and Pump-Repump-Probe
Spectroscopies to Explore the Light-Induced Dynamics of Peridinin
in Solution},
journal = {Journal of Physical Chemistry B},
year = {2006},
volume = {110},
pages = {512-521},
number = {1},
affiliation = {Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit,
De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands, and School
of Biological Sciences, Macquarie University, NSW 2109, Australia},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp053094d}
}
@ARTICLE{NataliaP.Pawlowicz08012008,
author = {Pawlowicz, Natalia P. and van Grondelle, Rienk and van Stokkum, Ivo
H. M. and Breton, Jacques and Jones, Michael R. and Groot, Marie
Louise},
title = {{Identification of the First Steps in Charge Separation in Bacterial
Photosynthetic Reaction Centers of Rhodobacter sphaeroides by Ultrafast
Mid-Infrared Spectroscopy: Electron Transfer and Protein Dynamics}},
journal = {Biophys. J.},
year = {2008},
volume = {95},
pages = {1268-1284},
number = {3},
abstract = {Time-resolved visible pump/mid-infrared (mid-IR) probe spectroscopy
in the region between 1600 and 1800 cm-1 was used to investigate
electron transfer, radical pair relaxation, and protein relaxation
at room temperature in the Rhodobacter sphaeroides reaction center
(RC). Wild-type RCs both with and without the quinone electron acceptor
QA, were excited at 600 nm (nonselective excitation), 800 nm (direct
excitation of the monomeric bacteriochlorophyll (BChl) cofactors),
and 860 nm (direct excitation of the dimer of primary donor (P) BChls
(PL/PM)). The region between 1600 and 1800 cm-1 encompasses absorption
changes associated with carbonyl (C=O) stretch vibrational modes
of the cofactors and protein. After photoexcitation of the RC the
primary electron donor P excited singlet state (P*) decayed on a
timescale of 3.7 ps to the state [IMG]f1.gif" ALT="Formula" BORDER="0">
(where BL is the accessory BChl electron acceptor). This is the first
report of the mid-IR absorption spectrum of [IMG]f2.gif" ALT="Formula"
BORDER="0"> the difference spectrum indicates that the 9-keto C=O
stretch of BL is located around 1670-1680 cm-1. After subsequent
electron transfer to the bacteriopheophytin HL in [~]1 ps, the state
[IMG]f3.gif" ALT="Formula" BORDER="0"> was formed. A sequential analysis
and simultaneous target analysis of the data showed a relaxation
of the [IMG]f3.gif" ALT="Formula" BORDER="0"> radical pair on the
[~]20 ps timescale, accompanied by a change in the relative ratio
of the [IMG]f4.gif" ALT="Formula" BORDER="0"> and [IMG]f5.gif" ALT="Formula"
BORDER="0"> bands and by a minor change in the band amplitude at
1640 cm-1 that may be tentatively ascribed to the response of an
amide C=O to the radical pair formation. We conclude that the drop
in free energy associated with the relaxation of [IMG]f3.gif" ALT="Formula"
BORDER="0"> is due to an increased localization of the electron hole
on the PL half of the dimer and a further consequence is a reduction
in the electrical field causing the Stark shift of one or more amide
C=O oscillators. },
doi = {10.1529/biophysj.108.130880},
eprint = {http://www.biophysj.org/cgi/reprint/95/3/1268.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/95/3/1268}
}
@ARTICLE{Pawlowicz10152007,
author = {Pawlowicz, N. P. and Groot, M.-L. and van Stokkum, I. H. M. and Breton,
J. and van Grondelle, R.},
title = {{Charge Separation and Energy Transfer in the {Photosystem II} Core
Complex Studied by Femtosecond Midinfrared Spectroscopy}},
journal = {Biophys. J.},
year = {2007},
volume = {93},
pages = {2732-2742},
number = {8},
abstract = {The core of photo{system II} (PSII) of green plants contains the reaction
center (RC) proteins D1D2-cytb559 and two core antennas CP43 and
CP47. We have used time-resolved visible pump/midinfrared probe spectroscopy
in the region between 1600 and 1800 cm1 to study the energy transfer
and charge separation events within PSII cores. The absorption difference
spectra in the region of the keto and ester chlorophyll modes show
spectral evolution with time constants of 3 ps, 27 ps, 200 ps, and
2 ns. Comparison of infrared (IR) difference spectra obtained for
the isolated antennas CP43 and CP47 and the D1D2-RC with those measured
for the PSII core allowed us to identify the features specific for
each of the PSII core components. From the presence of the CP43 and
CP47 specific features in the spectra up to time delays of 2030 ps,
we conclude that the main part of the energy transfer from the antennas
to the RC occurs on this timescale. Direct excitation of the pigments
in the RC evolution associated difference spectra to radical pair
formation of [IMG]f1.gif" ALT="Formula" BORDER="0"> on the same timescale
as multi-excitation annihilation and excited state equilibration
within the antennas CP43 and CP47, which occur within [~]13 ps. The
formation of the earlier radical pair [IMG]f2.gif" ALT="Formula"
BORDER="0"> as identified in isolated D1D2 complexes with time-resolved
mid-IR spectroscopy is not observed in the current data, probably
because of its relatively low concentration. Relaxation of the state
[IMG]f3.gif" ALT="Formula" BORDER="0"> caused by a drop in free energy,
occurs in 200 ps in closed cores. We conclude that the kinetic model
proposed earlier for the energy and electron transfer dynamics within
the D1D2-RC, plus two slowly energy-transferring antennas C43 and
CP47 explain the complex excited state and charge separation dynamics
in the PSII core very well. We further show that the time-resolved
IR-difference spectrum of [IMG]f1.gif" ALT="Formula" BORDER="0">
as observed in PSII cores is virtually identical to that observed
in the isolated D1D2-RC complex of PSII, demonstrating that the local
structure of the primary reactants has remained intact in the isolated
D1D2 complex. },
doi = {10.1529/biophysj.107.105452},
eprint = {http://www.biophysj.org/cgi/reprint/93/8/2732.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/93/8/2732}
}
@ARTICLE{Pawlowicz2010,
author = {Natalia P. Pawlowicz and Ivo H. M. van Stokkum and Jacques Breton
and Rienk van Grondelle and Michael R. Jones},
title = {An investigation of slow charge separation in a Tyrosine {M210} to
Tryptophan mutant of the Rhodobacter sphaeroides reaction center
by femtosecond mid-infrared spectroscopy},
journal = {Physical Chemistry Chemical Physics},
year = {2010},
volume = {12},
pages = {2693-2705},
number = {11},
doi = {DOI: 10.1039/b905934b}
}
@ARTICLE{Pawlowicz20094956,
author = {Natalia P. Pawlowicz and Ivo H. M. van Stokkum and Jacques Breton
and Rienk van Grondelle and Michael R. Jones},
title = {Identification of the Intermediate Charge-Separated State {P+{$\beta$}L-}
in a Leucine {M214} to Histidine Mutant of the {R}hodobacter sphaeroides
Reaction Center Using Femtosecond Midinfrared Spectroscopy},
journal = {Biophysical Journal},
year = {2009},
volume = {96},
pages = {4956 - 4965},
number = {12},
doi = {DOI: 10.1016/j.bpj.2009.03.031},
issn = {0006-3495},
url = {http://www.sciencedirect.com/science/article/B94RW-4WGVKGW-P/2/44157f270cf54de3077e7e0129440975}
}
@ARTICLE{Perez-Ruiz2006,
author = {Perez-Ruiz, Raul and Groeneveld, Michiel and van Stokkum, Ivo H.
