ArticleThe journal of physical chemistry. B2011
Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 33 citations in OpenAlex.
- The Effect of Xenon on the Voltage‒Current Characteristics of Tethered Lipid Bilayers.The Journal of membrane biology · 2025Article
- Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.Journal of chemical theory and computation · 2021Article
- Atomistic Characterization of Gramicidin Channel Formation.Journal of chemical theory and computation · 2021Article
- Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness.Biophysical journal · 2019Article
- A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.Molecules (Basel, Switzerland) · 2017Article
- Classical Molecular Dynamics with Mobile Protons.Journal of chemical information and modeling · 2017Article
- Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes.Journal of chemical theory and computation · 2017Article
- Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.Biophysical journal · 2017Article
- Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel.Biochimica et biophysica acta · 2016Article
- How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?Journal of chemical theory and computation · 2015Article
- Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.Journal of chemical theory and computation · 2015Article
- The membrane protein LeuT in micellar systems: aggregation dynamics and detergent binding to the S2 site.Journal of the American Chemical Society · 2013Article
- Atomic-level simulation of current-voltage relationships in single-file ion channels.The Journal of general physiology · 2013Article
- Voltage-dependent conformational changes in connexin channels.Biochimica et biophysica acta · 2012Review
- Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers.Biophysical journal · 2012Article
- Computer Simulations of Voltage-Gated Cation Channels.The journal of physical chemistry letters · 2012Article
- Molecular dynamics simulations of the Cx26 hemichannel: evaluation of structural models with Brownian dynamics.The Journal of general physiology · 2011Article
- Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments.The journal of physical chemistry. B · 2011Article
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8 authors at 4 institutions in 1 country.
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Abstract
Gramicidin A (gA) channels provide an ideal system to test molecular dynamics (MD) simulations of membrane proteins. The peptide backbone lines a cation-selective pore, and due to the small channel size, the average structure and extent of fluctuations of all atoms in the peptide will influence ion permeation. This raises the question of how well molecular mechanical force fields used in MD simulations and potential of mean force (PMF) calculations can predict structure and dynamics as well as ion permeation. To address this question, we undertook a comparative study of nuclear magnetic resonance (NMR) observables predicted by fully atomistic MD simulations on a gA dimer embedded in a sodium dodecyl sulfate (SDS) micelle with measurements of the gA dimer backbone and tryptophan side chain dynamics using solution-state (15)N NMR on gA dimers in SDS micelles (Vostrikov, V. V.; Gu, H.; Ingólfsson, H. I.; Hinton, J. F.; Andersen, O. S.; Roux, B.; Koeppe, R. E., II. J. Phys. Chem. B2011, DOI 10.1021/jp200906y , accompanying article). This comparison enables us to examine the robustness of the MD simulations done using different force fields as well as their ability to predict important features of the gA channel. We find that MD is able to predict NMR observables, including the generalized order parameters (S(2)), the (15)N spin-lattice (T(1)) and spin-spin (T(2)) relaxation times, and the (1)H-(15)N nuclear Overhauser effect (NOE), with remarkable accuracy. To examine further how differences in the force fields can affect the channel conductance, we calculated the PMF for K(+) and Na(+) permeation through a gA channel in a dimyristoylphosphatidylcholine (DMPC) bilayer. In this case, we find that MD is less successful in quantitatively predicting the single-channel conductance.
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