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

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.

Insulation of a synthetic hydrogen metabolism circuit in bacteria

“…In contrast, the interaction surface between the hydrogenase from Chlamydomonas reinhardtii and its cognate ferredoxin has been extensively modeled in silico , with evidence that this interaction has a strong electrostatic component [39,40]. Long et.…”

Identification of Global Ferredoxin Interaction Networks in Chlamydomonas reinhardtii

“…The Chlamydomonas genome encodes two [FeFe] hydrogenase enzymes, HYDA1 and HYDA2, that catalyze the reduction of two protons to hydrogen in all three pathways. In silico docking analysis and site-directed mutagenesis combined with in vitro hydrogen production assays have identified two amino acid residues (HYDA1 Lys-396 and FDX1 Glu-122) thought to mediate the electrostatic interaction between the two proteins (23,24). However, these site-directed mutagenesis and in silico docking studies were only informed by homology models of the Chlamydomonas hydrogenases and ferredoxins.…”

Enhancement of Bio-Hydrogen Production in Chlamydomonas Reinhardtii by Immobilization and Co-Culturing

“…Moreover, since the Calvin cycle has ceased, the system will be in a reduced state as the Calvin cycle can no longer function as a sink for carbon and energy, therefore the cell depends on the release of electrons from the system to avoid oxidative damage [28]. Thus, hydrogenase enzyme catalyzes the production of hydrogen by electrons received from ferredoxin to release the reductive pressure in the anaerobic environment [29]. In short, the regulation of the photosynthetic electron transport is an essential aspect of adjusting the cells metabolism to nutrient availability.…”