title: Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase.
abstract: 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.
authors.affiliation: LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Topin
authors.forename: Marc
authors.initials: M
authors.lastname: Rousset
authors.forename: Serge
authors.initials: S
authors.lastname: Antonczak
authors.forename: Jérôme
authors.initials: J
authors.lastname: Golebiowski
mesh_terms: D020134:Catalytic Domain; D003901:Desulfovibrio / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D004058:Diffusion; D006859:Hydrogen / Q000737:chemistry / Q000378:metabolism*; D006864:Hydrogenase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D007700:Kinetics; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism*; D017354:Point Mutation; D013816:Thermodynamics
chemical_list: D006859:Hydrogen; C043296:nickel-iron hydrogenase; D006864:Hydrogenase; D010100:Oxygen