ArticleBiophysical journal2006
Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers.
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Who cites it
107 citing papers in PubMed.
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- Transient protein structure guides surface diffusion pathways for electron transport in membrane supercomplexes.Nature communications · 2026Article
- Unleashing the potential of traditional Chinese medicine: a computational approach to discovering drug targets utilizing the CSLN and molecular dynamics.Molecular diversity · 2026Article
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- Human class B1 GPCR modulation by plasma membrane lipids.Communications biology · 2026Article
- Mutation-induced heme pocket destabilization in myoglobinopathy.Frontiers in bioinformatics · 2026Article
- Simulating Gas Permeation Through the Central Pore of AQP5.Advances in experimental medicine and biology · 2026Article
- Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling.bioRxiv : the preprint server for biology · 2025Article
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- Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen.Journal of chemical theory and computation · 2025Article
- Active-Site Oxygen Accessibility and Catalytic Loop Dynamics of Plant Aromatic Amino Acid Decarboxylases from Molecular Simulations.Biochemistry · 2024Article
- Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.Protein science : a publication of the Protein Society · 2024Article
- CaProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Lipid regulation of the glucagon receptor family.The Journal of endocrinology · 2024Review
- Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems.International journal of molecular sciences · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Programming xenon diffusion in maltose-binding protein.Biophysical journal · 2022Article
47 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Myoglobin (Mb) is perhaps the most studied protein, experimentally and theoretically. Despite the wealth of known details regarding the gas migration processes inside Mb, there exists no fully conclusive picture of these pathways. We address this deficiency by presenting a complete map of all the gas migration pathways inside Mb for small gas ligands (O2, NO, CO, and Xe). To accomplish this, we introduce a computational approach for studying gas migration, which we call implicit ligand sampling. Rather than simulating actual gas migration events, we infer the location of gas migration pathways based on a free-energy perturbation approach applied to simulations of Mb's dynamical fluctuations at equilibrium in the absence of ligand. The method provides complete three-dimensional maps of the potential of mean force of gas ligand placement anywhere inside a protein-solvent system. From such free-energy maps we identify each gas docking site, the pathways between these sites, to the heme and to the external solution. Our maps match previously known features of these pathways in Mb, but also point to the existence of additional exits from the protein matrix in regions that are not easily probed by experiment. We also compare the pathway maps of Mb for different gas ligands and for different animal species.
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