Master equation approach to protein folding and kinetic traps
Marek Cieplak, Malte Henkel, Jan Karbowski, Jayanth R. Banavar
Abstract
The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is governed by the longest relaxation time. For good folders, significant kinetic traps appear in the folding funnel whereas for bad folders, the traps also occur in non-native energy valleys.
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