Yesylevskyy S. Stochastic collective effects in the functioning of the ion channels and the process of protein folding

Dissertation is devoted to theoretical investigation of stochastic collective effects in the processes of ion translocation and folding General model of ion conduction in the multi-ion channels, which is based on the concept of quasi-ions, is developed. The theory is applied to the model of KcsA channel. The concept of the ion-conformational interaction is generalized to include the case of the multi-ion channels. It is shown, that barrier-less knock-on conduction can be considered as universal mechanism of permeation in the multi-ion channels. The novel method of protein folding simulation on lattice, called CMC algorithm, is developed. CMC describes stochastic collective moves, which occurs in the course of folding, correctly. The method is based on the structure-dependent micro-irreversible dynamics of clusters. It is shown that stochastic collective dynamics plays a crucial role in such dissimilar systems as the ion channel and the folding protein chains. This allows to hypothesize that stochasticcollective dynamics is a universal mechanism, which ensures functioning and self-assemblance of protein macromolecules.