title: Hydropathic analysis and comparison of KcsA and Shaker potassium channels.
abstract: The similarity in structure of potassium (K(+)) channels from different families has been revealed by only recently available crystallographic 3D structural data. The hydropathic analysis presented in this work illuminates whether homologous residues perform the same functions in channels that use different gating mechanisms. We calculated and compared the hydropathic profiles of two K(+) channels, KcsA and Kv1.2 (the latter a member of the Shaker family), at their pore-forming domain. Quantitative information describing important interactions stabilizing the protein beyond obvious secondary-structure elements was extracted from the analysis and applied as a template for subsequent molecular-dynamics (MD) analyses. For example, two key groups of interactions, defining the turns that connect the transmembrane helices and responsible for the orientation of the pore helix, were identified. Our results also indicate that Asp(80) and Asp(379) play a similar role in stabilizing the P-loop of KcsA and Kv1.2, respectively, but to significantly different extents.
authors.affiliation: Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0540, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Peng
authors.forename: J Neel
authors.initials: JN
authors.lastname: Scarsdale
authors.forename: Glen E
authors.initials: GE
authors.lastname: Kellogg
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D051663:Kv1.2 Potassium Channel / Q000737:chemistry / Q000378:metabolism; D008954:Models, Biological; D008969:Molecular Sequence Data; D015221:Potassium Channels / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017386:Sequence Homology, Amino Acid; D051637:Shaker Superfamily of Potassium Channels / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D051663:Kv1.2 Potassium Channel; D015221:Potassium Channels; D051637:Shaker Superfamily of Potassium Channels; C107790:prokaryotic potassium channel