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Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase
Author(s) -
Topin Jérémie,
Rousset Marc,
Antonczak Serge,
Golebiowski Jérôme
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.23248
Subject(s) - diffusion , hydrogenase , kinetic energy , thermodynamics , kinetics , chemistry , diffusion process , umbrella sampling , energetics , activation energy , chemical physics , molecular dynamics , materials science , physics , computational chemistry , enzyme , biochemistry , computer science , quantum mechanics , knowledge management , innovation diffusion
We have investigated O 2 and H 2 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 O 2 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. © 2012 Wiley Periodicals, Inc.