Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach

Abstract

Hydrogenases are metalloenzymes that catalyze the reversible reaction H(2)<->2H(+) + 2e(-), being potentially useful in H(2) production or oxidation. [NiFeSe] hydrogenases are a particularly interesting subgroup of the [NiFe] class that exhibit tolerance to O(2) inhibition and produce more H(2) than standard [NiFe] hydrogenases. However, the molecular determinants responsible for these properties remain unknown. Hydrophobic pathways for H(2) diffusion have been identified in [NiFe] hydrogenases, as have proton transfer pathways, but they have never been studied in [NiFeSe] hydrogenases. Our aim was, for the first time, to characterize the H(2) and proton pathways in a [NiFeSe] hydrogenase and compare them with those in a standard [NiFe] hydrogenase. We performed molecular dynamics simulations of H(2) diffusion in the [NiFeSe] hydrogenase from Desulfomicrobium baculatum and extended previous simulations of the [NiFe] hydrogenase from Desulfovibrio gigas (Teixeira et al. in Biophys J 91:2035-2045, 2006). The comparison showed that H(2) density near the active site is much higher in [NiFeSe] hydrogenase, which appears to have an alternative route for the access of H(2) to the active site. We have also determined a possible proton transfer pathway in the [NiFeSe] hydrogenase from D. baculatum using continuum electrostatics and Monte Carlo simulation and compared it with the proton pathway we found in the [NiFe] hydrogenase from D. gigas (Teixeira et al. in Proteins 70:1010-1022, 2008). The residues constituting both proton transfer pathways are considerably different, although in the same region of the protein. These results support the hypothesis that some of the special properties of [NiFeSe] hydrogenases could be related to differences in the H(2) and proton pathways.

Tracking the route of molecular oxygen in O 2 -tolerant membrane-bound [NiFe] hydrogenase

“…They have suggested that the concentration of the gaseous substrate in the enzyme affects the enzyme activity. Comparable conclusions have been drawn from the MD simulation results from [NiFeSe] hydrogenase ( 27 ). Baltazar et al ( 27 ) deduce from cavities with trapped H 2 molecules that they either hinder H 2 transport to the active site or promote access by storing gas molecules.…”

“…Comparable conclusions have been drawn from the MD simulation results from [NiFeSe] hydrogenase ( 27 ). Baltazar et al ( 27 ) deduce from cavities with trapped H 2 molecules that they either hinder H 2 transport to the active site or promote access by storing gas molecules. Considering the low solubility of H 2 in water, the hydrophobic tunnel system might aid in elevating the H 2 concentration above the surrounding medium level.…”

Synthetic Active Site Model of the [NiFeSe] Hydrogenase

“…It has been well-established that the protein structure surrounding an active site affects the reactivity of an enzyme,[ 14 ] and biomimetic molecules can be employed to learn about the structural and functional properties of the active site. [ 15 ] Our aim is to explore the effect of selenium on the enzyme active site using small molecule model chemistry.…”

Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

“…In the last decade, computational methods have been widely used to study gas migration in a number of proteins and MD simulations have successfully allowed the identification of several alternative routes for ligand diffusion (e.g. hydrogenase [26] – [28] , myoglobins [29] , [30] , oxidases [31] , [32] and laccases [33] ). Moreover, the combination of MD simulations with Implicit Ligand Sampling (ILS) [29] calculations allows the calculation of the energy cost of transferring any small, apolar molecule (like O 2 or H 2 ) from the solvent to the protein and consequently to compute a 3D free-energy landscape for that specific ligand molecule (e.g [29] , [33] , [34] ).…”