ArticleJournal of the American Chemical Society2015
Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Capturing Fast Gas Migration in Proteins.Molecules (Basel, Switzerland) · 2026Review
- Molecular dynamics simulations elucidate the role of the F-F' loop in substrate entry into CYP3A4.Communications chemistry · 2026Article
- Vibrational analyses of the reaction of oxymyoglobin with NO using a photolabile caged NO donor at cryogenic temperatures.Journal of inorganic biochemistry · 2024Article
- Free energy and kinetics of cAMP permeation through connexin26 via applied voltage and milestoning.Biophysical journal · 2021Article
- Structural Mechanism of ω-Currents in a Mutated Kv7.2 Voltage Sensor Domain from Molecular Dynamics Simulations.Journal of chemical information and modeling · 2021Article
- Water Dynamics in a Peptide-appended Pillar[5]arene Artificial Channel in Lipid and Biomimetic Membranes.Frontiers in chemistry · 2021Article
- Collective variable-based enhanced sampling and machine learning.The European physical journal. B · 2021Review
- Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor.Journal of chemical information and modeling · 2020Article
- The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin.Scientific reports · 2020Article
- Lessons Learned from 50 Years of Hemoglobin Research: Unstirred and Cell-Free Layers, Electrostatics, Baseball Gloves, and Molten Globules.Antioxidants & redox signaling · 2020Review
- Mapping saddles and minima on free energy surfaces using multiple climbing strings.The Journal of chemical physics · 2019Article
- Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach.The journal of physical chemistry letters · 2018Article
- Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme.PLoS computational biology · 2018Article
- Rate Constants and Mechanisms of Protein-Ligand Binding.Annual review of biophysics · 2017Review
- SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.The journal of physical chemistry. B · 2017Article
- Multiscale implementation of infinite-swap replica exchange molecular dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2016Review
- Kinetics of O2 Entry and Exit in Monomeric Sarcosine Oxidase via Markovian Milestoning Molecular Dynamics.Journal of chemical theory and computation · 2016Article
- Article
- Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.PLoS computational biology · 2015Article
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4 authors.
Funding
Abstract
We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to estimate the kinetics of entry, exit, and internal site-hopping. The tessellation is determined by analysis of the free-energy surface in that space using transition-path theory (TPT), which provides criteria for defining optimal milestones, allowing short, independent, cell-constrained MD simulations to provide properly weighted kinetic data. We coarse grain the resulting kinetic model at two levels: first, using crystallographically relevant internal cavities and their predicted interconnections and solvent portals; and second, as a three-state side-path scheme inspired by similar models developed from geminate recombination experiments. We show semiquantitative agreement with experiment on entry and exit rates and in the identification of the so-called "histidine gate" at position 64 through which ≈90% of flux between solvent and the distal pocket passes. We also show with six-dimensional calculations that the minimum free-energy pathway of escape through the histidine gate is a "knock-on" mechanism in which motion of the ligand and the gate are sequential and interdependent. In total, these results suggest that such TPT simulations are indeed a promising approach to overcome the practical time-scale limitations of MD to allow reliable estimation of transition mechanisms and rates among metastable states.
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