Novosibirsk, Russia, May, 30 – June, 4, 2011

International Conference
"Modern Problems of Applied Mathematics and Mechanics: Theory, Experiment and Applications", devoted to the 90th anniversary of professor Nikolai N. Yanenko

Chekmarev S.F.   Kalgin I.V.  

Turbulent phenomena in protein folding dynamics

Reporter: Chekmarev S.F.

Protein folding and hydrodynamic turbulence are two long-standing challenges, in molecular biophysics and fluid dynamics, respectively. The theories of these phenomena have been developed independently and used different formalisms. Here we show that the protein folding flows can be surprisingly similar to turbulent fluid flows. Studying a benchmark model protein (a SH3 domain), we have found that the flows for the slow folding trajectories of the protein have many properties of turbulent flows of a fluid. The flows have fractal nature and are filled with 3D eddies; the latter contain strange attractors, at which the tracer flow paths behave as saddle trajectories. Two regions of the space increment have been observed, in which the flux variations are self-similar with the scaling exponent h = 1/3, in surprising agreement with the Kolmogorov inertial range theory of turbulence. In one region, the cascade of protein rearrangements is directed from larger to smaller scales (protein net folding), and in the other, it is opposite directed (net unfolding). Based on the results of our study, we infer, and support this inference by simulations, that the origin of the similarity between the protein folding and turbulent motion of a fluid is in a cascade mechanism of structural transformations in the systems that underlies these phenomena.

Abstracts file: kalgin_chekmarev.doc
Full text file: kalgin_chekmarev.pdf

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