162 Dominant forces in protein folding

Dominant forces in protein folding.

T e purpose of this review is to assess the nature and magnitudes of the dominant forces in protein folding. Since proteins are only marginally stable at room temperature,’ no type of molecular interaction is unimportant, and even small interactions can contribute significantly (positively or negatively) to stability (Alber, 1989a,b; Matthews, 1987a,b). However, the present review aims to ident...

Dominant pathways in protein folding.

We present a method to investigate the kinetics of protein folding and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. By writing the solution of the Fokker-Planck equation in terms of a path integral, we derive a Hamilton-Jacobi variational principle from which we are able to compute the most probable pathway of folding. The method is appl...

Stochastic dynamics and dominant protein folding pathways

Quantitative protein dynamics from dominant folding pathways.

We develop a theoretical approach to the protein-folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps are removed, and simulating the entire reaction in atomistic details using existing computers becomes feasible. We discuss how to determine the most probable folding pathway, iden...

Protein folding under mechanical forces: a physiological view.

Mechanical forces regulate the function of numerous proteins relevant to physiology. The functions and folding of proteins have been under scrutiny for decades, but it was not until recently that mechanical forces have been considered. Here, we review different techniques for studying protein folding, highlighting their physiological significance.