Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 80, Issue 3, Pages 677-682Publisher
WILEY
DOI: 10.1002/prot.23248
Keywords
hydrogenase; simulation; free energy; diffusion; kinetics; TLES; umbrella sampling
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Funding
- ANR PNRB Hyliox
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We have investigated O2 and H2 transport across a NiFe hydrogenase at the atomic scale by means of computational methods. The Wild Type protein has been compared with the V74Q mutant. Two distinct methodologies have been applied to study the gas access to the active site. Temperature locally enhanced sampling simulations have emphasized the importance of protein dynamics on gas diffusion. The O2 diffusion free energy profiles, obtained by umbrella sampling, are in agreement with the known kinetic data and show that in the V74Q mutant, the inhibition process is lowered from both a kinetic and a thermodynamic point of view. Proteins 2011. (c) 2012 Wiley Periodicals, Inc.
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