On the transition coordinate for protein folding

Rose Du, Vijay S. Pande, Alexander Yu Grosberg, Toyoichi Tanaka, Eugene S. Shakhnovich

    Research output: Contribution to journalArticlepeer-review


    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 present 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.

    Original languageEnglish (US)
    Pages (from-to)334-350
    Number of pages17
    JournalJournal of Chemical Physics
    Issue number1
    StatePublished - Jan 1 1998

    ASJC Scopus subject areas

    • General Physics and Astronomy
    • Physical and Theoretical Chemistry


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