M. and Tormos, Rosa and Williams, Ren{\'{e}} M. and Miranda, Miguel
A.},
title = {Fast transient absorption spectroscopy of the early events in photoexcited
chiral benzophenone-naphthalene dyads},
journal = {Chemical Physics Letters},
year = {2006},
volume = {429},
pages = {276--281},
month = {Sep},
day = {29},
issue = {1-3},
url = {http://www.sciencedirect.com/science/article/B6TFN-4KJ6KN8-1/2/f108ed120c75e1d5f32acffc0f7abbdf}
}
@ARTICLE{Peterman1997,
author = {Peterman, Erwin J. G. and Monshouwer, Ren{\'{e}} and van Stokkum,
Ivo H. M. and van Grondelle, Rienk and van Amerongen, Herbert},
title = {Ultrafast singlet excitation transfer from carotenoids to chlorophylls
via different pathways in light-harvesting complex {II} of higher
plants},
journal = {Chemical Physics Letters},
year = {1997},
volume = {264},
pages = {279--284},
month = {Jan},
day = {10},
issue = {3-4},
url = {http://www.sciencedirect.com/science/article/B6TFN-3S9D8N3-1F/2/8859fbd9f7516a5533aa289d926f4a57}
}
@ARTICLE{PetkovaI._jp0735841,
author = {Petkova, I. and Mudadu, M.S. and Singh, A. and Thummel, R.P. and
van Stokkum, I. H. M. and Buma, W.J. and Waluk, J.},
title = {Structure and Photophysics of 2-(2'-Pyridyl)benzindoles: The Role
of Intermolecular Hydrogen Bonds},
journal = {Journal of Physical Chemistry A},
year = {2007},
volume = {111},
pages = {11400-11409},
number = {45},
affiliation = {Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka
44/52, 01-224 Warsaw, Poland, Institute of Organic Chemistry, Bulgarian
Academy of Sciences, Akad. G. Bontchev bl. IX, Sofia 1113, Bulgaria,
Van't Hoff Institute for Molecular Sciences, University of Amsterdam,
Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands, Department
of Chemistry, University of Houston, Houston, Texas, 77204-5003,
and Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081
HV Amsterdam, The Netherlands},
issn = {1089-5639},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0735841}
}
@ARTICLE{PetushkovV.N._jp034266e,
author = {Valentin N. Petushkov and Ivo H. M. van Stokkum and Bas Gobets and
Frank van Mourik and John Lee and Rienk van Grondelle and Antonie
J.W.G. Visser},
title = {Ultrafast Fluorescence Relaxation Spectroscopy of 6,7-Dimethyl-(8-ribityl)-lumazine
and Riboflavin, Free and Bound to Antenna Proteins from Bioluminescent
Bacteria},
journal = {Journal of Physical Chemistry B},
year = {2003},
volume = {107},
pages = {10934-10939},
number = {39},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp034266e}
}
@ARTICLE{PolivkaT_bi060265b,
author = {Pol{\'{i}}vka, T. and van Stokkum, I. H. M. and Zigmantas, D. and
van Grondelle, R. and Sundstr{\"{o}}m, V. and Hiller, R.G.},
title = {Energy Transfer in the Major Intrinsic Light-Harvesting Complex from
{{\it Amphidinium carterae}}},
journal = {Biochemistry},
year = {2006},
volume = {45},
pages = {8516-8526},
number = {28},
affiliation = {Institute of Physical Biology, University of South Bohemia, Czech
Republic, Institute of Plant Molecular Biology, Czech Academy of
Sciences, Czech Republic, Department of Chemical Physics, Lund University,
Sweden, Department of Physics and Astronomy, Vrije Universiteit,
Amsterdam, The Netherlands, Department of Chemistry, University of
California, Berkeley, California, Physical Biosciences Division,
Lawrence Berkeley National Laboratory, Berkeley, California 94720,
and Department of Biological Sciences, Macquarie University, NSW
2109, Australia},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi060265b}
}
@ARTICLE{pri93,
author = {Pribi{\'{c}}, R. and Van Stokkum, I. H. M. and Chapman, D. and Haris,
P.I. and Bloemendal, M.},
title = {Protein secondary structure from Fourier Transform Infrared and/or
Circular Dichroism spectra},
journal = {Analytical Biochemistry},
year = {1993},
volume = {214},
pages = {366-378}
}
@INPROCEEDINGS{pr94,
author = {Pribi{\'{c}}, R. and Van Stokkum, I. H. M. and Van den Bos, A.},
title = {Inference regions of nonlinear parameters in global analysis},
booktitle = {Proceedings {SYSID} 1994, 10th {IFAC} Symposium on System Identification},
year = {1994},
editor = {Blanke, M. and S{\"o}derstr{\"o}m, T.},
pages = {2423-2428},
publisher = {Danish Automation Society, Copenhagen}
}
@ARTICLE{Romero2009L35,
author = {Elisabet Romero and Milena Mozzo and Ivo H. M. van Stokkum and Jan
P. Dekker and Rienk van Grondelle and Roberta Croce},
title = {The Origin of the Low-Energy Form of Photosystem {I} Light{-}Harvesting
Complex {Lhca}4: Mixing of the Lowest Exciton with a Charge{-}Transfer
State},
journal = {Biophysical Journal},
year = {2009},
volume = {96},
pages = {L35 - L37},
number = {5},
doi = {DOI: 10.1016/j.bpj.2008.11.043},
issn = {0006-3495},
url = {http://www.sciencedirect.com/science/article/B94RW-4VRPN44-1/2/d4374b92f183d213568b0fee8c25e7ad}
}
@ARTICLE{ISI:000288447100008,
author = {Romero, Elisabet and van Stokkum, Ivo H. M. and Dekker, Jan P. and
van Grondelle, Rienk},
title = {{Ultrafast carotenoid band shifts correlated with Chl(z) excited
states in the photo{system II} reaction center: are the carotenoids
involved in energy transfer?}},
journal = {Physical Chemistry Chemical Physics},
year = {2011},
volume = {{13}},
pages = {{5573-5575}},
number = {{13}},
abstract = {{We show a correlation between the electronic excitation of the peripheral
chlorophylls (Chls(Z)) of the photo{system II} reaction center and
a shift of the S(2) absorption bands of beta-carotene, and suggest
that the carotenoids may enhance the excitation energy transfer rate
from these chlorophylls to the central cofactors.}},
address = {{THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF,
CAMBS, ENGLAND}},
affiliation = {{Romero, E (Reprint Author), Vrije Univ Amsterdam, Fac Sci, Dept Phys
\& Astron, De Boelelaan 1081, NL-1081 HV Amsterdam, Netherlands.
Romero, E Romero, E; van Stokkum, IHM; Dekker, JP; van Grondelle,
R, Vrije Univ Amsterdam, Fac Sci, Dept Phys \& Astron, NL-1081 HV
Amsterdam, Netherlands.}},
doc-delivery-number = {{735VB}},
doi = {{10.1039/c0cp02896g}},
funding-acknowledgement = {{Marie Curie Research Training Network INTRO2 of the E.U.\{{[}\}MRTN
- CT - 505069]; Netherlands Organization for Scientific Research
(NWO)}},
funding-text = {{This work was supported by the Marie Curie Research Training Network
INTRO2 (MRTN - CT - 505069) (E. R.) of the E.U. and by The Netherlands
Organization for Scientific Research (NWO).}},
issn = {{1463-9076}},
journal-iso = {{Phys. Chem. Chem. Phys.}},
keywords-plus = {{PRIMARY ELECTRON-DONOR; CHARGE SEPARATION; FLUORESCENCE; SPECTROSCOPY;
ARRANGEMENT; RESOLUTION; DYNAMICS; SPECTRA; LIGHT; LH2}},
language = {{English}},
number-of-cited-references = {{21}},
publisher = {{ROYAL SOC CHEMISTRY}},
subject-category = {{Chemistry; Physics}},
times-cited = {{1}},
type = {{Article}},
unique-id = {{ISI:000288447100008}}
}
@ARTICLE{Romero2010,
author = {Romero, E. and van Stokkum, I. H. M. and Novoderezhkin, V. I. and
Dekker, J. P. and van Grondelle, R.},
title = {Two Different Charge Separation Pathways in Photosystem {II}},
journal = {Biochemistry},
year = {2010},
volume = {49},
pages = {4300-4307},
number = {20},
abstract = {Charge separation is an essential step in the conversion of solar
energy into chemical energy in photosynthesis. To investigate this
process, we performed transient absorption experiments at 77 K with
various excitation conditions on the isolated {Photosystem II} reaction
center preparations from spinach. The results have been analyzed
by global and target analysis and demonstrate that at least two different
excited states, (Chl(D1)Phe(D1))* and (P(D1)P(D2)Chl(D1))*, give
rise to two different pathways for ultrafast charge separation. We
propose that the disorder produced by slow protein motions causes
energetic differentiation among reaction center complexes, leading
to different charge separation pathways. Because of the low temperature,
two excitation energy trap states are also present, generating charge-separated
states on long time scales. We conclude that these slow trap states
are the same as the excited states that lead to ultrafast charge
separation, indicating that at 77 K charge separation can be either
activation-less and last or activated and slow.}
}
@ARTICLE{vanRotterdam2002,
author = {van Rotterdam, Bart J. and Crielaard, Wim and van Stokkum, Ivo H.
M. and Hellingwerf, Klaas J. and Westerhoff, Hans V.},
title = {Simplicity in complexity: the photosynthetic reaction center performs
as a simple 0.2 {V} battery},
journal = {FEBS Letters},
year = {2002},
volume = {510},
pages = {105--107},
month = {Jan},
day = {02},
issue = {1-2},
keywords = {Photosynthesis},
url = {http://www.sciencedirect.com/science/article/B6T36-44KWT43-1/2/c245f3b0071c42271e5a0db0da98a34c}
}
@ARTICLE{ruban2007,
author = {Ruban, Alexander V. and Berera, Rudi and Ilioaia, Cristian and van
Stokkum, Ivo H. M. and Kennis, John T. M. and Pascal, Andrew A. and
van Amerongen, Herbert and Robert, Bruno and Horton, Peter and van
Grondelle, Rienk},
title = {Identification of a mechanism of photoprotective energy dissipation
in higher plants},
journal = {Nature},
year = {2007},
volume = {450},
pages = {575-578},
number = {7169},
url = {http://www.nature.com/nature/journal/v450/n7169/abs/nature06262.html}
}
@ARTICLE{AlisaRupenyan05152008,
author = {Rupenyan, Alisa and van Stokkum, Ivo H. M. and Arents, Jos C. and
van Grondelle, Rienk and Hellingwerf, Klaas and Groot, Marie Louise},
title = {{Characterization of the Primary Photochemistry of Proteorhodopsin
with Femtosecond Spectroscopy}},
journal = {Biophys. J.},
year = {2008},
volume = {94},
pages = {4020-4030},
number = {10},
abstract = {Proteorhodopsin is an ion-translocating member of the microbial rhodopsin
family. Light absorption by its retinal chromophore initiates a photocycle,
driven by trans/cis isomerization, leading to transmembrane translocation
of a proton toward the extracellular side of the cytoplasmic membrane.
Here we report a study on the photoisomerization dynamics of the
retinal chromophore of proteorhodopsin, using femtosecond time-resolved
spectroscopy, by probing in the visible- and in the midinfrared spectral
regions. Experiments were performed both at pH 9.5 (a physiologically
relevant pH value in which the primary proton acceptor of the protonated
Schiff base, Asp97, is deprotonated) and at pH 6.5 (with Asp97 protonated).
Simultaneous analysis of the data sets recorded in the two spectral
regions and at both pH values reveals a multiexponential excited
state decay, with time constants of [~]0.2 ps, [~]2 ps, and [~]20
ps. From the difference spectra associated with these dynamics, we
conclude that there are two chromophore-isomerizaton pathways that
lead to the K-state: one with an effective rate of [~](2 ps)-1 and
the other with a rate of [~](20 ps)-1. At high pH, both pathways
are equally effective, with an estimated quantum yield for K-formation
of [~]0.7. At pH 6.5, the slower pathway is less productive, which
results in an isomerization quantum yield of 0.5. We further observe
an ultrafast response of residue Asp227, which forms part of the
counterion complex, corresponding to a strengthening of its hydrogen
bond with the Schiff base on K-state formation; and a feature that
develops on the 0.2 ps and 2 ps timescale and probably reflects a
response of an amide {II} band in reaction to the isomerization process.
