Brownian Dynamics and Molecular Dynamics Study of the Association Between Hydrogenase and Ferredoxin from the Chlamydomonas reinhardtii

Hai Long, Christopher H. Chang, Paul W. King, Maria L. Ghirardi, Kwiseon Kim

Research output: Contribution to journalArticlepeer-review

36 Scopus Citations

Abstract

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer.

Original languageAmerican English
Pages (from-to)3753-3766
Number of pages14
JournalBiophysical Journal
Volume95
Issue number8
DOIs
StatePublished - 15 Oct 2008

NREL Publication Number

  • NREL/JA-530-41890

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