On the theory of folding kinetics for short proteins

Vijay S. Rande, Alexander Yu Grosberg, Toyoichi Tanaka

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Background: Recent data have suggested two principles that are central to the work we describe here. First, proteins are the result of evolutionary 'sequence selection1 to optimize the energy of the native state. Second, the overlap with the native state is a qualitatively suitable reaction coordinate for modeling folding kinetics. The former principle is bolder and better established. Results: Employing only these two principles, we have constructed a nonphenomenological, correlated energy landscape theory that predicts single barrier protein folding kinetics. Moreover, we are able to analytically describe the nature of the free energetic barrier between the denatured and native states of a protein and to detail the nature of folding kinetics for short proteins. Our model predicts Hammond behavior and also describes how mutations can lead to drastic differences in folding times. Conclusions: We find that folding and unfolding kinetics can be characterized by a single thermodynamic parameter and, moreover, that Monte Carlo simulation data on folding and unfolding rates with different temperatures and mutations collapse with this characterization. Our results also delineate a regime in which kinetics may proceed via a single unique nucleus.

    Original languageEnglish (US)
    Pages (from-to)109-114
    Number of pages6
    JournalFolding and Design
    Volume2
    Issue number2
    DOIs
    StatePublished - 1997

    Keywords

    • Correlated energy landscape
    • Folding/unfolding kinetics

    ASJC Scopus subject areas

    • Biochemistry
    • Molecular Medicine

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