Multiscale Simulations Give Insight into the Hydrogen In and Out Pathways of [NiFe]-Hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans

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• 作者：Francesco Oteri ; Marc Baaden ; Elisabeth Lojou ; Sophie Sacquin-Mora
• 刊名：Journal of Physical Chemistry B
• 出版年：2014
• 出版时间：December 4, 2014
• 年：2014
• 卷：118
• 期：48
• 页码：13800-13811
• 全文大小：544K
• ISSN：1520-5207

文摘

[NiFe]-hydrogenases catalyze the cleavage of molecular hydrogen into protons and electrons and represent promising tools for H₂-based technologies such as biofuel cells. However, many aspects of these enzymes remain to be understood, in particular how the catalytic center can be protected from irreversible inactivation by O₂. In this work, we combined homology modeling, all-atom molecular dynamics, and coarse-grain Brownian dynamics simulations to investigate and compare the dynamic and mechanical properties of two [NiFe]-hydrogenases: the soluble O₂-sensitive enzyme from Desulfovibrio fructosovorans, and the O₂-tolerant membrane-bound hydrogenase from Aquifex aeolicus. We investigated the diffusion pathways of H₂ from the enzyme surface to the central [NiFe] active site, and the possible proton pathways that are used to evacuate hydrogen after the oxidation reaction. Our results highlight common features of the two enzymes, such as a Val/Leu/Arg triad of key residues that controls ligand migration and substrate access in the vicinity of the active site, or the key role played by a Glu residue for proton transfer after hydrogen oxidation. We show specificities of each hydrogenase regarding the enzymes internal tunnel network or the proton transport pathways.