title: General rules for the arrangements and gating motions of pore-lining helices in homomeric ion channels.
abstract: The pore-lining helix (PLH) bundles are central to the function of all ion channels, as their conformational rearrangements dictate channel gating. Here we explore all plausible oligomeric arrangements of the PLH bundles within homomeric ion channels by building models using generic restraints. In particular, the distance between two neighbouring PLHs was bounded both below and above in order to avoid steric clash and allow proper packing. The resulting models provide a theoretical representation of the accessible space for oligomeric arrangements. While the represented space is confined, it encompasses nearly all the ion channel PLH bundles for which the structures are currently known. For a multitude of channels, gating models suggested by paths within the confined accessible space are in qualitative agreement with those established in previous structural and computational studies.
authors.affiliation: Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Dai
authors.affiliation: Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
authors.forename: Huan-Xiang
authors.initials: HX
authors.lastname: Zhou
mesh_terms: D000409:Alanine / Q000737:chemistry; D002118:Calcium / Q000737:chemistry; D003198:Computer Simulation; D015640:Ion Channel Gating; D007473:Ion Channels / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D008967:Molecular Biology; D009038:Motion; D011188:Potassium / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D007473:Ion Channels; D007477:Ions; D008024:Ligands; D000409:Alanine; D011188:Potassium; D002118:Calcium
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