ArticleThe Journal of chemical physics2007
Free energy simulations of single and double ion occupancy in gramicidin A.
Article in The Journal of chemical physics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 36 citations in OpenAlex.
- Free-Energy Simulations Resolve the Low-Affinity NaBiophysical journal · 2019Article
- KScientific reports · 2018Article
- Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A.Membranes · 2016Article
- Use of Molecular Dynamics for the Refinement of an Electrostatic Model for the In Silico Design of a Polymer Antidote for the Anticoagulant Fondaparinux.Journal of medical engineering · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Molecular dynamics simulations of membrane proteins.Biophysical reviews · 2012Review
- Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels.Biophysical journal · 2011Article
- Energetics of double-ion occupancy in the gramicidin A channel.The journal of physical chemistry. B · 2010Article
- Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites.Biochimica et biophysica acta · 2009Article
- The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements.Interdisciplinary sciences, computational life sciences · 2009Article
- Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.The Journal of chemical physics · 2009Article
- Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations.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
- Optimization of cutting schemes for the evaluation of molecular electrostatic potentials in proteins via Moving-Domain QM/MM.Journal of molecular modeling · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Simultaneous occupancy of the two binding sites in gramicidin A by monovalent cations is a well known property of this channel, but the energetic feasibility of this process in molecular dynamics simulations has not been established so far. Here the authors study the energetics of single and double ion occupancy in gramicidin A by constructing the potential of mean force for single and pair of cations. As representatives of small and large ions, they consider both Na+ and K+ ions in the calculations. Binding constants of ions are estimated from the free energy profiles. Comparisons with the experimental results indicate 3-4 kT discrepancy in the binding energies. They also study the coordination of the ions in their respective binding sites and the dynamic behavior of the channel water during the double ion binding process.
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