Biopolym. Cell. 2009; 25(5):390-397.
Molecular Biophysics
Semi-quantitative model of the gating of KcsA ion channel. 1. Geometry and energetics of the gating
1Kharkyanen V. N., 1Yesylevskyy S. O., 1Berezetskaya N. M., 2Boiteux C., 2Ramseyer Ch.
  1. Institute of Physics, NAS of Ukraine
    46, Prospect Nauki, Kyiv, Ukraine, 03028
  2. UMR CNRS 6624, Faculte des Sciences et Techniques, Universite de Franche-Comte
    16 route de Gray, La Bouloie, 25030 Besancon Cedex, France


The aim of this series of papers is to develop the semi-quantitative theory of the gating of KcsA channel. For this purpose the available structural and electrophysiological data and the results of molecular dynamics simulations were used in the context of the concept of dynamical self-organization. In the first paper we describe the simplified model of the geometry and energetics of the gating process. This work is the first successful attempt of combining the structure and dynamics of a real protein and the general concept of dynamic self-organization.
Keywords: ion channel, KcsA channel, dynamic self-organization, channel gating


[1] Doyle D. A., Cabral J. M., Pfuzner R. A., Kuo A., Gulbis J. M., Cohen S. L., Chait B. T., MacKinnon R. The structure of the potassium channel: molecular basis of K+ conduction and selectivity Science 1998 280, N 3:69–77.
[2] Holyoake J., Domene C., Bright J. N., Sansom M. S. KcsA closed and open: modelling and simulation studies Eur. Biophys. J 2004 33, N 3:238–246.
[3] Liu Y.-S., Sompornpisut P., Perozo E. Structure of the KcsA channel intracellular gate in the open state Nat. Struct. Biol 2001 8, N 10:883–887.
[4] Compoint M., Carloni P., Ramseyer C., Girardet C. Molecular dynamics study of the KcsA channel at 2.0 resolution: stability and concerted motions within the pore Biochim. et Biophys. Acta 2004 1661, N 1:26–39.
[5] Compoint M., Picaud F., Ramseyer C., Girardet C. Targeted molecular dynamics of an open-state KcsA channel J. Chem. Phys 2005 122, N 13:134707.
[6] Mashl R. J., Tang Y., Schnitzer J., Jakobsson E. Hierarchical approach to predicting permeation in ion channels Biophys. J 2001 81, N 5:2473–2483.
[7] Zhou Y., Moralis-Cabral J. H., Kaufman A., MacKinnon R. Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 resolution Nature 2001 414, N 6859:43–48.
[8] Yesylevskyy S. O., Kharkyanen V. N. Quasi-particles in the selectivity filter can explain permeation in a channel with multiple occupancy Phys. Chem. Chem. Phys 2004 N 6:3111–3122.
[9] Chinarov V. A., Gaididei Y. B., Kharkyanen V. N., Sit'ko S. P. Ion pores in biological membranes as self-organizing bistable systems Phys. Rev. A 1992 46, N 8:5232–5241.
[10] Christophorov L. N., Holzwarth A. R., Kharkyanen V. N., van Mourik F. Structure-function self-organization in nonequilibrium macromolecular systems Chem. Phys 2000 256, N 1:45–60.
[11] Yesylevskyy S. O., Kharkyanen V. N. Barrier-less knock-on conduction in ion channels: peculiarity or general mechanism? Chem. Phys 2005 312, N 1–3:127–133.
[12] Case D. A., Pearlman D. A., Caldwell J. W., Cheatham III T. E., Ross W. S., Simmerling C. L., Darden T. A., Merz K. M., Stanton R. V., Cheng A. L., Vincent J. J., Crowley M., Tsui V., Radmer R. J., Duan Y., Pitera J., Massova I., Seibel G. L., Singh U. C., Weiner P. K.,Kollman P. A. AMBER6 San Francisco: Univ. California press, 1999.