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Originally published as Biophys J. BioFAST on May 26, 2006.
doi:10.1529/biophysj.106.084376
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Biophysical Journal 91:2035-2045 (2006)
© 2006 The Biophysical Society

Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase

Vitor H. Teixeira, António M. Baptista and Cláudio M. Soares

Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa, Oeiras, Portugal

Correspondence: Address reprint requests to Dr. Cláudio M. Soares, Tel.: 35-1-21-446-9610; E-mail: claudio{at}itqb.unl.pt.

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. H2 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.




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Thiolate-bridged dinuclear iron(tris-carbonyl)-nickel complexes relevant to the active site of [NiFe] hydrogenase
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