Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase
Jérémie Topin
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
Search for more papers by this authorMarc Rousset
CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditérannée, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
Search for more papers by this authorSerge Antonczak
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
Search for more papers by this authorCorresponding Author
Jérôme Golebiowski
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France===Search for more papers by this authorJérémie Topin
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
Search for more papers by this authorMarc Rousset
CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditérannée, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
Search for more papers by this authorSerge Antonczak
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
Search for more papers by this authorCorresponding Author
Jérôme Golebiowski
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France
LCMBA-UMR CNRS 6001, Institut de Chimie de Nice, Université de Nice-Sophia Antipolis, Faculté des Sciences, 06108 Nice Cedex 2, France===Search for more papers by this authorAbstract
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. © 2012 Wiley Periodicals, Inc.
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