Interaction at a Distance: Xenon Migration in Mb

TL;DR

This study uses molecular dynamics simulations to explore how internal cavities in myoglobin influence ligand migration, revealing complex, non-additive effects and dynamic communication pathways that relate to protein allostery.

Contribution

It demonstrates that ligand migration energetics in myoglobin depend on cavity occupation, directionality, and dynamic interactions, providing new insights into internal protein communication.

Findings

Ligand migration barriers depend on cavity occupation and transition direction.

Multiple barriers exist for the same transition, indicating a distribution of transition times.

Residue Phe138 acts as a gate controlling ligand movement.

Abstract

The transport of ligands, such as NO or O$_2$, through internal cavities is essential for the function of globular proteins, including hemoglobin, myoglobin (Mb), neuroglobin, truncated hemoglobins, or cytoglobin. For Mb, several internal cavities (Xe1 through Xe4) were observed experimentally through X-ray crystallography experiments. At a functional level, they were linked to ligand storage and internal ligand diffusion. Barriers for ligand diffusion and relative stabilization energies for the ligand in the initial and final pocket linking a transition may differ depending on the occupation state of the remaining pockets. This is considered in the present work from biased (umbrella sampling) and unbiased molecular dynamics simulations. It is found that the energetics of a particular ligand migration pathway may depend on the direction in which the transition is followed (forward or reverse) and the occupation state of other cavities. Furthermore, the barrier for a particular transition can depend in a non-additive fashion on the occupation of either cavity A or B or simultaneous occupation of both cavities, A and B. Multiple repeats for the Xe1$\rightarrow$Xe2 transition reveals that the activation barrier is a distribution of barrier heights rather than one single value which is confirmed by a distribution of transition times for the same transition from unbiased simulations. Dynamic cross correlation maps for this transition demonstrate that correlated motions occur between adjacent residues or through space. Residue Phe138 is characterized as a gate between Xe1 and Xe2 for the Xe1$\rightarrow$Xe2 transition. It is also found that the volumes of the internal cavities vary along the diffusion pathway which points towards dynamic communication between the ligand and the protein. The findings are discussed in the context of protein allostery.