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A novel fluctuational approach to analysis of the permeation in ion channels

Molecular dynamics simulations is an important tool for understanding the function-structure relationship in biological macro-molecules. To link different time scales in the simulations and consider rare events in macro-molecules, different techniques introducing constant biasing forces are applied. For potassium KscA ion channel the application of standard biased techniques leads to inconsistent results. A novel fluctuational approach which utilizes the duality of Hamiltonian formalism between the theory of optimal control and the theory of most probable fluctuations is suggested here. The transition of an ion between two sites of the KcsA channel is considered by using the novel approach, and the barrier between the two sites is evaluated. This approach can be applied to other channels, for example to sodium ion channels, but it would require further modifications.