},
doi = {10.1529/biophysj.107.121376},
eprint = {http://www.biophysj.org/cgi/reprint/94/10/4020.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/94/10/4020}
}
@ARTICLE{alisaJPCB09,
author = {Rupenyan, Alisa and van Stokkum, Ivo H. M. and Arents, Jos C. and
van Grondelle, Rienk and Hellingwerf, Klaas J. and Groot, Marie Louise},
title = {Reaction Pathways of Photoexcited Retinal in Proteorhodopsin Studied
by {Pump-Dump-Probe} Spectroscopy},
journal = {The Journal of Physical Chemistry B},
year = {2009},
volume = {113},
pages = {16251-16256},
number = {50},
doi = {doi: 10.1021/jp9065289}
}
@ARTICLE{ISI:000290652100031,
author = {Rupenyan, Alisa B. and Vreede, Jocelyne and van Stokkum, Ivo H. M.
and Hospes, Marijke and Kennis, John T. M. and Hellingwerf, Klaas
J. and Groot, Marie Louise},
title = {{Proline 68 Enhances Photoisomerization Yield in Photoactive Yellow
Protein}},
journal = {Journal of Physical Chemistry B},
year = {2011},
volume = {{115}},
pages = {{6668-6677}},
number = {{20}},
month = {{May 26}},
address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
affiliation = {{Rupenyan, AB (Reprint Author), Swiss Fed Inst Technol, Lab Phys Chem,
Wolfgang Pauli Str 10, CH-8093 Zurich, Switzerland. Vreede, J, Univ
Amsterdam, Vant Hoff Inst Mol Sci, NL-1010 WV Amsterdam, Netherlands.
Hospes, M; Hellingwerf, KJ, Univ Amsterdam, Swammerdam Inst Life
Sci, Lab Microbiol, NL-1010 WV Amsterdam, Netherlands. Rupenyan,
AB; van Stokkum, IHM; Kennis, JTM; Hellingwerf, KJ; Groot, ML, Vrije
Univ Amsterdam, Fac Sci, Dept Phys \& Astron, NL-1081 HV Amsterdam,
Netherlands.}},
author-email = {{a.b.rupenyan@uva.nl}},
doc-delivery-number = {{764SE}},
doi = {{10.1021/jp112113s}},
funding-acknowledgement = {{Netherlands Organization for Scientific Research; Human Frontier
Science Program}},
funding-text = {{This research was supported by The Netherlands Organization for Scientific
Research and the Human Frontier Science Program. J.V. thanks Gerrit
Groenhof at the Max Planck Institute for Biophysical Chemistry, Goettingen,
Germany, for kindly providing the force field parameters of the chromophore.
A.B.R. thanks Jos Thieme from VU University Amsterdam for technical
support.}},
issn = {{1520-6106}},
journal-iso = {{J. Phys. Chem. B}},
keywords-plus = {{TRANSIENT ABSORPTION-SPECTROSCOPY; ECTOTHIORHODOSPIRA-HALOPHILA;
PHOTOCYCLE; DYNAMICS; CHROMOPHORE; FLUORESCENCE; MUTANTS; WATER;
ISOMERIZATION; INTERMEDIATE}},
language = {{English}},
number-of-cited-references = {{50}},
publisher = {{AMER CHEMICAL SOC}},
subject-category = {{Chemistry}},
times-cited = {{0}},
type = {{Article}},
unique-id = {{ISI:000290652100031}}
}
@INPROCEEDINGS{i98z,
author = {Salverda, JM and van Mourik, F and van Stokkum, I. H. M. and Wendling,
M and van Grondelle, R},
title = {Polarized and colored photon echo measurements on the {LH2} antenna
of {R}ps. acidophila and {R}s. molischianum},
booktitle = {Photosynthesis: Mechanisms and Effects},
year = {1998},
editor = {Garab, G},
pages = {45-48},
publisher = {Kluwer Academic Publishers, Dordrecht}
}
@ARTICLE{SautterA._ja0448216,
author = {Sautter, A. and Kaletas, B.K. and Schmid, D.G. and Dobrawa, R. and
Zimine, M. and Jung, G. and van Stokkum, I. H. M. and DeCola, L.
and Williams, R.M. and W{\"u}rthner, F.},
title = {Ultrafast Energy-Electron Transfer Cascade in a Multichromophoric
Light-Harvesting Molecular Square},
journal = {Journal of the American Chemical Society},
year = {2005},
volume = {127},
pages = {6719-6729},
number = {18},
issn = {0002-7863},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja0448216}
}
@ARTICLE{SchererT._j100092a025,
author = {Scherer, T. and van Stokkum, I. H. M. and Brouwer, A. M. and Verhoeven,
J. W.},
title = {Excited-State Conformational Dynamics of Flexibly and Semirigidly
Bridged Electron Donor-Acceptor Systems in Solution. Influence of
Temperature and Solvent Viscosity},
journal = {Journal of Physical Chemistry},
year = {1994},
volume = {98},
pages = {10539-10549},
number = {41},
issn = {0022-3654},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/j100092a025}
}
@ARTICLE{jorispub1,
author = {Sicam, Victor Arni D. P. and Snellenburg, Joris J. and Van Der Heijde,
Rob G. L. and Van Stokkum, Ivo H. M.},
title = {{Pseudo Forward Ray-Tracing: A New Method for Surface Validation
in Cornea Topography}},
journal = {Optometry \& Vision Science},
year = {2007},
volume = {84},
pages = {E915-E923},
number = {9},
abstract = {http://www.optvissci.com/pt/re/ovs/abstract.00006324-200709000-00020.htm},
copyright = {http://copyrighttoolbox.surf.nl/copyrighttoolbox/authors/sample-wording/educational-use/provisions/},
file = {sicam-snellenburg.pdf:http\://www.nat.vu.nl/~jsnel/paper/sicam-snellenburg.pdf:PDF},
url = {http://meta.wkhealth.com/pt/pt-core/template-journal/lwwgateway/media/landingpage.htm?an=00006324-200709000-00020}
}
@ARTICLE{Stahl20093215,
author = {Andreas D. Stahl and Mariangela Di Donato and Ivo van Stokkum and
Rienk van Grondelle and Marie Louise Groot},
title = {A Femtosecond Visible/Visible and Visible/Mid-Infrared Transient
Absorption Study of the Light Harvesting Complex {II}},
journal = {Biophysical Journal},
year = {2009},
volume = {97},
pages = {3215 - 3223},
number = {12},
doi = {DOI: 10.1016/j.bpj.2009.09.037},
issn = {0006-3495},
url = {http://www.sciencedirect.com/science/article/B94RW-4XX39TB-N/2/823955b52a75d6e56afb34b3c37cb395}
}
@TECHREPORT{lecture,
author = {Ivo H. M. van Stokkum},
title = {Global and Target Analysis of Time-resolved Spectra, Lecture notes
for the Troisi{\`{e}}me Cycle de la Physique en Suisse Romande},
institution = {Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit,
Amsterdam, The Netherlands},
year = {2005},
url = {http://www.nat.vu.nl/~ivo/pub/2005/lecturenotes3cycle.pdf}
}
@INPROCEEDINGS{i99,
author = {van Stokkum, I. H. M.},
title = {Added value of singles in {3D PET}},
booktitle = {Proceedings of the 1999 International meeting on fully three-dimensional
image reconstruction in radiology and nuclear medicine},
year = {1999},
pages = {115-118}
}
@ARTICLE{ieee1x,
author = {van Stokkum, I. H. M.},
title = {Parameter Precision in Global Analysis of Time Resolved Spectra},
journal = {IEEE Transactions on Instrumentation and Measurement},
year = {1997},
volume = {46},
pages = {764-768},
number = {4}
}
@INPROCEEDINGS{ieee2x,
author = {van Stokkum, I. H. M.},
title = {Parameter Precision in Global Analysis of Time Resolved Spectra},
booktitle = {Quality Measurements: The Indispensable Bridge between Theory and
Reality},
year = {1996},
volume = {1},
pages = {168-173},
organization = {IEEE Instrumentation and Measurement Technology Conference}
}
@ARTICLE{vanStokkum1990b,
author = {van Stokkum, Ivo H. M.},
title = {Modelling the response of auditory midbrain neurons in the grassfrog
to temporally structured monaural stimuli},
journal = {Hearing Research},
year = {1990},
volume = {43},
pages = {231--250},
month = {Jan},
issue = {2-3},
keywords = {Anuran},
url = {http://www.sciencedirect.com/science/article/B6T73-4CF5W2R-G/2/0bb61683a06f2e5ca035405c6d0e92c1}
}
@PHDTHESIS{thesisivo,
author = {van Stokkum, I. H. M.},
title = {Analysis of auditory brainstem neurons in the grassfrog},
school = {Catholic University of Nijmegen},
year = {1989}
}
@ARTICLE{vanStokkum1987,
author = {van Stokkum, Ivo H. M.},
title = {Sensitivity of neurons in the dorsal medullary nucleus of the grassfrog
to spectral and temporal characteristics of sound},
journal = {Hearing Research},
year = {1987},
volume = {29},
pages = {223--235},
issue = {2-3},
keywords = {Amplitude modulation},
url = {http://www.sciencedirect.com/science/article/B6T73-485GM6P-S7/2/382f5f3bd1189b5e9242b6ecbad822db}
}
@ARTICLE{pse_short,
author = {Ivo H. M. van Stokkum and Henri E. Bal},
title = {A Problem Solving Environment for interactive modelling of multiway
data},
journal = {Concurrency and computation: practice and experience},
year = {2006},
volume = {18},
pages = {263-269}
}
@ARTICLE{vanStokkumI.H.M._bi9707943,
author = {van Stokkum, I. H. M. and Beekman, L.M.P. and Jones, M.R. and van
Brederode, M.E. and van Grondelle, R.},
title = {Primary Electron Transfer Kinetics in Membrane-Bound Rhodobacter
sphaeroides Reaction Centers: A Global and Target Analysis},
journal = {Biochemistry},
year = {1997},
volume = {36},
pages = {11360-11368},
number = {38},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9707943}
}
@ARTICLE{ivo93,
author = {van Stokkum, I. H. M. and Brouwer, A.M. and Van Ramesdonk, H.J. and
Scherer, T.},
title = {Multiresponse parameter estimation and compartmental analysis of
time resolved fluorescence spectra: Application to conformational
dynamics of charge-separated species in solution},
journal = {Proc. Kon. Ned. Akad. v. Wetensch},
year = {1993},
volume = {96},
pages = {43-68}
}
@ARTICLE{ivo88b,
author = {van Stokkum, I. H. M. and Epping, W.J.M.},
title = {Responses of auditory brainstem neurons in the grassfrog to clicks},
journal = {Acta Biologica Hungarica},
year = {1988},
volume = {29},
pages = {291-304}
}
@ARTICLE{ISI:000289774200005,
author = {van Stokkum, Ivo H. M. and Gauden, Magdalena and Crosson, Sean and
van Grondelle, Rienk and Moffat, Keith and Kennis, John T. M.},
title = {{The Primary Photophysics of the Avena sativa Phototropin 1 LOV2
Domain Observed with Time-resolved Emission Spectroscopy}},
journal = {Photochemistry and Photobiology},
year = {2011},
volume = {{87}},
pages = {{534-541}},
number = {{3}},
month = {{May-jun}},
abstract = {{The phototropins are blue-light receptors that base their light-dependent
action on the reversible formation of a covalent bond between a flavin
mononucleotide (FMN) cofactor and a conserved cysteine in light,
oxygen or voltage (LOV) domains. The primary reactions of the Avena
sativa phototropin 1 LOV2 domain were investigated by means of time-resolved
and low-temperature fluorescence spectroscopy. Synchroscan streak
camera experiments revealed a fluorescence lifetime of 2.2 ns in
LOV2. A weak long-lived component with emission intensity from 600
to 650 nm was assigned to phosphorescence from the reactive FMN triplet
state. This observation allowed determination of the LOV2 triplet
state energy level at physiological temperature at 16600 cm(-1).
