Structural dynamics in proteins

Our aim is to advance our understanding of the photochemistry and photophysics of light-activated enzymes as a window into the fundamental question of how protein dynamics impact on enzyme catalytic function. 

Enzymes accelerate chemical reactions with rate enhancements of up to 1017 compared to the equivalent reaction in solution, by providing specialised environments in which the reactivity of substrates is different from that in solution. Enzymes are uniquely suited to the function they perform and any change in primary structure made by mutagenesis typically leads to a sub-optimal performance.

Structural dynamics in proteins

We use the protein Photoactive Yellow Protein to advance our understanding of the molecular interactions within proteins that control functionality, by applying fulltime scale multi-pulse spectroscopy both in the visible and midinfrared spectral regions. Photoactive Yellow Protein is an excellent model system for studying how proteins transform light energy into a biological signal. The chemistry involved in PYP is a trans/cis isomerisation of its cofactor, a p-coumaric acid (pCa). Our research involves the study of the isomerization process in PYP and of the role of the amino acids that line the chromophore-binding pocket in this reaction with atomic detail. For recent publications, see

Converting Light into a Metastable Structural Change. M. L. Groot and K. J. Hellingwerf in Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies" Editors: S. Haacke (Strasbourg University), I. Burghardt (Frankfurt University) Publishers: Pan Stanford Publishing (http://www.panstanford.com/)

Short Hydrogen Bonds and Negative Charge in Photoactive Yellow Protein Promote Fast Isomerization but not High Quantum Yield. J.Y. Zhu, J. Vreede, M. Hospes, J. Arents, J.T.M. Kennis, I.H.M. van Stokkum, K.J. Hellingwerf, and M.L. Groot, Journal of Physical Chemistry B, 2015. 119(6): p. 2372-2383

A.D. Stahl, M. Hospes, K. Singhal, I. van Stokkum, R. van Grondelle, M.L. Groot, and K.J. Hellingwerf, On the Involvement of Single-Bond Rotation in the Primary Photochemistry of Photoactive Yellow Protein.Biophysical Journal, 2011. 101(5): p. 1184-1192.

A.B. Rupenyan, J. Vreede, I.H.M. van Stokkum, M. Hospes, J.T.M. Kennis, K.J. Hellingwerf, and M.L. Groot, Proline 68 Enhances Photoisomerization Yield in Photoactive Yellow Protein.Journal of Physical Chemistry B, 2011. 115(20): p. 6668-6677.

L.J.G.W. van Wilderen, M.A. Van der Horst, I.H.M. van Stokkum, K.J. Hellingwerf, R. van Grondelle, and M.L. Groot, Ultrafast infrared spectroscopy reveals a key step for successful entry into the photocycle for photoactive yellow protein.Proceedings of the National Academy of Sciences of the United States of America, 2006. 103(41): p. 15050-15055.

A key complex in natural photosynthesis is the reaction center of the purple bacterium Rhodobacter sphaeroides (BRC). This light-powered enzyme is a cytochrome c:ubiquinone oxidoreductase that converts sunlight into chemical energy through a series of sequential electron transfer processes that occur over time scales from less than 1 picosecond up to milliseconds. Roles for light-induced, reaction-induced and diffusional conformational protein dynamics in this process have been suggested. We aim to determine the precise role of protein dynamics in the electron transfer process by mapping out the protein response on the full relevant time scale for both catalytic electron transfer events, and determine the coupling of such protein motions to light absorption, electron transfer and the lipid bilayer membrane, using multi-pulse vibrational spectroscopy.

 Afbeelding structural dynamics in proteins 2

Structure of the Rhodobacter sphaeroides photosynthetic reaction center, reproduced from http://www.photobiology.info/Jones.html. On the left the ribbons indicate the proteins α-helical structures. On the right the protein scaffold has been omitted from the figure to better visualize the electron transfer cofactors. Black