Genes or environment: How the protein surroundings affects their function (Genen)

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Funder's project number: 332742

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Project timetable

Project start date: 01/09/2020

Project end date: 31/08/2024

Summary

Life on earth would be impossible without the catalytic action of enzymes. A good enzyme ishighly selective and efficient. To improve an enzyme or to design a new one, requires a detailedunderstanding of the underlying reaction mechanism. As the time and spatial resolution requiredto gain the essential atomistic insights into enzymatic activity are notoriously difficult to achieveexperimentally, most of our current knowledge is based on inference from tedious experimentation[1],which isindirect, or from computer simulations[2], which are direct, but rely on approximations thatare difficult to validate.Recently, Serial Femtosecond time-resolved X-ray crystallography (SFX) at free electron lasers [3]and synchrotrons [4] have opened up a new experimental window into the regime of chemical dynamics.However, although the relevant time and length scales are now accessible simultaneously, the enzymedynamics can only be probed inside crystals. Because crystal packing could restrict the conformationalflexibility of the enzyme, the structural changes associated with catalysis might be different fromsolution. Indeed, by comparing x-ray scattering from phytochrome photoreceptor proteins in solutionon the one hand, and x-ray diffraction from these proteins in crystals on the other hand, we showedthat the photo-inducedstructural changes are not the same in solution as in the crystal[5]. Sinceenzymes are evolved to work in solution rather than in crystals, it is fair to askif the mechanismsobserved in crystals are similar, or even relevant for the enzymatic action in solution?With the enormous investments into and expectations of SFX, it is of utmost importance toanswer this question now andunderstand what are the effects of the crystal environment onthe enzymatic reactivity. We propose to address this crucial question bycombining state-of-the-art experiments with advanced computer simulations. Differences between reaction rates andspectroscopic signatures of intermediates in crystal and solution will be rationalized with MolecularDynamics (MD) simulations, and verified with laser spectroscopic techniques. With these atomisticinsights we will develop amodel for extrapolating reaction mechanisms from crystals to solution.

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