On selectivity and gating of ionic channels.

A novel conceptual model is introduced in which ion permeation is coupled to the protein wall vibration and the later in turn modulates exponentially strongly the permeation via radial oscillations of the potential of mean force. In the framework of this model of ion-wall-water interaction we discuss problems of selectivity between alike ions and coupling of ion permeation to gating.

[1]  Dezso Boda,et al.  The effect of protein dielectric coefficient on the ionic selectivity of a calcium channel. , 2006, The Journal of chemical physics.

[2]  O. Andersen,et al.  Gramicidin channels. , 2005, Annual review of physiology.

[3]  R. MacKinnon,et al.  Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution , 2001, Nature.

[4]  Brownian dynamics simulations of ionic current through an open channel , 2005 .

[5]  Boaz Nadler,et al.  Connecting a Discrete Ionic Simulation to a Continuum , 2003, SIAM J. Appl. Math..

[6]  B. Chait,et al.  The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.

[7]  Francisco Bezanilla,et al.  Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement , 2005, Nature.

[8]  Shin-Ho Chung,et al.  Modeling diverse range of potassium channels with Brownian dynamics. , 2002, Biophysical journal.

[9]  Ben Corry,et al.  Understanding ion channel selectivity and gating and their role in cellular signalling. , 2006, Molecular bioSystems.

[10]  W. Sung,et al.  Ion transport and channel transition in biomembranes , 2002 .

[11]  P. H. Barry,et al.  Ligand-gated channels , 2005, IEEE Transactions on NanoBioscience.

[12]  Robert S. Eisenberg,et al.  Ionic current through an open channel: a low-dimensional model of coupling with vibrations of the wall , 2004, SPIE International Symposium on Fluctuations and Noise.

[13]  S. Kuyucak,et al.  Role of protein flexibility in ion permeation: a case study in gramicidin A. , 2006, Biophysical journal.

[14]  Solvated chloride ions at contact , 1987 .

[15]  P. Kollman,et al.  The effect of water models on the interaction of the sodium–chloride ion pair in water: Molecular dynamics simulations , 1990 .

[16]  A Stochastic Model of Conductance Transitions in Voltage-Gated IonChannels , 2002, Journal of biological physics.

[17]  Jack A. Tuszynski,et al.  Introduction to Molecular Biophysics , 2003 .

[18]  Abraham Nitzan,et al.  The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents. , 2003, Biophysical journal.

[19]  Shin-Ho Chung,et al.  Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus brownian dynamics. , 2000, Biophysical journal.

[20]  B. Roux,et al.  Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields. , 2006, Biophysical journal.

[21]  Anthony Auerbach,et al.  Gating of acetylcholine receptor channels: brownian motion across a broad transition state. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Shin-Ho Chung,et al.  Three computational methods for studying permeation, selectivity and dynamics in biological ion channels. , 2005, Soft matter.

[23]  R. Dutzler,et al.  X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity , 2002, Nature.

[24]  Boris Martinac,et al.  Mechanosensitive ion channels: molecules of mechanotransduction , 2004, Journal of Cell Science.

[25]  B. R. Fink,et al.  Clinical and Experimental Pharmacology and Physiology , 1974 .

[26]  Shin-Ho Chung,et al.  Proceedings of the Australian Physiological and Pharmacological Society Symposium: Ion Channels PREDICTING CHANNEL FUNCTION FROM CHANNEL STRUCTURE USING BROWNIAN DYNAMICS SIMULATIONS , 2001, Clinical and experimental pharmacology & physiology.

[27]  B. Roux,et al.  Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands , 2004, Nature.

[28]  B. Roux,et al.  Gramicidin channels , 2005, IEEE Transactions on NanoBioscience.

[29]  Bob Eisenberg,et al.  Monte Carlo simulations of ion selectivity in a biological Na channel: Charge–space competition , 2002 .

[30]  P. Läuger.  Structural fluctuations and current noise of ionic channels. , 1985, Biophysical journal.

[31]  S. Chung,et al.  Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics. , 2000, Biophysical journal.

[32]  R. Eisenberg,et al.  Ion channels as electrostatic amplifiers of charge fluctuations , 2006, physics/0611240.