ArticleBiophysical journal2006
Pathways of H2 toward the active site of [NiFe]-hydrogenase.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics.The journal of physical chemistry letters · 2025Article
- PathInHydro, a Set of Machine Learning Models to Identify Unbinding Pathways of Gas Molecules in [NiFe] Hydrogenases.Journal of chemical information and modeling · 2025Article
- Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase.Journal of chemical information and modeling · 2024Article
- Article
- Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase fromFrontiers in microbiology · 2022Article
- QM/MM study of the binding of HJournal of molecular modeling · 2021Article
- Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2020Article
- Studying OScientific reports · 2020Article
- From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production.Sustainable energy & fuels · 2018Review
- Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.PLoS computational biology · 2014Article
- Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2012Article
- Analyses of the large subunit histidine-rich motif expose an alternative proton transfer pathway in [NiFe] hydrogenases.PloS one · 2012Article
- Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits.European biophysics journal : EBJ · 2010Article
- Review
- Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2009Article
- Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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