title: A comparison between two prokaryotic potassium channels (KirBac1.1 and KcsA) in a molecular dynamics (MD) simulation study.
abstract: 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.
authors.affiliation: Theoretical Biological Physics, Department of Physics, Royal Institute of Technology, AlbaNova University Centre, SE-106 91 Stockholm, Sweden.
authors.forename: Mikko
authors.initials: M
authors.lastname: Hellgren
authors.forename: Lars
authors.initials: L
authors.lastname: Sandberg
authors.forename: Olle
authors.initials: O
authors.lastname: Edholm
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015221:Potassium Channels / Q000737:chemistry* / Q000145:classification; D011387:Prokaryotic Cells / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D015221:Potassium Channels; C107790:prokaryotic potassium channel