Exploring the origin of the ion selectivity of the KcsA potassium channel

The availability of structural information about biological ion channels provides an opportunity to gain a detailed understanding of the control of ion selectivity by biological systems. However, accomplishing this task by computer simulation approaches is very challenging. First, although the activation barriers for ion transport can be evaluated by microscopic simulations, it is hard to obtain accurate results by such approaches. Second, the selectivity is related to the actual ion current and not directly to the individual activation barriers. Thus, it is essential to simulate the ion currents and this cannot be accomplished at present by microscopic MD approaches. In order to address this challenge, we developed and refined an approach capable of evaluating ion current while still reflecting the realistic features of the given channel. Our method involves generation of semimacroscopic free energy surfaces for the channel/ions system and Brownian dynamics (BD) simulations of the corresponding ion current. In contrast to most alternative macroscopic models, our approach is able to reproduce the difference between the free energy surfaces of different ions and thus to address the selectivity problem. Our method is used in a study of the selectivity of the KcsA channel toward the K+ and Na+ ions. The BD simulations with the calculated free energy profiles produce an appreciable selectivity. To the best of our knowledge, this is the first time that the trend in the selectivity in the ion current is produced by a computer simulation approach. Nevertheless, the calculated selectivity is still smaller than its experimental estimate. Recognizing that the calculated profiles are not perfect, we examine how changes in these profiles can account for the observed selectivity. It is found that the origin of the selectivity is more complex than generally assumed. The observed selectivity can be reproduced by increasing the barrier at the exit and the entrance of the selectivity filter, but the necessary changes in the barrier approach the limit of the error in the PDLD/S‐LRA calculations. Other options that can increase the selectivity are also considered, including the difference between the Na+…Na+ and K+…K+ interaction. However, this interesting effect does not appear to lead to a major difference in selectivity since the Na+ ions at the limit of strong interaction tend to move in a less concerted way than the K+ ions. Changes in the relative binding energies at the different binding sites are also not so effective in changing the selectivity. Finally, it is pointed out that using the calculated profiles as a starting point and forcing the model to satisfy different experimentally based constraints, should eventually provide more detailed understanding of the different complex factors involved in ion selectivity of biological channels. Proteins 2003;52:412–426. © 2003 Wiley‐Liss, Inc.

[1]  R Elber,et al.  Sodium in gramicidin: an example of a permion. , 1995, Biophysical journal.

[2]  Christopher Miller,et al.  Na+ Block and Permeation in a K+ Channel of Known Structure , 2002, The Journal of general physiology.

[3]  R. Kubo The fluctuation-dissipation theorem , 1966 .

[4]  J. Neyton,et al.  Discrete Ba2+ block as a probe of ion occupancy and pore structure in the high-conductance Ca2+ -activated K+ channel , 1988, The Journal of general physiology.

[5]  B. Roux,et al.  Energetics of ion conduction through the K + channel , 2022 .

[6]  Serdar Kuyucak,et al.  Molecular and Brownian dynamics study of ion selectivity and conductivity in the potassium channel , 1999 .

[7]  Arieh Warshel,et al.  A surface constrained all‐atom solvent model for effective simulations of polar solutions , 1989 .

[8]  Arieh Warshel,et al.  Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .

[9]  W. W. Parson,et al.  Electrostatic interactions in an integral membrane protein. , 2002, Biochemistry.

[10]  G. Uhlenbeck,et al.  On the Theory of the Brownian Motion II , 1945 .

[11]  A. Warshel,et al.  Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A. , 1989, Biophysical journal.

[12]  V. Luzhkov,et al.  Ion permeation mechanism of the potassium channel , 2000, Nature.

[13]  Arieh Warshel,et al.  A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations , 1992 .

[14]  I. Shrivastava,et al.  K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study. , 2002, Biophysical journal.

[15]  Shin-Ho Chung,et al.  Ion channels: recent progress and prospects , 2002, European Biophysics Journal.

[16]  H Luecke,et al.  Dipoles localized at helix termini of proteins stabilize charges. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Peter C. Jordan Microscopic approaches to ion transport through transmembrane channels: the model system gramicidin , 1987 .

[18]  B. Wallace,et al.  HOLE: a program for the analysis of the pore dimensions of ion channel structural models. , 1996, Journal of molecular graphics.

[19]  Shin-Ho Chung,et al.  Continuum electrostatics fails to describe ion permeation in the gramicidin channel. , 2002, Biophysical journal.

[20]  A. Warshel,et al.  What are the dielectric “constants” of proteins and how to validate electrostatic models? , 2001, Proteins.

[21]  M. M. Marino,et al.  Ab initio study of hydrogen adsorption on Be (0001) , 1991 .

[22]  E. Perozo,et al.  pH-dependent gating in the Streptomyces lividans K+ channel. , 1998, Biochemistry.

[23]  C. Miller,et al.  KcsA: it's a potassium channel. , 2001, The Journal of general physiology.

[24]  A. Warshel,et al.  Simulations of ion current in realistic models of ion channels: The KcsA potassium channel , 2002, Proteins.

[25]  Shin-Ho Chung,et al.  Permeation of ions across the potassium channel: Brownian dynamics studies. , 1999, Biophysical journal.

[26]  A. Warshel,et al.  Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center , 1999, Proteins.

[27]  A. Warshel,et al.  The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. , 1998, Biophysical journal.

[28]  H. Sullivan Ionic Channels of Excitable Membranes, 2nd Ed. , 1992, Neurology.

[29]  G. R. Smith,et al.  Effective diffusion coefficients of K+ and Cl- ions in ion channel models. , 1999, Biophysical chemistry.

[30]  Alistair P. Rendell,et al.  The potassium channel: Structure, selectivity and diffusion , 2000 .

[31]  M. Tissandier,et al.  The Proton's Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster-Ion Solvation Data , 1998 .

[32]  R. Keynes The ionic channels in excitable membranes. , 1975, Ciba Foundation symposium.

[33]  R. Latorre,et al.  Conduction and selectivity in potassium channels , 2005, The Journal of Membrane Biology.

[34]  Arieh Warshel,et al.  Computer Modeling of Chemical Reactions in Enzymes and Solutions , 1991 .

[35]  M. Sansom,et al.  Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations. , 2001, Biochimica et biophysica acta.

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

[37]  Arieh Warshel,et al.  Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs , 1993, J. Comput. Chem..

[38]  W. Im,et al.  Ion channels, permeation, and electrostatics: insight into the function of KcsA. , 2000, Biochemistry.

[39]  Peter C. Jordan Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study. , 1990, Biophysical journal.

[40]  E. M.,et al.  Statistical Mechanics , 2021, Manual for Theoretical Chemistry.

[41]  A. Warshel,et al.  Electrostatic effects in macromolecules: fundamental concepts and practical modeling. , 1998, Current opinion in structural biology.

[42]  Richard Horn,et al.  Ionic selectivity revisited: The role of kinetic and equilibrium processes in ion permeation through channels , 2005, The Journal of Membrane Biology.

[43]  J. Åqvist,et al.  Ion-water interaction potentials derived from free energy perturbation simulations , 1990 .

[44]  Christopher Miller See potassium run , 2001, Nature.

[45]  Roderick MacKinnon,et al.  Energetic optimization of ion conduction rate by the K+ selectivity filter , 2001, Nature.

[46]  K. Schulten,et al.  Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations , 1999 .

[47]  E. Perozo,et al.  Structural rearrangements underlying K+-channel activation gating. , 1999, Science.

[48]  V. Luzhkov,et al.  K(+)/Na(+) selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations. , 2001, Biochimica et biophysica acta.