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Protein folding dynamics via quantification of kinematic energy landscape

Sëma Kachalo·Hsiao-Mei Lu·Jie Liang
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Abstract

We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802,075 conformations of 16-mers over 7-orders of time span. We find that (i) folding rates of these protein-like sequences of same length can differ by 4-orders of magnitude, (ii) folding rates of sequences of the same conformation can differ by a factor of 190, and (iii) parameters of the native structures, designability, and thermodynamic properties are weak predictors of the folding rates, rather, basin analysis of the kinematic energy landscape defined by the moves can provide excellent account of the observed folding rates.

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Sëma Kachalo, Hsiao-Mei Lu, Jie Liang. 2006-01-12. Protein folding dynamics via quantification of kinematic energy landscape. https://doi.org/10.1103/physrevlett.96.058106

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