FMN dissolved in aqueous solution showed pH-dependent fluorescence
lifetimes of 2.7 ns at pH 2 and 3.9-4.1 ns at pH 3-8. Here, too,
a weak phosphorescence band was observed. The fluorescence quantum
yield of LOV2 increased from 0.13 to 0.41 upon cooling the sample
from 293 to 77 K. A pronounced phosphorescence emission around 600
nm was observed in the LOV2 domain between 77 and 120 K in the steady-state
emission.}},
address = {{COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA}},
affiliation = {{Kennis, JTM (Reprint Author), Vrije Univ Amsterdam, Fac Sci, Dept
Phys \& Astron, Amsterdam, Netherlands. van Stokkum, IHM; Gauden,
M; van Grondelle, R; Kennis, JTM, Vrije Univ Amsterdam, Fac Sci,
Dept Phys \& Astron, Amsterdam, Netherlands. Crosson, S; Moffat,
K, Univ Chicago, Dept Biochem \& Mol Biol, Chicago, IL 60637 USA.
Moffat, K, Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA.}},
author-email = {{j.t.m.kennis@vu.nl}},
doc-delivery-number = {{753LD}},
doi = {{10.1111/j.1751-1097.2011.00903.x}},
funding-acknowledgement = {{Chemical Sciences Council of the Netherlands Foundation for Scientific
Research (NWO-CW); Earth and Life Sciences Council of the Netherlands
Foundation for Scientific Research (NWO-ALW); Foundation of Fundamental
Research on Matter (FOM); NIH\{{[}\}GM 36452]; NSF}},
funding-text = {{The construct of oat phot1 LOV2 was generously provided by Kevin
Gardner of University of Texas and Southwestern Medical Center, Dallas.
M.G. was supported by the Chemical Sciences Council of the Netherlands
Foundation for Scientific Research (NWO-CW). J.T.M.K. was supported
by the Earth and Life Sciences Council of the Netherlands Foundation
for Scientific Research (NWO-ALW) via a VIDI grant, and through the
Foundation of Fundamental Research on Matter (FOM). K.M. was supported
through NIH grant GM 36452, S.C. was supported through an NSF Predoctoral
Fellowship.}},
issn = {{0031-8655}},
journal-iso = {{Photochem. Photobiol.}},
keywords-plus = {{BLUE-LIGHT RECEPTOR; ALGA CHLAMYDOMONAS-REINHARDTII; FLAVIN-BINDING
PHOTORECEPTOR; J-ALPHA HELIX; STRUCTURAL-CHANGES; SIGNALING MECHANISM;
RHODOBACTER-SPHAEROIDES; HISTIDINE KINASES; PHOT-LOV1 DOMAIN; AQUEOUS-SOLUTION}},
language = {{English}},
number-of-cited-references = {{90}},
publisher = {{WILEY-BLACKWELL}},
subject-category = {{Biochemistry \& Molecular Biology; Biophysics}},
times-cited = {{0}},
type = {{Article}},
unique-id = {{ISI:000289774200005}}
}
@ARTICLE{vanStokkum1989,
author = {van Stokkum, Ivo H. M. and Gielen, C. C. A. M.},
title = {A model for the peripheral auditory nervous system of the grassfrog},
journal = {Hearing Research},
year = {1989},
volume = {41},
pages = {71--85},
month = {Aug},
issue = {1},
keywords = {Anuran},
url = {http://www.sciencedirect.com/science/article/B6T73-485H319-X/2/74482d7e19e3233e617f40a8fa5d65f2}
}
@ARTICLE{i_2006,
author = {I. H. M. van Stokkum and B. Gobets and T. Gensch and F. van Mourik
and K. J. Hellingwerf and R. van Grondelle and J. T. M. Kennis},
title = {Symposium-in-Print: Green Fluorescent Protein and Homologs. (Sub)-Picosecond
Spectral Evolution of Fluorescence in Photoactive Proteins Studied
with a Synchroscan Streak Camera System},
journal = {Photochemistry and Photobiology},
year = {2006},
volume = {82},
pages = {380-388},
file = {PhotochemPhotobiol82_380_388.pdf:http\://www.nat.vu.nl/~ivo/pub/2006/PhotochemPhotobiol82_380_388.pdf:PDF}
}
@ARTICLE{vanStokkum1995,
author = {van Stokkum, I. H. M. and van der Graaf, W. A. and Lenstra, D.},
title = {Weighted fit of optical spectra},
journal = {Optics Communications},
year = {1995},
volume = {121},
pages = {103--108},
month = {Dec},
day = {01},
issue = {4-6},
url = {http://www.sciencedirect.com/science/article/B6TVF-3XY2PXG-3/2/8594545ebf321bb087dc365196c77820}
}
@ARTICLE{i95,
author = {van Stokkum, I. H. M. and Lambrou, G.N. and Van den Berg, T.J.T.P.},
title = {Hemodynamic parameter estimation from ocular fluorescein angiograms},
journal = {Graefe's Archive for Clinical and Experimental Ophthalmology},
year = {1995},
volume = {233},
pages = {123-130}
}
@ARTICLE{pse_long,
author = {Ivo H. M. van Stokkum and Delmar S. Larsen and Rienk van Grondelle},
title = {Global and Target Analysis of Time-resolved Spectra},
journal = {Biochimica et Biophysica Acta},
year = {2004},
volume = {1657},
pages = {82-104, and erratum, {{\bf 1658}}, 262}
}
@ARTICLE{vanStokkum2004a,
author = {van Stokkum, Ivo H. M. and Larsen, Delmar S. and van Grondelle, Rienk},
title = {Erratum to ''{G}lobal and target analysis of time-resolved spectra''
[{Biochimica et Biophysica Acta} 1658/2-3 (2004) 82-104]},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {2004},
volume = {1658},
pages = {262--262},
month = {Oct},
day = {04},
issue = {3},
url = {http://www.sciencedirect.com/science/article/B6T1S-4D5P0FB-1/2/6dd0f74e3ce7f0159dd7dfacf7d6c0c7}
}
@ARTICLE{vanStokkum2004b,
author = {van Stokkum, Ivo H. M. and Larsen, Delmar S. and van Grondelle, Rienk},
title = {Global and target analysis of time-resolved spectra},
journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
year = {2004},
volume = {1657},
pages = {82--104},
month = {Jul},
day = {09},
issue = {2-3},
keywords = {Global analysis},
url = {http://www.sciencedirect.com/science/article/B6T1S-4CK7MW0-3/2/ccec4c719e748c44b43c827df76e0b45}
}
@ARTICLE{vanStokkumI.H.M._bi00033a024,
author = {van Stokkum, I. H. M. and Linsdell, H. and Hadden, J. M. and Haris,
P. I. and Chapman, D. and Bloemendal, M.},
title = {Temperature-Induced Changes in Protein Structures Studied by Fourier
Transform Infrared Spectroscopy and Global Analysis},
journal = {Biochemistry},
year = {1995},
volume = {34},
pages = {10508-10518},
number = {33},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi00033a024}
}
@ARTICLE{target,
author = {van Stokkum, I. H. M. and Lozier, RH},
title = {Target analysis of the bacteriorhodopsin photocycle using a spectrotemporal
model},
journal = {J. Phys. Chem. B},
year = {2002},
volume = {106},
pages = {3477-3485}
}
@ARTICLE{vanStokkum1991,
author = {van Stokkum, Ivo H. M. and Melssen, Willem J.},
title = {Measuring and modelling the response of auditory midbrain neurons
in the grassfrog to temporally structured binaural stimuli},
journal = {Hearing Research},
year = {1991},
volume = {52},
pages = {113--132},
month = {Mar},
issue = {1},
keywords = {Anuran},
url = {http://www.sciencedirect.com/science/article/B6T73-485H32M-1C/2/43f2844a196d6d0aee11be1f7bec9ce6}
}
@INPROCEEDINGS{beekb,
author = {van Stokkum, I. H. M. and F. van Mourik and M.-L. Groot and R. van
Grondelle},
title = {Low-intensity fluorescence spectra from the photosystem {II} reaction
centre measured using a picosecond synchroscan streak camera. Effects
of sample degradation on the observed lifetimes},
booktitle = {Photosynthesis: from Light to Biosphere},
year = {1995},
editor = {P. Mathis},
volume = {1},
pages = {887-890},
publisher = {Dordrecht, Kluwer}
}
@ARTICLE{vanStokkum2009150,
author = {Ivo H. M. van Stokkum and Katharine M. Mullen and Velitchka V. Mihaleva},
title = {Global analysis of multiple gas chromatography-mass spectrometry
({GC/MS}) data sets: A method for resolution of co-eluting components
with comparison to {MCR-ALS}},
journal = {Chemometrics and Intelligent Laboratory Systems},
year = {2009},
volume = {95},
pages = {150 - 163},
number = {2},
doi = {DOI: 10.1016/j.chemolab.2008.10.004},
issn = {0169-7439},
keywords = {Multivariate curve resolution alternating least squares},
url = {http://www.sciencedirect.com/science/article/B6TFP-4TT9G9Y-2/2/023c3de71d2471d96ef8e1b4c377ff36}
}
@INCOLLECTION{streakreview,
author = {I. H. M. van Stokkum and B. van Oort and F. van Mourik and B. Gobets
and H. van Amerongen},
title = {{(Sub)-Picosecond Spectral Evolution of Fluorescence Studied with
a Synchroscan Streak-Camera System and Target Analysis}},
booktitle = {{Biophysical Techniques in Photosynthesis, Volume {II}, Series Advances
