Sub-diffusive dynamics of protein folding and protein folding under confinement.

摘要

Conformational dynamics is of fundamental importance for the folding and the function of proteins. Structural changes occur over a wide range of time scales, and folding itself is the slowest, long-time process, Rates vary with the extent of folding, as measured by an order parameter, Q.;The dynamics of the order parameter is studied in detail using a coarse-grained model of the protein and classical molecular dynamics simulations. A description of folding is attempted in terms of the Smoluchowski equation (SE), based on a picture of diffusion of the order parameter under the influence of a thermodynamic force. A new method is developed to obtain the order parameter dependent diffusion coefficient, D(Q), from short-time simulations. D(Q) is shown to change significantly as the protein folds. It is found that folding obeys neither the one-dimensional SE nor a normal-diffusion continuous time random walk (CTRW), because the order parameter follows sub-diffusion. The anomalous nature of the order parameter dynamics is incorporated into the ordinary SE based on the idea that the folding pathways have fractal character. Obtaining the free energy from the statistical temperature molecular dynamics (STMD) enhanced sampling algorithm and D(Q) from short-time simulations, mean first passage times of folding (MFPT) calculated from our fractal SE theory are in quantitative agreement with simulated long-time folding dynamics.;Protein folding occurs in a crowded and heterogeneous environment inside the cell. Interactions of the protein with other cellular biomolecules may hamper the folding process. Chaperones are known to help a large fraction of newly synthesized proteins in their proper folding. To understand the mechanism of chaperonin-mediated protein folding, the thermodynamics and kinetics of a frustrated model protein are studied inside a chaperonin cavity modeled as a sphere of tunable hydrophobicity. Using the inherent structure (IS) approach, we found that folding is preferred over misfolding inside a slightly hydrophobic chaperonin cavity. The occupation probabilities of the misfolded states are entropically suppressed due to smaller associated configurational volumes.