title: Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase.
abstract: Possible proton transport pathways in Clostridium pasteurianum (CpI) [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to evaluate the functional pathway and provide insight into the hydrogen bonding features defining an active proton transport pathway. Three pathways were evaluated, two of which consist of water wires and one of predominantly amino acid residues. Our simulations suggest that protons are not transported through water wires. Instead, the five-residue motif (Glu282, Ser319, Glu279, H2O, Cys299) was found to be the likely pathway, consistent with previously made experimental observations. The pathway was found to have a persistent hydrogen bonded core (residues Cys299 to Ser319), with less persistent hydrogen bonds at the ends of the pathway for both H2 release and H2 uptake. Single site mutations of the four residues have been shown experimentally to deactivate the enzyme. The theoretical evaluation of these mutations demonstrates redistribution of the hydrogen bonds in the pathway, resulting in enzyme deactivation. Finally, coupling between the protein dynamics near the proton transport pathway and the redox partner binding regions was also found as a function of H2 uptake and H2 release states, which may be indicative of a correlation between proton and electron movement within the enzyme.
authors: Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors: Bojana
authors: B
authors: Ginovska-Pangovska
authors: Ming-Hsun
authors: MH
authors: Ho
authors: John C
authors: JC
authors: Linehan
authors: Yuhui
authors: Y
authors: Cheng
authors: Michel
authors: M
authors: Dupuis
authors: Simone
authors: S
authors: Raugei
authors: Wendy J
authors: WJ
authors: Shaw
mesh_terms: D020816:Amino Acid Motifs; D003013:Clostridium / Q000201:enzymology / Q000378:metabolism; D006859:Hydrogen / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010084:Oxidation-Reduction; D017434:Protein Structure, Tertiary; D011522:Protons; D014867:Water / Q000737:chemistry*
chemical_list: D011522:Protons; D014867:Water; D006859:Hydrogen; D006864:Hydrogenase
keywords: (CpI); (DdH); (ESP); Clostridium pasteurianum; Desulfovibrio desulfuricans; Electrostatic potential; Hydrogen bonding; Molecular dynamics; Mutations; Proton transport; [FeFe]-hydrogenase