in Photosynthesis and Respiration}},
publisher = {Springer, Dordrecht},
year = {2008},
editor = {Aartsma, Thijs J. and Matysik, J{\"{o}}rg},
volume = {26},
pages = {223-240},
isbn = {978-1-4020-8249-8},
url = {http://www.springer.com/west/home/new+%26+forthcoming+titles+%28default%29?SGWID=4-40356-22-173795609-0}
}
@ARTICLE{vanStokkum200970,
author = {Ivo H. M. van Stokkum and Emmanouil Papagiannakis and Mikas Vengris
and Jante M. Salverda and Tom{\'{a}}s Pol{\'{i}}vka and Donatas Zigmantas
and Delmar S. Larsen and Stefania S. Lampoura and Roger G. Hiller
and Rienk van Grondelle},
title = {Inter-pigment interactions in the peridinin chlorophyll protein studied
by global and target analysis of time resolved absorption spectra},
journal = {Chemical Physics},
year = {2009},
volume = {357},
pages = {70 - 78},
number = {1-3},
doi = {DOI: 10.1016/j.chemphys.2008.10.005},
issn = {0301-0104},
keywords = {Peridinin chlorophyll protein},
url = {http://www.sciencedirect.com/science/article/B6TFM-4TP49RS-1/2/547d9b815d70999da20a291a2b76c3dc}
}
@ARTICLE{vanStokkumI.H.M._j100054a021,
author = {van Stokkum, I. H. M. and Scherer, T. and Brouwer, A. M. and Verhoeven,
J. W.},
title = {Conformational dynamics of flexibly and semirigidly bridged electron
donor-acceptor systems as revealed by spectrotemporal parametrization
of fluorescence},
journal = {Journal of Physical Chemistry},
year = {1994},
volume = {98},
pages = {852-866},
number = {3},
issn = {0022-3654},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/j100054a021}
}
@ARTICLE{vanStokkum1990a,
author = {van Stokkum, Ivo H. M. and Spoelder, Hans J. W. and Bloemendal, Michael
and van Grondelle, Rienk and Groen, Frans C. A.},
title = {Estimation of protein secondary structure and error analysis from
circular dichroism spectra},
journal = {Analytical Biochemistry},
year = {1990},
volume = {191},
pages = {110--118},
month = {Nov},
day = {15},
issue = {1},
url = {http://www.sciencedirect.com/science/article/B6W9V-4F031H9-7X/2/c5ac776796f63ea06b6bf35705f49643}
}
@ARTICLE{sytina2008,
author = {Sytina, Olga A. and Heyes, Derren J. and Hunter, C. Neil and Alexandre,
Maxime T. and van Stokkum, Ivo H. M. and van Grondelle, Rienk and
Groot, Marie{-}Louise},
title = {Conformational changes in an ultrafast light-driven enzyme determine
catalytic activity},
journal = {Nature},
year = {2008},
volume = {456},
pages = {1001-1004},
number = {7224},
url = {http://www.nature.com/nature/journal/v456/n7224/abs/nature07354.html}
}
@ARTICLE{doi:10.1021/jp108317u,
author = {Sytina, Olga A. and van Stokkum, Ivo H. M. and van Grondelle, Rienk
and Groot, Marie Louise},
title = {Single and Multi-Exciton Dynamics in Aqueous Protochlorophyllide
Aggregates},
journal = {The Journal of Physical Chemistry A},
year = {2011},
volume = {{115}},
pages = {{3936-3946}},
number = {{16}},
month = {{Apr 28}},
doi = {10.1021/jp108317u},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp108317u},
url = {http://pubs.acs.org/doi/abs/10.1021/jp108317u}
}
@ARTICLE{Sytina2010,
author = {Sytina, O. A. and van Stokkum, I. H. M. and Heyes, D. J. and Hunter,
C. N. and van Grondelle, R. and Groot, M. L.},
title = {Protochlorophyllide Excited-State Dynamics in Organic Solvents Studied
by Time-Resolved Visible and Mid-Infrared Spectroscopy},
journal = {Journal of Physical Chemistry B},
year = {2010},
volume = {114},
pages = {4335-4344},
number = {12},
abstract = {Protochlorophyllide (PChlide) is a precursor in the biosynthesis of
chlorophyll. Complexed with NADPH to the enzyme protochlorophyllide
oxidoreductase (POR), it is reduced to chlorophyllide, a process
that Occurs via a set of spectroscopically distinct intermediate
states and is initiated from the excited state of PChlide. To obtain
a better understanding of these catalytic events, we characterized
the excited state dynamics of PChlide in the solvents tetrahydrofuran
(THF), methanol, and Tris/Triton buffer using ultrafast transient
absorption in the visible and mid-infrared spectral regions and time-resolved
fluorescence emission experiments. For comparison, we present time-resolved
transient absorption measurements of chlorophyll a in THE From the
combined analysis of these experiments, we derive that during the
2-3 ns excited state lifetime an extensive multiphasic quenching
of the emission occurs due to solvation of the excited state, which
is in agreement with the previously proposed internal charge transfer
(ICT) character of the S I state (Zhao, G. J.; Han, K. L. Biophys.
J. 2008, 94, 38). The solvation process in methanol occurs in conjunction
with a strengthening of a hydrogen bond to the Pchlide keto carbonyl
group. We demonstrate that the internal conversion from the S2 to
S1 excited states is remarkably slow and stretches out on to the
700 fs time scale, causing a rise of blue-shifted signals in the
transient absorption and a gain of emission in the time-resolved
fluorescence. A triplet state is populated oil the nanosecond time
scale with a maximal yield of similar to 23%. The consequences of
these observations for the catalytic pathway and the role of the
triplet and ICT state in activation of the enzyme are discussed.}
}
@ARTICLE{ISI:000291656900023,
author = {Toh, K. C. and Stojkovic, Emina A. and van Stokkum, Ivo H. M. and
Moffat, Keith and Kennis, John T. M.},
title = {{Fluorescence quantum yield and photochemistry of bacteriophytochrome
constructs}},
journal = {Physical Chemistry Chemical Physics},
year = {2011},
volume = {{13}},
pages = {{11985-11997}},
number = {{25}},
abstract = {{Bacteriophytochromes (Bphs) are red-light photoreceptor proteins
with a photosensory core that consists of three distinct domains,
PAS, GAF and PHY, and covalently binds biliverdin (BV) to a conserved
cysteine in the PAS domain. In a recent development, PAS-GAF variants
were engineered for use as a near-infrared fluorescent marker in
mammalian tissues (Tsien and co-workers, Science, 2009, 324, 804-807).
Here, we report the fluorescence quantum yield and photochemistry
of two highly-related Bphs from Rps. palustris, RpBphP2 (P2) and
RpBphP3 (P3) with distinct photoconversion and fluorescence properties.
We applied ultrafast spectroscopy to wild type P3 and P2 PAS-GAF
proteins and their P3 D216A, Y272F and P2 D202A PAS-GAF-PHY mutant
proteins. In these mutants hydrogen-bond interactions between a conserved
aspartate (Asp) which connects the BV chromophore with the PHY domains
are disrupted. The excited-state lifetime of the truncated P3 and
P2 PAS-GAF proteins was significantly longer than in their PAS-GAF-PHY
counterparts that constitute the full photosensory core. Mutation
of the conserved Asp to Ala in the PAS-GAF-PHY protein had a similar
but larger effect. The fluorescence quantum yields of the P3 D216A
and Y272F mutants were 0.066, higher than that of wild type P3 (0.043)
and similar to the engineered Bph of Tsien and co-workers. We conclude
that elimination of a key hydrogen-bond interaction between Asp and
a conserved Arg in the PHY domain is responsible for the excited-state
lifetime increase in all Bph variants studied here. H/D exchange
resulted in a 1.4-1.7 fold increase of excited-state lifetime. The
results support a reaction model in which deactivation of the BV
chromophore proceeds via excited-state proton transfer from the BV
pyrrole nitrogens to the backbone of the conserved Asp or to a bound
water. This work may aid in rational structure-and mechanism-based
conversion of constructs based on P3 and other BPhs into efficient
near-IR, deep tissue, fluorescent markers.}},
address = {{THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF,
CAMBS, ENGLAND}},
affiliation = {{Kennis, JTM (Reprint Author), Vrije Univ Amsterdam, Dept Phys \&
Astron, Biophys Sect, De Boelelaan 1081, NL-1081 HV Amsterdam, Netherlands.
Toh, KC; van Stokkum, IHM; Kennis, JTM, Vrije Univ Amsterdam, Dept
Phys \& Astron, Biophys Sect, NL-1081 HV Amsterdam, Netherlands.
