Biopolymers and cell. 2009; 25 (5): 390 - 397

Semi-quantitative model of the gating of KcsA ion channel. 1. Geometry and energetics of the gating

V. N. Kharkyanen¹, S. O. Yesylevskyy¹, N. M. Berezetskaya¹, C. Boiteux², Ch. Ramseyer²

¹Institute of Physics of National Academy of Sciences of Ukraine
Prospect Nauky 46, Kyiv, Ukraine, 03680

²UMR 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.