title: Multi-ion distributions in the cytoplasmic domain of inward rectifier potassium channels.
abstract: Inward rectifier potassium (Kir) channels act as cellular diodes, allowing unrestricted flow of potassium (K(+)) into the cell while preventing currents of large magnitude in the outward direction. The rectification mechanism by which this occurs involves a coupling between K(+) and intracellular blockers-magnesium (Mg(2+)) or polyamines-that simultaneously occupy the permeation pathway. In addition to the transmembrane pore, Kirs possess a large cytoplasmic domain (CD) that provides a favorable electronegative environment for cations. Electrophysiological experiments have shown that the CD is a key regulator of both conductance and rectification. In this study, we calculate and compare averaged equilibrium probability densities of K(+) and Cl(-) in open-pore models of the CDs of a weak (Kir1.1-ROMK) and a strong (Kir2.1-IRK) rectifier through explicit-solvent molecular-dynamics simulations in ~1 M KCl. The CD of both channels concentrates K(+) ions greater than threefold inside the cytoplasmic pore while IRK shows an additional K(+) accumulation region near the cytoplasmic entrance. Simulations carried out with Mg(2+) or spermine (SPM(4+)) show that these ions interact with pore-lining residues, shielding the surface charge and reducing K(+) in both channels. The results also show that SPM(4+) behaves differently inside these two channels. Although SPM(4+) remains inside the CD of ROMK, it diffuses around the entire volume of the pore. In contrast, this polyatomic cation finds long-lived conformational states inside the IRK pore, interacting with residues E224, D259, and E299. The strong rectifier CD is also capable of sequestering an additional SPM(4+) at the cytoplasmic entrance near a cluster of negative residues D249, D274, E275, and D276. Although understanding the actual mechanism of rectification blockade will require high-resolution structural information of the blocked state, these simulations provide insight into how sequence variation in the CD can affect the multi-ion distributions that underlie the mechanisms of conduction, rectification affinity, and kinetics.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
authors.forename: J L
authors.initials: JL
authors.lastname: Robertson
authors.affiliation: Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.
authors.forename: L G
authors.initials: LG
authors.lastname: Palmer
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois. Electronic address: roux@uchicago.edu.
authors.forename: B
authors.initials: B
authors.lastname: Roux
mesh_terms: D002712:Chlorides / Q000378:metabolism; D003593:Cytoplasm / Q000187:drug effects / Q000378:metabolism*; D004553:Electric Conductivity; D008274:Magnesium / Q000494:pharmacology; D056004:Molecular Dynamics Simulation; D016062:Porosity; D011188:Potassium / Q000378:metabolism; D026902:Potassium Channel Blockers / Q000494:pharmacology; D024661:Potassium Channels, Inwardly Rectifying / Q000737:chemistry* / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D013096:Spermine / Q000494:pharmacology
chemical_list: D002712:Chlorides; D026902:Potassium Channel Blockers; D024661:Potassium Channels, Inwardly Rectifying; D013096:Spermine; D008274:Magnesium; D011188:Potassium