# Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics

## TL;DR

This study uses simulations to explore how hydrogen binds to and unbinds from [NiFe] hydrogenases, revealing symmetric pathways and a dual-state bottleneck that could help improve biofuel production.

## Contribution

The discovery of a dual-state bottleneck and symmetric ligand pathways in [NiFe] hydrogenases provides new insights into their function and potential modulation.

## Key findings

- Symmetric binding and unbinding pathways for H2 were observed in [NiFe] hydrogenases.
- The bottleneck between residues V74 and L122 can shift between two states, affecting ligand access.
- Simulated association rate constants matched experimental results, validating the method.

## Abstract

[NiFe] hydrogenases make up a family of enzymes that
can be used
to produce biofuel, thus making them important for industrial applications.
In this work, we utilized unbiased molecular dynamics simulations
to capture binding and unbinding events of the substrate, H2, to and from the [NiFe] hydrogenases from two different organisms.
We obtained multiple (un)­binding events and reproduced experimental
association rate constants. We observed symmetry between the binding
and unbinding pathways used by H2 to access and leave the
catalytic site. Moreover, we found that the main bottleneck for ligand
binding, the distance between residues V74 and L122, can shift between
two states with different bottleneck widths, a feature which can be
exploited to modulate the access of small molecules to the catalytic
site. The pathway probabilities presented here can be used to benchmark
enhanced sampling methods which investigate protein–ligand
binding.