Abstract
Incorrect folding of proteins in the macromolecular crowding environment in living cells would cause cellular disasters. All cells have developed their structurally and functionally distinct classes of molecular chaperones to help nonnative proteins fold to their native structures, one of which is the most studied GroEL/ES complex. In the present article, large-scale all-atom explicit solvent molecular dynamics (MD) simulations have been carried out on rhodanese folding in a series of chaperonin mutants for 200ns to understand the mechanism therein. In accordance with experimental results, two factors have been identified to play a significant role, the geometrical confinement effect of the folding cavity and the charge effect of the inner surface of the cavity. Our analysis of the properties during simulation suggests that the GroEL/ES complex directly exerts force on the contacting residues of the substrate, thus assists substrate folding.
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