On the transition coordinate for protein folding

Rose Du, Vijay S. Pande, Alexander Yu. Grosberg, Toyoichi Tanaka, Eugene S. Shakhnovich
1998 Journal of Chemical Physics  
To understand the kinetics of protein folding, we introduce the concept of a "transition coordinate" which is defined to be the coordinate along which the system progresses most slowly. As a practical implementation of this concept, we define the transmission coefficient for any conformation to be the probability for a chain with the given conformation to fold before it unfolds. Since the transmission coefficient can serve as the best possible measure of kinetic distance for a system, we
more » ... two methods by which we can determine how closely any parameter of the system approximates the transmission coefficient. As we determine that the transmission coefficient for a short-chain heteropolymer system is dominated by entropic factors, we have chosen to illustrate the methods mentioned by applying them to geometrical properties of the system such as the number of native contacts and the looplength distribution. We find that these coordinates are not good approximations of the transmission coefficient and therefore, cannot adequately describe the kinetics of protein folding.
doi:10.1063/1.475393 fatcat:rfnex36gxzdvpmr5oqnqkmtbwq