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A comparison between two prokaryotic potassium channels (KirBac1.1 and KcsA) in a molecular dynamics (MD) simulation study
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.ORCID iD: 0000-0002-7448-4664
2006 (English)In: Biophysical Chemistry, ISSN 0301-4622, E-ISSN 1873-4200, Vol. 120, no 1, 1-9 p.Article in journal (Refereed) Published
Abstract [en]

The two potassium ion channels KirBac1.1 and KcsA are compared in a Molecular Dynamics (MD) simulation study. The location and motion of the potassium ions observed in the simulations are compared to those in the X-ray structures and previous simulations. In our simulations several of the crystallography resolved ion sites in KirBac1.1 are occupied by ions. In addition to this, two in KirBac1.1 unresolved sites where occupied by ions at sites that are in close correspondence to sites found in KcsA. There is every reason to believe that the conserved alignment of the selectivity filter in the potassium ion channel family corresponds to a very similar mechanism for ion transport across the filter. The gate residues, Phe146 in KirBac1.1 and Ala111 in KcsA acted in the simulations as effective barriers which never were passed by ions nor water molecules.

Place, publisher, year, edition, pages
2006. Vol. 120, no 1, 1-9 p.
Keyword [en]
potassium channel, molecular dynamics simulation, KcsA, KirBac 1.1, particle mesh ewald, k+ channel, ion conduction, crystal-structure, state, conformation, permeation, hydration, mechanism, binding
URN: urn:nbn:se:kth:diva-15497DOI: 10.1016/j.bpc.2005.10.002ISI: 000235831600001ScopusID: 2-s2.0-32844467750OAI: diva2:333538
QC 20100525Available from: 2010-08-05 Created: 2010-08-05Bibliographically approved

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Edholm, Olle
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