Stojkovic, EA; Moffat, K, Univ Chicago, Dept Biochem \& Mol Biol,
Chicago, IL 60637 USA. Moffat, K, Univ Chicago, Inst Biophys Dynam,
Chicago, IL 60637 USA.}},
author-email = {{j.t.m.kennis@vu.nl}},
doc-delivery-number = {{777WX}},
doi = {{10.1039/c1cp00050k}},
funding-acknowledgement = {{Earth and Life Sciences Council of the Netherlands Foundation for
Scientific Research (NWO-ALW); NIH\{{[}\}GM036452]}},
funding-text = {{K.C.T. and J.T.M.K. were supported by the Earth and Life Sciences
Council of the Netherlands Foundation for Scientific Research (NWO-ALW)
through a VIDI grant to J.T.M.K. E.A.S and K.M. were supported by
NIH grant GM036452 to K.M.}},
issn = {{1463-9076}},
journal-iso = {{Phys. Chem. Chem. Phys.}},
keywords-plus = {{CYANOBACTERIAL PHYTOCHROME CPH1; CHROMOPHORE-BINDING DOMAIN; TIME-RESOLVED
SPECTROSCOPY; EXCITED-STATE DYNAMICS; ENERGY-TRANSFER; CRYSTAL-STRUCTURE;
RESONANCE RAMAN; GROUND-STATE; AGROBACTERIUM-TUMEFACIENS; MIDINFRARED
SPECTROSCOPY}},
language = {{English}},
number-of-cited-references = {{79}},
publisher = {{ROYAL SOC CHEMISTRY}},
subject-category = {{Chemistry; Physics}},
times-cited = {{0}},
type = {{Article}},
unique-id = {{ISI:000291656900023}}
}
@ARTICLE{doi:10.1021/jp106891x,
author = {Toh, K. C. and Stojkovi{\'{c}}, Emina A. and Rupenyan, Alisa B. and
van Stokkum, Ivo H. M. and Salumbides, Marian and Groot, Marie-Louise
and Moffat, Keith and Kennis, John T. M.},
title = {Primary Reactions of Bacteriophytochrome Observed with Ultrafast
Mid-Infrared Spectroscopy},
journal = {The Journal of Physical Chemistry A},
year = {2011},
volume = {{115}},
pages = {{3778-3786}},
number = {{16}},
month = {{Apr 28}},
doi = {10.1021/jp106891x},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp106891x},
url = {http://pubs.acs.org/doi/abs/10.1021/jp106891x}
}
@ARTICLE{Toh2010,
author = {Toh, K. C. and Stojkovi{\'{c}}, E. A. and van Stokkum, I. H. M. and
Moffat, K. and Kennis, J. T. M.},
title = {Proton-transfer and hydrogen-bond interactions determine fluorescence
quantum yield and photochemical efficiency of bacteriophytochrome},
journal = {Proceedings of the National Academy of Sciences of the United States
of America},
year = {2010},
volume = {107},
pages = {9170-9175},
number = {20},
abstract = {Phytochromes are red-light photoreceptor proteins that regulate a
variety of responses and cellular processes in plants, bacteria,
and fungi. Thephytochromelight activation mechanism involves isomerization
around the C15=C16 double bond of an open-chain tetrapyrrole chromophore,
resulting in a flip of its D-ring. In an important new development,
bacteriophytochrome (Bph) has been engineered for use as a fluorescent
marker in mammalian tissues. Here we report that an unusual Bph,
RpBphP3 from Rhodopseudomonas palustris, denoted P3, is fluorescent.
This Bph modulates synthesis of light-harvesting complex in combination
with a second Bph exhibiting classical photochemistry, RpBphP2, denoted
P2. We identify the factors that determine the fluorescence and isomerization
quantum yields through the application of ultrafast spectroscopy
to wild-type and mutants of P2 and P3. The excited-state lifetime
of the biliverdin chromophore in P3 was significantly longer at 330-500
ps than in P2 and other classical phytochromes and accompanied by
a significantly reduced isomerization quantum yield. H/D exchange
reduces the rate of decay from the excited state of biliverdin by
a factor of 1.4 and increases the isomerization quantum yield. Comparison
of the properties of the P2 and P3 variants shows that the quantum
yields of fluorescence and isomerization are determined by excited-state
deprotonation of biliverdin at the pyrrole rings, in competition
with hydrogen-bond rupture between the D-ring and the apoprotein.
This work provides a basis for structure-based conversion of Bph
into an efficient near-IR fluorescent marker.}
}
@ARTICLE{K.C.Toh07012008,
author = {Toh, K. C. and van Stokkum, Ivo H. M. and Hendriks, Johnny and Alexandre,
Maxime T. A. and Arents, J. C. and Perez, Marcela Avila and van Grondelle,
Rienk and Hellingwerf, Klaas J. and Kennis, John T. M.},
title = {{On the Signaling Mechanism and the Absence of Photoreversibility
in the AppA BLUF Domain}},
journal = {Biophys. J.},
year = {2008},
volume = {95},
pages = {312-321},
number = {1},
abstract = {The flavoprotein AppA from Rhodobacter sphaeroides contains an N-terminal,
FAD-binding BLUF photoreceptor domain. Upon illumination, the AppA
BLUF domain forms a signaling state that is characterized by red-shifted
absorbance by 10 nm, a state known as AppARED. We have applied ultrafast
spectroscopy on the photoaccumulated AppARED state to investigate
the photoreversible properties of the AppA BLUF domain. On light
absorption by AppARED, the FAD singlet excited state FADRED* decays
monoexponentially in 7 ps to form the neutral semiquinone radical
FADH*, which subsequently decays to the original AppARED molecular
ground state in 60 ps. Thus, FADRED* is deactivated rapidly via electron
and proton transfer, probably from the conserved tyrosine Tyr-21
to FAD, followed by radical-pair recombination. We conclude that,
in contrast to many other photoreceptors, the AppA BLUF domain is
not photoreversible and does not enter alternative reaction pathways
upon absorption of a second photon. To explain these properties,
we propose that a molecular configuration is formed upon excitation
of AppARED that corresponds to a forward reaction intermediate previously
identified for the dark-state BLUF photoreaction. Upon excitation
of AppARED, the BLUF domain therefore enters its forward reaction
coordinate, readily re-forming the AppARED ground state and suppressing
reverse or side reactions. The monoexponential decay of FAD* indicates
that the FAD-binding pocket in AppARED is significantly more rigid
than in dark-state AppA. Steady-state fluorescence experiments on
wild-type, W104F, and W64F mutant BLUF domains show tryptophan fluorescence
maxima that correspond with a buried conformation of Trp-104 in dark
and light states. We conclude that Trp-104 does not become exposed
to solvent during the BLUF photocycle. },
doi = {10.1529/biophysj.107.117788},
eprint = {http://www.biophysj.org/cgi/reprint/95/1/312.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/95/1/312}
}
@ARTICLE{Valkunas200917,
author = {Leonas Valkunas and Ivo H. M. van Stokkum and Rudi Berera and Rienk
van Grondelle},
title = {Exciton migration and fluorescence quenching in {{LHCII}} aggregates:
Target analysis using a simple nonlinear annihilation scheme},
journal = {Chemical Physics},
year = {2009},
volume = {357},
pages = {17 - 20},
number = {1-3},
doi = {DOI: 10.1016/j.chemphys.2008.07.025},
issn = {0301-0104},
keywords = {Non{-}photochemical quenching},
url = {http://www.sciencedirect.com/science/article/B6TFM-4T7XGVW-1/2/b8bf22a5db39eab19c2be203d614d719}
}
@ARTICLE{vananh2009,
author = {Van Anh, Nguyen and Schlosser, Felix and Groeneveld, Michiel M. and
van Stokkum, Ivo H. M. and W{\"u}rthner, Frank and Williams, Ren{\'{e}} M.},
title = {Photoinduced Interactions in a Pyrene-Calix[4]arene-Perylene Bisimide
Dye System: Probing Ground-State Conformations with Excited-State
Dynamics of Charge Separation and Recombination},
journal = {The Journal of Physical Chemistry C},
year = {2009},
volume = {113},
pages = {18358-18368},
number = {42},
doi = {doi: 10.1021/jp9055279}
}
@INPROCEEDINGS{bed96,
author = {Van Brederode, ME and Beekman, LMP and Kuciauskas, D and Jones, MR
and van Stokkum, I. H. M. and van Grondelle, R},
title = {Characteristics of the electron transfer reactions in the {M210W}
reaction centre only mutant of Rhodobacter sphaeroides},
booktitle = {The Reaction Center of Photosynthetic Bacteria: Structure and Dynamics},
year = {1996},
editor = {Michel-Beyerle, ME},
pages = {225-237},
publisher = {Springer-Verlag, Berlin}
}
@ARTICLE{VanBrederodeM.E._bi9703756,
author = {Van Brederode, M.E. and Jones, M.R. and Van Mourik, F. and Van Stokkum,
I. H. M. and Van Grondelle, R.},
title = {A New Pathway for Transmembrane Electron Transfer in Photosynthetic
Reaction Centers of Rhodobacter sphaeroides Not Involving the Excited
Special Pair},
journal = {Biochemistry},
year = {1997},
volume = {36},
pages = {6855-6861},
number = {23},
issn = {0006-2960},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9703756}
}
@ARTICLE{PetraA.W.VanDenBerg10012001,
author = {Van Den Berg, Petra A.W. and Mulrooney, Scott B. and Gobets, Bas
and Van Stokkum, Ivo H. M. and Van Hoek, Arie and Williams, Charles
H., JR. and Visser, Antonie J.W.G.},
title = {{Exploring the conformational equilibrium of E. coli thioredoxin
