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Molecular dynamics simulation of the antiamoebin ion channel: Linking structure and conductance
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. NASA, Ames Res Ctr, Exobiol Branch, Moffett Field, USA.
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2011 (English)In: Biophysical Journal, ISSN 0006-3495, Vol. 100, no 10, 2394-2402 p.Article in journal (Refereed) Published
Abstract [en]

Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K+ and CI- with their first solvation shells intact. The free energy barrier encountered by K+ is only 2.2 kcal/mol whereas Cl- encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.

Place, publisher, year, edition, pages
2011. Vol. 100, no 10, 2394-2402 p.
Keyword [en]
antiamebic agent, ion channel, lipid, peptide, water, article, biomechanics, channel gating, chemistry, diffusion, electric conductivity, ion transport, metabolism, molecular dynamics, pliability, porosity, protein quaternary structure, protein stability, structure activity relation, thermodynamics, Ion Channel Gating, Ion Channels, Lipids, Molecular Dynamics Simulation, Peptides, Protein Structure, Quaternary, Structure-Activity Relationship
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URN: urn:nbn:se:kth:diva-151220DOI: 10.1016/j.bpj.2011.03.054ISI: 000290830900010PubMedID: 21575573ScopusID: 2-s2.0-79959643733OAI: diva2:747796

QC 20140917

Available from: 2014-09-17 Created: 2014-09-15 Last updated: 2014-09-17Bibliographically approved

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Bjelkmar, Pär
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Theoretical & Computational Biophysics

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