College Van Quark tot Biomaterie / Biofysica

Marloes Groot
Faculteit Exacte Wetenschappen,
kamer S124
De Boelelaan 1081
1081 HV Amsterdam
tel nr +31 20 5982570
fax nr +31 20 5987999


Selected publications:


 O.A. Sytina, D. J. Heyes, C.N. Hunter, M. T. Alexandre, I. H.M. van Stokkum, R. van Grondelle and M. L. Groot
Conformational changes in an ultrafast light-driven enzyme determine catalytic activity     Nature 456, 1001-1008, 2008

J. T. M. Kennis and M. L. Groot, Curr Opin Struct Biol 2007 17, 623
’Ultrafast spectroscopy of biological photoreceptors’

M. L. Groot, L.J.G.W. van Wilderen, M. Di Donato, Photochem. Photobiol. Sci., 2007, 6, 501 – 507
’Femtosecond time-resolved and dispersed infrared spectroscopy on proteins’

L.J.G.W. van Wilderen, M.A. van der Horst, I.H.M. Van Stokkum, K.J. Hellingwerf, R. van Grondelle, M.L. Groot, Proc. Natl. Acad. Sci. USA , 2006, 103, 41, 15050-15055
Ultrafast infrared spectroscopy reveals key step for successful entry into photocycle for Photoactive Yellow Protein’

M. L. Groot, N. P. Pawlowicz, L. van Wilderen, J. Breton, I. H. M. van Stokkum and R. van Grondelle, Proc. Natl. Acad. Sci. USA, 2005 102, 37, 13087-13092
'Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy'

D. J. Heyes, C. N. Hunter, I.H.M. van Stokkum, R. van Grondelle and M.L. Groot, 2003 Nature Structural Biology 10,491-492
‘Ultrafast enzymatic reaction dynamics in protochlorophyllide oxidoreductase’

All publications















Research statement:


I am interested in elementary reactions in proteins and enzymes. Using several spectroscopic techniques, mainly visible pump-midinfrared probe spectroscopy and vis/vis spectroscpy we study several protein complexes such as:

  • PS1, PS2: The structure-dynamics-function relationship in photosynthetic complexes, in collaboration with dr J. Breton (Saclay, FR) and Prof. B. Diner (DuPont, USA).

  • PYP: Photoactive Yellow Protein (in collaboration with prof. K Hellingwerf, UVA) is a bacterial blue-light sensor. Light absorption by PYP’s intrinsic chromophore, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. We have been able to show that the low quantum yield of isomerization in PYP (0.3) is most likely determined by the hydrogen bond strength of the chromophore with one of the protein residues.

  • GFP: The color of the fluorescent light emitted by Green Fluorescent Protein (GFP) depends on a light-induced proton transfer reaction occurring in a ‘proton-wire’ that is formed by the chromophore, a water molecule (W22), Ser205 and Glu222. We have been able to show that the chain of proton transfer reactions starts at the acceptor end of the wire.

  • PR: We have started spectroscopic research on proteorhodopsin with the aim to resolve what controls their multi-functionality, see publication 2.

  • POR: Proton and hydride transfer in the chlorophyll biosynthetic enzyme NADPH:protochlorophyllide oxidoreductase. We have reported the first ultrafast visible pump-probe data on this important enzyme.  We have found that the catalytic mechanism, involving formation of a transition state and proton and hydride transfer, proceeds with time constants of 3ps and 400ps. This project is a collaboration with prof. Hunter ( University of Sheffield , UK ) and dr D. Heyes ( University of Manchester , UK )


Femtosecond mid-infrared spectroscopy
At LCVU we have
developed an experimental setup for the study of protein dynamics via visible pump/midinfrared probe spectroscopy. This setup has sufficient sensitivity to follow reaction induced structural changes with atomic resolution, on a time scale from 100 femtoseconds (10-13s) up to 10 nanoseconds (10.10-9s). Our setup is unique because, in combination with a home-developed Lissajous sample scanner, we are able to acquire datasets under single pulse conditions, and we can monitor the absorption changes in the visible part of the spectrum at the same time. We are therefore uniquely positioned to study protein and chromophore dynamics via their changes in the vibrational absorption, both for cyclic and for non-cyclic (photoconversion) reactions. The vibrational spectrum of a protein or a protein-bound chromophore contains a wealth of information about its structure, the interaction with the environment and the electronic properties of the molecule. Therefore time-resolved IR spectroscopy is a powerful tool that can reveal many dynamic structural details of chromophores. In addition, it can reveal the response of those parts of the protein that are affected by the reactions that are taking place.

Deep tissue imaging
Recently we have started a new research line in the field of Biomedical Photonics. Using nonlinear or coherent microscopic techniques, we want to develop new tools for studies on the level of cells and tissue in the field of biomedical research. To this end we collaborate with neurobiologists prof. H. Mansvelder, and dr R. Toonen of the CNCR (VU-FALW), dr E Peterman of VU-FEW/LCVU and prof. G. van Dongen and R. Brakenhoff of the VUMC