Dynamics of Protein Folding in the Space of Experimentally Measured Variables: Turbulence Phenomena
S. F. Chekmarev1,2
1Kutateladze Institute of Thermophysics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
2Novosibirsk National Research State University, Novosibirsk, 630090, Russia
Keywords: динамика укладки белков, молекулярная динамика, ферстеровский резонансный перенос энергии, потоки вероятностей переходов, турбулентность, структурные функции, protein folding, molecular dynamics, Forster resonance energy transfer, probability transition flows, turbulence, structure functions
Abstract
The process of folding of villin subdomain HP-35 has been studied using the method of molecular dynamics. To characterize protein conformations, two variables are introduced which correspond to the distances between fluorophores in experiments on protein folding with the Forster resonance energy. The simulation results show that the flow field of the probabilities of transitions between protein states is filled with eddies. It has been found that in contrast to the previously studied cases of hydrodynamic turbulence and turbulence in protein folding in the three-dimensional conformational space, the structure functions of the flows of various orders depend linearly on the increment in the conformational space. An explanation of this linear dependence based on the -model is proposed, and it is shown that this dependence is not due to the choice of variables for describing the folding process.
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