Pathways of H2 toward the active site of [NiFe]-hydrogenase

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Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H2), but little is known about the diffusion of H2 toward the active site. Here we analyze pathways for H2 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 H2 molecules that reach the active site made their approach from the side of the Ni ion. H2 is able to reach distances of <4 Å from the active site, although after 6 Å permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H2 inside the protein and at lower distances from the active site. This valine can be a control point in the H2 access to the active center.

Original languageEnglish
Pages (from-to)2035-2045
Number of pages11
JournalBiophysical Journal
Issue number6
Publication statusPublished - 1 Jan 2006


  • nickel-iron hydrogenase
  • alanine
  • hydrogen
  • hydrogenase
  • iron
  • mutant protein
  • nickel
  • solvent
  • valine
  • ion
  • nickel iron hydrogenase


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