title: Proton pathways in a [NiFe]-hydrogenase: A theoretical study.
abstract: We present here a theoretical study to investigate possible proton pathways in the [NiFe]-hydrogenase from Desulfovibrio gigas. The approach used in this study consists of a combination of Poisson-Boltzmann and Monte Carlo simulations together with a distance-based network analysis to find possible groups involved in the proton transfer. Results obtained at different pH values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration around the metal centres. The electrostatic interactions in this protein are strong, as shown by the unusual shape of the titration curves of several sites. Some residue pairs show strongly correlated protonations, indicating the sharing and probably exchange of a proton between them. The conjugation of the PB and MC simulations with the distance-based analysis allows a detailed characterization of the possible proton pathways. We discuss previous suggestions and propose a new complete pathway for the proton transfer between the active site and the surface. This pathway is mainly composed of histidines and glutamic acid residues.
authors.affiliation: Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, E.A.N, Ap. 127, 2780-157 Oeiras, Portugal.
authors.forename: Vitor H
authors.initials: VH
authors.lastname: Teixeira
authors.forename: Cláudio M
authors.initials: CM
authors.lastname: Soares
authors.forename: António M
authors.initials: AM
authors.lastname: Baptista
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D045286:Desulfovibrio gigas / Q000201:enzymology; D018698:Glutamic Acid / Q000378:metabolism; D006639:Histidine / Q000378:metabolism; D006864:Hydrogenase / Q000737:chemistry*; D008958:Models, Molecular; D009010:Monte Carlo Method; D010084:Oxidation-Reduction; D011522:Protons; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D011522:Protons; D014867:Water; D018698:Glutamic Acid; D006639:Histidine; C043296:nickel-iron hydrogenase; D006864:Hydrogenase