ArticleBiophysical journal2007
Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Article
- Computational methods and theory for ion channel research.Advances in physics: X · 2022Article
- Multi-ion versus single-ion conduction mechanisms can yield current rectification in biological ion channels.Journal of biological physics · 2014Article
- Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications.Physiological reviews · 2013Review
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Nonselective conduction in a mutated NaK channel with three cation-binding sites.Biophysical journal · 2012Article
- Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations.PloS one · 2011Article
- Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites.Biochimica et biophysica acta · 2009Article
- The selectivity of K+ ion channels: testing the hypotheses.Biophysical journal · 2008Article
- Brownian dynamics study of flux ratios in sodium channels.European biophysics journal : EBJ · 2008Article
- Conduction of Na+ and K+ through the NaK channel: molecular and Brownian dynamics studies.Biophysical journal · 2008Article
- Estimating the dielectric constant of the channel protein and pore.European biophysics journal : EBJ · 2008Article
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Authors and funding
2 authors.
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Abstract
In the narrow segment of an ion conducting pathway, it is likely that a permeating ion influences the positions of the nearby atoms that carry partial or full electronic charges. Here we introduce a method of incorporating the motion of charged atoms lining the pore into Brownian dynamics simulations of ion conduction. The movements of the carbonyl groups in the selectivity filter of the KcsA channel are calculated explicitly, allowing their bond lengths, bond angles, and dihedral angels to change in response to the forces acting upon them. By systematically changing the coefficients of bond stretching and of angle bending, the carbon and oxygen atoms can be made to fluctuate from their fixed positions by varying mean distances. We show that incorporating carbonyl motion in this way does not alter the mechanism of ion conduction and only has a small influence on the computed current. The slope conductance of the channel increases by approximately 25% when the root mean-square fluctuations of the carbonyl groups are increased from 0.01 to 0.61 A. The energy profiles and the number of resident ions in the channel remain unchanged. The method we utilized here can be extended to allow the movement of glutamate or aspartate side chains lining the selectivity filters of other ionic channels.
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