Interaction at a Distance: Xenon Migration in Mb
Haydar Taylan Turan, Eric Boittier, Markus Meuwly

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, 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…
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
Taxonomy
TopicsHemoglobin structure and function · Molecular Junctions and Nanostructures · Supramolecular Chemistry and Complexes
