title: Digitalized K(+) Occupancy in the Nanocavity Holds and Releases Queues of K(+) in a Channel.
abstract: The mechanisms of ion permeation through potassium channels have been extensively examined. Molecular dynamics (MD) simulations have demonstrated that rapidly permeating ions collide near the selectivity filter (SF) ("knock-on" mechanism), but this oversimplified mechanism is insufficient to account for the experimentally observed single-channel current amplitudes. Here, we analyzed the MD-simulated ion trajectories through a Kv1.2 potassium channel using an event-oriented analysis method, and surprisingly, we found that the nanocavity (NC) governs ion permeation in a digital fashion. The NC has a maximal diameter of 10 Å and stands between the intracellular bulk solution and the SF, which holds only up to one K(+) during permeation. Accordingly, the K(+) concentration in the intracellular solution is translated as a digitalized zero or one K(+) in the NC. When the ion number in the NC is zero, the multiple ions in the SF are mostly immobilized. By contrast, when the number of ions in the NC is one, the structured water in the NC mediates the ion-occupied status to the queueing ions in the SF, and the ions then initiate a collective outward motion. Accordingly, the one ion in the NC serves as a catalytic intermediate for permeation, which quantitatively accounts for the experimentally obtained conductance-concentration relationships. We conclude that the ion movements are coherent across the entire pore.
authors.affiliation: Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui , Fukui 910-1193, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Sumikama
authors.affiliation: Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui , Fukui 910-1193, Japan.
authors.forename: Shigetoshi
authors.initials: S
authors.lastname: Oiki
mesh_terms: D000818:Animals; D015195:Drug Design; D015640:Ion Channel Gating; D007700:Kinetics; D051663:Kv1.2 Potassium Channel / Q000737:chemistry; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D050997:Nanomedicine; D011188:Potassium / Q000737:chemistry*; D015221:Potassium Channels / Q000737:chemistry*; D011336:Probability; D011487:Protein Conformation; D051381:Rats; D012984:Software
chemical_list: D051663:Kv1.2 Potassium Channel; D015221:Potassium Channels; D011188:Potassium