Protein folding pathways and state transitions described by classical equations of motion of an elastic network model.

ABSTRACT: Protein topology defined by the matrix of residue contacts has proved to be a fruitful basis for the study of protein dynamics. The widely implemented coarse-grained elastic network model of backbone fluctuations has been used to describe crystallographic temperature factors, allosteric couplings, and some aspects of the folding pathway. In the present study, we develop a model of protein dynamics based on the classical equations of motion of a damped network model (DNM) that describes the folding path from a completely unfolded state to the native conformation through a single-well potential derived purely from the native conformation. The kinetic energy gained through the collapse of the protein chain is dissipated through a friction term in the equations of motion that models the water

SUBMITTER: Williams G 

PROVIDER: S-EPMC3009412 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature