ArticleBiophysical journal2006
Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations.
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 17 papers.
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17 citing papers in PubMed, 45 citations in OpenAlex.
- Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions.International journal of molecular sciences · 2016Article
- Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A.Membranes · 2016Article
- Force fields for simulating the interaction of surfaces with biological molecules.Interface focus · 2016Review
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- Article
- Molecular dynamics study of binding of µ-conotoxin GIIIA to the voltage-gated sodium channel Na(v)1.4.PloS one · 2014Article
- Density-functional theory study of gramicidin A ion channel geometry and electronic properties.Journal of the Royal Society, Interface · 2013Article
- Computational studies of marine toxins targeting ion channels.Marine drugs · 2013Review
- Molecular dynamics simulations of membrane proteins.Biophysical reviews · 2012Review
- Position of the third Na+ site in the aspartate transporter GltPh and the human glutamate transporter, EAAT1.PloS one · 2012Article
- Free energy simulations of ligand binding to the aspartate transporter Glt(Ph).Biophysical journal · 2011Article
- Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels.Biophysical journal · 2011Article
- Molecular simulations of ion channels: a quantum chemist's perspective.The Journal of general physiology · 2010Article
- The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements.Interdisciplinary sciences, computational life sciences · 2009Article
- Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites.Biochimica et biophysica acta · 2009Article
- Importance of the peptide backbone description in modeling the selectivity filter in potassium channels.Biophysical journal · 2009Article
- Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)].The Journal of chemical physics · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The rigid force fields currently used in molecular dynamics (MD) simulations of biomolecules are optimized for globular proteins. Whether they can also be used in MD simulations of membrane proteins is an important issue that needs to be resolved. Here we address this issue using the gramicidin A channel, which provides an ideal test case because of the simplicity of its structure and the availability of a wealth of functional data. Permeation properties of gramicidin A can be summarized as "it conducts monovalent cations, rejects anions, and binds divalent cations." Hence, a comprehensive test should consider the energetics of permeation for all three types of ions. To that end, we construct the potential of mean force for K(+), Cl(-), and Ca(2+) ions along the channel axis. For an independent check of the potential-of-mean-force results, we also calculate the free energy differences for these ions at the channel center and binding sites relative to bulk. We find that "rejection of anions" is satisfied but there are difficulties in accommodating the other two properties using the current MD force fields.
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