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Multiscale Simulation Reveals Multiple Pathways for H2 and O2 Transport in a [NiFe]-Hydrogenase

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases
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Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases
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A search for ligand diffusion pathway in myoglobin using a metadynamics simulation
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Finding Gas Diffusion Pathways in Proteins: Application to O2 and H2 Transport in CpI [FeFe]-Hydrogenase and the Role of Packing Defects
inferredcites →https://doi.org/10.1016/s0031-8914(40)90098-2openalex-snapshot
Brownian motion in a field of force and the diffusion model of chemical reactions
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Volume changes on protein folding
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Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase,
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The Binding and Release of Oxygen and Hydrogen Peroxide Are Directed by a Hydrophobic Tunnel in Cholesterol Oxidase
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Structure/Function Relationships of [NiFe]- and [FeFe]-Hydrogenases
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The missing term in effective pair potentials
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Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
inferredcites →https://doi.org/10.1021/ja043701vopenalex-snapshot
The Tunnel of Acetyl-Coenzyme A Synthase/Carbon Monoxide Dehydrogenase Regulates Delivery of CO to the Active Site
inferredcites →https://doi.org/10.1021/ja9018258openalex-snapshot
Introduction of Methionines in the Gas Channel Makes [NiFe] Hydrogenase Aero-Tolerant
inferredcites →https://doi.org/10.1021/ja905671xopenalex-snapshot
Mapping the Network of Pathways of CO Diffusion in Myoglobin
inferredcites →https://doi.org/10.1021/jp0761665openalex-snapshot
Coarse Master Equations for Peptide Folding Dynamics
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The GROMOS Biomolecular Simulation Program Package
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Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics
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Dynamic electrochemical investigations of hydrogen oxidation and production by enzymes and implications for future technology
inferredcites →https://doi.org/10.1039/b903840jopenalex-snapshot
[NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism
inferredcites →https://doi.org/10.1042/bst0330080openalex-snapshot
Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase
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Computing time scales from reaction coordinates by milestoning
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Reactive flux and folding pathways in network models of coarse-grained protein dynamics
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Progress and challenges in the automated construction of Markov state models for full protein systems
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A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter
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Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations
inferredcites →https://doi.org/10.1073/pnas.0408098102openalex-snapshot
Reaction coordinates and rates from transition paths
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Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels
inferredcites →https://doi.org/10.1073/pnas.0710825105openalex-snapshot
Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
inferredcites →https://doi.org/10.1073/pnas.0803689105openalex-snapshot
Experimental approaches to kinetics of gas diffusion in hydrogenase
inferredcites →https://doi.org/10.1073/pnas.0903809106openalex-snapshot
Multiple pathways guide oxygen diffusion into flavoenzyme active sites
inferredcites →https://doi.org/10.1073/pnas.0903938106openalex-snapshot
Kinetic gating of the proton pump in cytochrome c oxidase
inferredcites →https://doi.org/10.1073/pnas.0905959106openalex-snapshot
A kinetic and thermodynamic understanding of O 2 tolerance in [NiFe]-hydrogenases
inferredcites →https://doi.org/10.1073/pnas.90.20.9547openalex-snapshot
Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin.
inferredcites →https://doi.org/10.1074/jbc.m701308200openalex-snapshot
Exploring Molecular Oxygen Pathways in Hansenula polymorpha Copper-containing Amine Oxidase
inferredcites →https://doi.org/10.1074/jbc.m802321200openalex-snapshot
On the Oxygen Reactivity of Flavoprotein Oxidases
inferredcites →https://doi.org/10.1074/jbc.m803676200openalex-snapshot
Oxygen-tolerant H2 Oxidation by Membrane-bound [NiFe] Hydrogenases of Ralstonia Species
inferredcites →https://doi.org/10.1080/10409230390242380openalex-snapshot
Nitrogen Fixation: The Mechanism of the Mo-Dependent Nitrogenase
inferredcites →https://doi.org/10.1088/1367-2630/7/1/034openalex-snapshot
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
inferredcites →https://doi.org/10.1103/physrevlett.96.108101openalex-snapshot
Intrinsic Rates and Activation Free Energies from Single-Molecule Pulling Experiments
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On the Approximation Quality of Markov State Models
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T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
inferredcites →https://doi.org/10.1529/biophysj.106.084376openalex-snapshot
Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase
inferredcites →https://doi.org/10.1529/biophysj.106.085746openalex-snapshot
Imaging the Migration Pathways for O2, CO, NO, and Xe Inside Myoglobin
inferredcites →https://doi.org/10.1529/biophysj.107.108712openalex-snapshot
O2 Migration Pathways Are Not Conserved across Proteins of a Similar Fold

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