reductase: Characterization of two catalytically important states
by ultrafast flavin fluorescence spectroscopy}},
journal = {Protein Sci},
year = {2001},
volume = {10},
pages = {2037-2049},
number = {10},
doi = {10.1110/ps.06701},
file = {2037.pdf:http\://www.proteinscience.org/cgi/reprint/10/10/2037.pdf:PDF},
url = {http://www.proteinscience.org/cgi/content/abstract/10/10/2037}
}
@ARTICLE{gen95,
author = {Van Haeringen, B and de Lange, F. and van Stokkum, I. H. M. and Srai,
SKS and Evans, RW and van Grondelle, R. and Bloemendal, M},
title = {Dynamic structure of human serum transferrin from transient electric
birefringence},
journal = {Proteins, Structure, Function, and Genetics},
year = {1995},
volume = {23},
pages = {233-240}
}
@INCOLLECTION{ivo92a,
author = {Van Kan, P.J.M. and Groot, M.L. and Van Stokkum, I. H. M. and Kwa,
S.L.S. and Van Grondelle, R. and Dekker, J.P.},
title = {Chlorophyll triplet states in the {CP47} core antenna protein of
photosystem {II}},
booktitle = {Research in Photosynthesis},
publisher = {Kluwer Academic Publishers,Dordrecht},
year = {1992},
editor = {N. Murata},
volume = {1},
pages = {271-274}
}
@INPROCEEDINGS{beeka,
author = {Van Kan, P.J.M. and Van Stokkum, I. H. M. and Styring, S.},
title = {Time-resolved {EPR} spectroscopy of the triplet state of the primary
electron donor {P680} in {PS {II}}},
booktitle = {Photosynthesis: from Light to Biosphere},
year = {1995},
editor = {P. Mathis},
volume = {1},
pages = {543-546},
publisher = {Dordrecht, Kluwer}
}
@INCOLLECTION{ivo92b,
author = {Van Mourik, F. and Corten, E.P.M. and Van Stokkum, I. H. M. and Visschers,
R.W. and Loach, P.A. and Kraayenhof, R. and Van Grondelle, R.},
title = {Self assembly of the {LH-1} antenna of Rhodospirillum rubrum, a time-resolved
study of the aggregation of the {B820} subunit form},
booktitle = {Research in Photosynthesis},
publisher = {Kluwer Academic Publishers,Dordrecht},
year = {1992},
editor = {N. Murata},
volume = {1},
pages = {101-104}
}
@ARTICLE{VanMourik2004,
author = {Van Mourik, Frank and Groot, Marie-Louise and Van Grondelle, Rienk
and Dekker, Jan P. and Van Stokkum, Ivo H. M.},
title = {{Global and target analysis of fluorescence measurements on photosystem
2 reaction centers upon red excitation }},
journal = {Physical Chemistry Chemical Physics},
year = {2004},
volume = {6},
pages = {4820 - 4824}
}
@ARTICLE{ivo86,
author = {Van Stokkum, I. H. M. and Johannesma, P.I.M. and Eggermont, J.J.},
title = {Representation of time-dependent correlation and recurrence-time
functions: A new method to analyse non-stationary point-processes},
journal = {Biological Cybernetics},
year = {1986},
volume = {55},
pages = {17-24}
}
@ARTICLE{MikasVengris09012004,
author = {Vengris, Mikas and van der Horst, Michael A. and Zgrablic, Goran
and van Stokkum, Ivo H. M. and Haacke, Stefan and Chergui, Majed
and Hellingwerf, Klaas J. and van Grondelle, Rienk and Larsen, Delmar
S.},
title = {{Contrasting the Excited-State Dynamics of the Photoactive Yellow
Protein Chromophore: Protein versus Solvent Environments}},
journal = {Biophysical Journal},
year = {2004},
volume = {87},
pages = {1848-1857},
number = {3},
doi = {10.1529/biophysj.104.043224},
file = {1848.pdf:http\://www.biophysj.org/cgi/reprint/87/3/1848.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/87/3/1848}
}
@INCOLLECTION{bookpulse,
author = {Mikas Vengris and Ivo van Stokkum and Xiang He and Alasdair Bell
and Peter Tonge and Rienk van Grondelle and Delmar Larsen},
title = {Ultrafast excited and ground-state isomerization dynamics of the
Green Fluorescent Protein chromophore in solution},
booktitle = {Ultrafast Phenomena XIV},
year = {2005},
pages = {610-612},
url = {http://www.springerlink.com/content/m6u40244600kuj81}
}
@ARTICLE{VengrisM._jp037902h,
author = {Vengris, M. and van Stokkum, I. H. M. and He, X. and Bell, A.F. and
Tonge, P.J. and van Grondelle, R. and Larsen, D.S.},
title = {Ultrafast Excited and Ground-State Dynamics of the Green Fluorescent
Protein Chromophore in Solution},
journal = {Journal of Physical Chemistry A},
year = {2004},
volume = {108},
pages = {4587-4598},
number = {21},
issn = {1089-5639},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp037902h}
}
@ARTICLE{HMVisser09011995,
author = {Visser, HM and Somsen, OJG and van Mourik, F and Lin, S and van Stokkum,
I. H. M. and van Grondelle, R},
title = {{Direct observation of sub-picosecond equilibration of excitation
energy in the light-harvesting antenna of Rhodospirillum rubrum}},
journal = {Biophys. J.},
year = {1995},
volume = {69},
pages = {1083-1099},
number = {3},
file = {1083.pdf:http\://www.biophysj.org/cgi/reprint/69/3/1083.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/69/3/1083}
}
@ARTICLE{VisserH.Matthieu_j100041a055,
author = {Visser, H. Matthieu and Groot, Marie-Louise and van Mourik, Frank
and van Stokkum, Ivo H. M. and Dekker, Jan P. and van Grondelle,
Rienk},
title = {Subpicosecond Transient Absorption Difference Spectroscopy on the
Reaction Center of Photosystem {II}: Radical Pair Formation at 77
{K}},
journal = {Journal of Physical Chemistry},
year = {1995},
volume = {99},
pages = {15304-15309},
number = {41},
issn = {0022-3654},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/j100041a055}
}
@ARTICLE{Visser1996,
author = {Visser, H. M. and Kleima, F. J. and van Stokkum, I. H. M. and van
Grondelle, R. and van Amerongen, H.},
title = {Probing the many energy-transfer processes in the photosynthetic
light-harvesting complex {II} at 77 {K} using energy-selective sub-picosecond
transient absorption spectroscopy},
journal = {Chemical Physics},
year = {1996},
volume = {210},
pages = {297--312},
month = {Oct},
day = {01},
issue = {1-2},
url = {http://www.sciencedirect.com/science/article/B6TFM-3VB3S3T-S/2/ed5bbd5a910c358d091db41dfb33e456}
}
@ARTICLE{ieee1,
author = {Vos, F.M. and van der Heijde, G.L. and Spoelder, H.J.W. and van Stokkum,
I. H. M. and Groen, F.C.A.},
title = {A new instrument to measure the shape of the cornea based on pseudorandom
color coding},
journal = {IEEE Transactions on Instrumentation and Measurement},
year = {1997},
volume = {46},
pages = {794 - 797},
number = {4}
}
@INPROCEEDINGS{ieee2,
author = {Vos, F.M. and van der Heijde, G.L. and Spoelder, H.J.W. and van Stokkum,
I. H. M. and Groen, F.C.A.},
title = {A new PRBA-based instrument to measure the shape of the cornea},
booktitle = {Quality Measurements: The Indispensable Bridge between Theory and
Reality},
year = {1996},
volume = {1},
pages = {416 - 421},
organization = {IEEE Instrumentation and Measurement Technology Conference}
}
@ARTICLE{vanWalree2002,
author = {van Walree, Cornelis A. and Kaats-Richters, Veronica E. M. and Jenneskens,
Leonardus W. and Williams, Ren{\'{e}} M. and van Stokkum, Ivo H.
M.},
title = {Intramolecular excimer and exciplex emission of 1,4-dipyrenyl substituted
cyclohexasilane},
journal = {Chemical Physics Letters},
year = {2002},
volume = {355},
pages = {65--70},
month = {Mar},
day = {25},
issue = {1-2},
url = {http://www.sciencedirect.com/science/article/B6TFN-457D1TP-5/2/91d224654917d6b1195f8afbfcca05a8}
}
@ARTICLE{FrankL.deWeerd03012002,
author = {de Weerd, Frank L. and van Stokkum, Ivo H. M. and van Amerongen,
Herbert and Dekker, Jan P. and van Grondelle, Rienk},
title = {{Pathways for Energy Transfer in the Core Light-Harvesting Complexes
CP43 and CP47 of Photosystem {II}}},
journal = {Biophysical Journal},
year = {2002},
volume = {82},
pages = {1586-1597},
number = {3},
file = {1586.pdf:http\://www.biophysj.org/cgi/reprint/82/3/1586.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/82/3/1586}
}
@ARTICLE{deWeerd2002,
author = {de Weerd, Frank L. and van Stokkum, Ivo H. M. and van Grondelle,
Rienk},
title = {Subpicosecond dynamics in the excited state absorption of all-trans-{$\beta$}-Carotene},
journal = {Chemical Physics Letters},
year = {2002},
volume = {354},
pages = {38--43},
month = {Mar},
day = {05},
issue = {1-2},
url = {http://www.sciencedirect.com/science/article/B6TFN-45B55WW-1/2/eb0879bc26e075d0db2c1d3149c851b1}
}
@ARTICLE{ChantalDvanderWeijDeWit03152008,
author = {van der Weij-De Wit, Chantal D. and Doust, Alexander B. and van Stokkum,
Ivo H. M. and Dekker, Jan P. and Wilk, Krystyna E. and Curmi, Paul
M. G. and van Grondelle, Rienk},
title = {{Phycocyanin Sensitizes both Photosystem I and Photosystem {II} in
Cryptophyte Chroomonas {CCMP270} Cells}},
journal = {Biophys. J.},
year = {2008},
volume = {94},
pages = {2423-2433},
number = {6},
abstract = {This article presents an investigation of the energy migration dynamics
in intact cells of the unicellular photosynthetic cryptophyte Chroomonas
CCMP270 by steady-state and time-resolved fluorescence measurements.
