ArticleBiophysical journal2011
Brownian dynamics simulations of ion transport through the VDAC.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 56 citations in OpenAlex.
- Fast prediction of antibiotic permeability through membrane channels using Brownian dynamics.Biophysical journal · 2023Article
- The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating.Journal of the American Chemical Society · 2022Article
- A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States.International journal of molecular sciences · 2022Article
- The Open State Selectivity of the Bean Seed VDAC Depends on Stigmasterol and Ion Concentration.International journal of molecular sciences · 2021Article
- QligFEP: an automated workflow for small molecule free energy calculations in Q.Journal of cheminformatics · 2019Article
- Gating of Connexin Channels by transjunctional-voltage: Conformations and models of open and closed states.Biochimica et biophysica acta. Biomembranes · 2018Review
- Ten Years of High Resolution Structural Research on the Voltage Dependent Anion Channel (VDAC)-Recent Developments and Future Directions.Frontiers in physiology · 2018Review
- CHARMM-GUI 10 years for biomolecular modeling and simulation.Journal of computational chemistry · 2017Review
- Modulation of Asymmetric Flux in Heterotypic Gap Junctions by Pore Shape, Particle Size and Charge.Frontiers in physiology · 2017Article
- Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1.Biophysical journal · 2016Article
- Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC).Biochimica et biophysica acta · 2016Review
- Voltage regulation of connexin channel conductance.Yonsei medical journal · 2015Review
- Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites.PloS one · 2015Article
- Computational investigation of cholesterol binding sites on mitochondrial VDAC.The journal of physical chemistry. B · 2014Article
- Channeling your inner energy.Nature structural & molecular biology · 2014Article
- Article
- Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.The Journal of general physiology · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- β-Barrel mobility underlies closure of the voltage-dependent anion channel.Structure (London, England : 1993) · 2012Article
- Voltage-dependent conformational changes in connexin channels.Biochimica et biophysica acta · 2012Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.