Characterizing the Rate-Limiting Step of Trp-Cage Folding by All-Atom Molecular Dynamics Simulations

Abstract

In this study, the detailed mechanisms of the rapid-folding Trp-cage mini-protein were investigated by extensive all-atom molecular dynamics simulations of both wild-type and mutant proteins using a recently developed point-charge force field within the AMBER simulation package and the generalized Born treatment of solvation. Among the 77 100-ns simulations performed on the wild-type protein, 5 of the simulation trajectories yielded structures with main-chain RMSDs of 1.0−2.0 Å from the native NMR structure. A gradual reduction in the value of the main-chain RMSD distribution was observed during the simulations, which is consistent with the folding funnel theory. The folding time of ∼3 μs based on native tertiary contacts is in reasonable agreement with an experimental value of ∼4 μs. Detailed analysis suggests that packing of the structurally important Trp25 side chain is involved in the rate-limiting step and unfolding of the misfolded states and overcoming the additional entropic barrier also contributed to the rate-limiting steps. This is reinforced by the faster folding rate of the W25F mutant. Two putative folding pathways were observed from the simulations, and their folding rates differed by about 200-fold, leading to a 3.2 kcal/mol folding free energy barrier difference. Of this, approximately 2.2 kcal/mol was due to unfolding of the misfolded states, and about 1.0 kcal/mol was due to overcoming the entropic cost to move Trp25 side chain into the native orientation. Although formation of the main-chain contacts was not the rate-limiting step, we observed a hierarchical process in which the short-range native contacts formed faster than the long-range ones. These observations are consistent with the contact-order theory.