By kinetic modeling of the fluorescence data on chlorophyll and phycocyanin
645 excitation (at 400 and 582 nm respectively), it has been possible
to show the excited state energy distribution in the photosynthetic
antenna of this alga. Excitation energy from phycocyanin 645 is distributed
nearly equally between photosystem I and photosystem {II} with very
high efficiency on a 100-ps timescale. The excitation energy trapping
times for both photosystem I ([~]30 ps) and photosystem I (200 and
[~]540 ps) correspond well to those obtained from experiments on
isolated photosystems. The results are compared with previous results
for another cryptophyte species, Rhodomonas CS24, and suggest a similar
membrane organization for the cryptophytes with the phycobiliproteins
tightly packed in the thylakoid lumen around the periphery of the
photosystems. },
doi = {10.1529/biophysj.107.113993},
eprint = {http://www.biophysj.org/cgi/reprint/94/6/2423.pdf},
url = {http://www.biophysj.org/cgi/content/abstract/94/6/2423}
}
@ARTICLE{vanderWeij-DeWitC.D._jp061546w,
author = {van der Weij{-}DeWit, C.D. and Doust, A.B. and van Stokkum, I. H. M.
and Dekker, J.P. and Wilk, K.E. and Curmi, P.M.G. and Scholes, G.D.
and van Grondelle, R.},
title = {How Energy Funnels from the Phycoerythrin Antenna Complex to Photosystem
{I} and Photosystem {II} in Cryptophyte Rhodomonas {CS24} Cells},
journal = {Journal of Physical Chemistry B},
year = {2006},
volume = {110},
pages = {25066-25073},
number = {49},
issn = {1520-6106},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp061546w}
}
@INPROCEEDINGS{i98q,
author = {Wendling, M and van Mourik, F and van Stokkum, I. H. M. and Salverda,
JM and Michel, H and van Grondelle, R},
title = {Low-intensity pump-probe measurements on the {B800} band of Rhodospirillim
molischianum},
booktitle = {Photosynthesis: Mechanisms and Effects},
year = {1998},
editor = {Garab, G},
pages = {49-52},
publisher = {Kluwer Academic Publishers, Dordrecht}
}
@ARTICLE{MarkusWendling01012003,
author = {Wendling, Markus and Mourik, Frank van and van Stokkum, Ivo H. M.
and Salverda, Jante M. and Michel, Hartmut and Grondelle, Rienk van},
title = {{Low-Intensity Pump-Probe Measurements on the {B800} Band of Rhodospirillum
molischianum}},
journal = {Biophysical Journal},
year = {2003},
volume = {84},
pages = {440-449},
number = {1},
file = {440.pdf:http\://www.biophysj.org/cgi/reprint/84/1/440.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/84/1/440}
}
@ARTICLE{Wientjes20111372,
author = {Emilie Wientjes and Ivo H.M. van Stokkum and Herbert van Amerongen
and Roberta Croce},
title = {Excitation-Energy Transfer Dynamics of Higher Plant Photosystem {I}
Light-Harvesting Complexes},
journal = {Biophysical Journal},
year = {2011},
volume = {100},
pages = {1372 - 1380},
number = {5},
doi = {DOI: 10.1016/j.bpj.2011.01.030},
issn = {0006-3495},
url = {http://www.sciencedirect.com/science/article/B94RW-528YMC8-2/2/95612d92a10fbf4c3fa51698310b4052}
}
@ARTICLE{L.J.G.W.vanWilderen10102006,
author = {van Wilderen, L. J. G. W. and van der Horst, M. A. and van Stokkum,
I. H. M. and Hellingwerf, K. J. and van Grondelle, R. and Groot,
M. L.},
title = {{Ultrafast infrared spectroscopy reveals a key step for successful
entry into the photocycle for photoactive yellow protein}},
journal = {PNAS},
year = {2006},
volume = {103},
pages = {15050-15055},
number = {41},
doi = {10.1073/pnas.0603476103},
file = {15050.pdf:http\://www.pnas.org/cgi/reprint/103/41/15050.pdf:PDF},
url = {http://www.pnas.org/cgi/content/abstract/103/41/15050}
}
@ARTICLE{vanWilderenJPCB2009,
author = {van Wilderen, Luuk J. G. W. and Key, Jason M. and van Stokkum, Ivo
H. M. and van Grondelle, Rienk and Groot, Marie{-}Louise},
title = {{Dynamics of Carbon Monoxide Photodissociation in {B}radyrhizobium
japonicum {FixL} Probed by Picosecond Midinfrared Spectroscopy}},
journal = {{Journal of Physical Chemistry B}},
year = {2009},
volume = {{113}},
pages = {{3292-3297}},
number = {{11}}
}
@ARTICLE{WurpelG.W.H._ja015919c,
author = {Wurpel, G.W.H. and Brouwer, A.M. and van Stokkum, I. H. M. and Farran,
A. and Leigh, D.A.},
title = {Enhanced Hydrogen Bonding Induced by Optical Excitation: Unexpected
Subnanosecond Photoinduced Dynamics in a Peptide-Based [2]Rotaxane},
journal = {Journal of the American Chemical Society},
year = {2001},
volume = {123},
pages = {11327-11328},
number = {45},
issn = {0002-7863},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja015919c}
}
@ARTICLE{YatskouM.M._jp010411h,
author = {Yatskou, M.M. and Koehorst, R.B.M. and van Hoek, A. and Donker, H.
and Schaafsma, T.J. and Gobets, B. and van Stokkum, I. and van Grondelle,
R.},
title = {Spectroscopic Properties of a Self-Assembled Zinc Porphyrin Tetramer
{II.} Time-Resolved Fluorescence Spectroscopy},
journal = {Journal of Physical Chemistry A},
year = {2001},
volume = {105},
pages = {11432-11440},
number = {51},
issn = {1089-5639},
url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp010411h}
}
@ARTICLE{SergeyYeremenko06012006,
author = {Yeremenko, Sergey and van Stokkum, Ivo H. M. and Moffat, Keith and
Hellingwerf, Klaas J.},
title = {{Influence of the Crystalline State on Photoinduced Dynamics of Photoactive
Yellow Protein Studied by Ultraviolet-Visible Transient Absorption
Spectroscopy}},
journal = {Biophysical Journal},
year = {2006},
volume = {90},
pages = {4224-4235},
number = {11},
doi = {10.1529/biophysj.105.074765},
file = {4224.pdf:http\://www.biophysj.org/cgi/reprint/90/11/4224.pdf:PDF},
url = {http://www.biophysj.org/cgi/content/abstract/90/11/4224}
}
@ARTICLE{Zoon2010,
author = {Peter D. Zoon and Ivo H. M. van Stokkum and Manuel Parent and Olivier
Mongin and Mireille Blanchard-Desce and Albert M. Brouwer},
title = {Fast photo-processes in triazole-based push-pull systems},
journal = {Physical Chemistry Chemical Physics},
year = {2010},
volume = {12},
pages = {2706-2715},
number = {11},
doi = {DOI: 10.1039/b921322h}
}
@article{ ISI:000289697500032,
Author = {van der Weij-de Wit, C. D. and Dekker, J. P. and van Grondelle, R. and
van Stokkum, I. H. M.},
Title = {{Charge Separation is Virtually Irreversible in {Photosystem II} Core
Complexes with Oxidized Primary Quinone Acceptor}},
Journal = {{Journal of Physical Chemistry A}},
Year = {2011},
Volume = {{115}},
Number = {{16}},
Pages = {{3947-3956}},
Month = {{APR 28}},
Abstract = {{X-ray structures of the {Photosystem II} (PSII) core revealed relatively
large interpigment distances between the CP43 and CP47 antenna compleyes
and the reaction center (RC) with respect to the interpigment distances
in a single unit. This finding questions the possibility of fast energy
equilibration among the antenna and the RC, which has been the basic
explanation for the measured PSII fluorescence kinetics for more than
two decades. In this study, we present time-resolved fluorescence
measurements obtained with a streak-camera setup on PSH core complexes
from Thermosynechococcus elongatus at room temperature (RT) and at 77 K.
Kinetic modeling of the RT data obtained with oxidized quinone acceptor
Q(A) reveals that the kinetics are best described by fast primary charge
separation at a time scale of 1.5 ps and slow energy transfer from the
antenna into the RC, which results in an energy equilibration time
between the antenna and the RC of about 44 ps. This model is consistent
with structure-based computations. Primary radical pair formation was
found to be a virtually irreversible process. Energy equilibration
within the CP43 and CP47 complexes is shown to occur at a time scale of
8 ps. Kinetic modeling of the 77K data reveals similar energy transfer
time scales in the antenna units and among the antenna and the RC as at
RT, respectively, 7 and 37 ps. We conclude that the energy transfer from
the CP43/CP47 antenna to; the RC is the dominant factor in the total
charge separation kinetics in intact PSII cores.}},
Publisher = {{AMER CHEMICAL SOC}},
Address = {{1155 16TH ST, NW, WASHINGTON, DC 20036 USA}},
Type = {{Article}},
Language = {{English}},
Affiliation = {{van Grondelle, R (Reprint Author), Vrije Univ Amsterdam, Fac Sci, Dept Phys \& Astron, De Boelelaan 1081, NL-1081 HV Amsterdam, Netherlands.
van der Weij-de Wit, CD; Dekker, JP; van Grondelle, R; van Stokkum, IHM, Vrije Univ Amsterdam, Fac Sci, Dept Phys \& Astron, NL-1081 HV Amsterdam, Netherlands.}},
DOI = {{10.1021/jp1083746}},
ISSN = {{1089-5639}},
Keywords-Plus = {{EXCITATION-ENERGY TRANSFER; REACTION CENTERS; ELECTRON-TRANSFER;
CRYSTAL-STRUCTURE; FLUORESCENCE SPECTROSCOPY; PICOSECOND FLUORESCENCE;
LOW-TEMPERATURE; TARGET ANALYSIS; KINETICS; CP47}},
Funding-Acknowledgement = {{Netherlands Organization of Scientific Research (NWO) via the foundation
of Earth and Life Sciences (ALW); Foundation for Fundamental Research on
Matter (FOM)}},
Funding-Text = {{We thank Eberhard Schlodder (Technische Universitat Berlin) for kindly
providing the samples and for useful discussions. Marloes Groot is
thanked for critical reading of the text. This research is supported by
The Netherlands Organization of Scientific Research (NWO) via the
foundation of Earth and Life Sciences (ALW) and the Foundation for
Fundamental Research on Matter (FOM).}},
Number-of-Cited-References = {{48}},
Times-Cited = {{0}},
Journal-ISO = {{J. Phys. Chem. A}},
Doc-Delivery-Number = {{752NB}},
Unique-ID = {{ISI:000289697500032}},
}
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