title: Pathways of H2 toward the active site of [NiFe]-hydrogenase.
abstract: Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H(2)), but little is known about the diffusion of H(2) toward the active site. Here we analyze pathways for H(2) permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H(2) easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H(2) molecules that reach the active site made their approach from the side of the Ni ion. H(2) is able to reach distances of <4 A from the active site, although after 6 A permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H(2) inside the protein and at lower distances from the active site. This valine can be a control point in the H(2) access to the active center.
authors.affiliation: Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa, Oeiras, Portugal.
authors.forename: Vitor H
authors.initials: VH
authors.lastname: Teixeira
authors.forename: António M
authors.initials: AM
authors.lastname: Baptista
authors.forename: Cláudio M
authors.initials: CM
authors.lastname: Soares
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D045286:Desulfovibrio gigas / Q000201:enzymology; D006859:Hydrogen / Q000737:chemistry*; D006864:Hydrogenase / Q000737:chemistry* / Q000235:genetics; D007477:Ions; D007501:Iron / Q000737:chemistry*; D008958:Models, Molecular; D009154:Mutation; D009532:Nickel / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D007477:Ions; D009532:Nickel; D006859:Hydrogen; D007501:Iron; C043296:nickel-iron hydrogenase; D006864:Hydrogenase