On the role of conformational geometry in protein folding

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

    Research output: Contribution to journalArticle

    Abstract

    Using a lattice model of protein folding, we find that once certain native contacts have been formed, folding to the native state is inevitable, even if the only energetic bias in the system is nonspecific, homopolymeric attraction to a collapsed state. These conformations can be quite geometrically unrelated to the native state (with as low as only 53% of the native contacts formed). We demonstrate these results by examining the Monte Carlo kinetics of both heteropolymers under Go interactions and homopolymers, with the folding of both types of polymers to the native state of the heteropolymer. Although we only consider a 48-mer lattice model, our findings shed light on the effects of geometrical restrictions, including those of chain connectivity and steric excluded volume, on protein folding. These effects play a complementary role to that of the rugged energy landscape. In addition, the results of this work can aid in the interpretation of experiments and computer simulations of protein folding performed at elevated temperatures.

    Original languageEnglish (US)
    Pages (from-to)10375-10380
    Number of pages6
    JournalJournal of Chemical Physics
    Volume111
    Issue number22
    StatePublished - Dec 8 1999

    Fingerprint

    Protein folding
    folding
    proteins
    Geometry
    geometry
    Homopolymerization
    Conformations
    Polymers
    Kinetics
    Computer simulation
    attraction
    constrictions
    computerized simulation
    Experiments
    kinetics
    polymers
    Temperature
    simulation
    interactions

    ASJC Scopus subject areas

    • Atomic and Molecular Physics, and Optics

    Cite this

    Du, R., Pande, V. S., Grosberg, A. Y., Tanaka, T., & Shakhnovich, E. (1999). On the role of conformational geometry in protein folding. Journal of Chemical Physics, 111(22), 10375-10380.

    On the role of conformational geometry in protein folding. / Du, Rose; Pande, Vijay S.; Grosberg, Alexander Yu; Tanaka, Toyoichi; Shakhnovich, Eugene.

    In: Journal of Chemical Physics, Vol. 111, No. 22, 08.12.1999, p. 10375-10380.

    Research output: Contribution to journalArticle

    Du, R, Pande, VS, Grosberg, AY, Tanaka, T & Shakhnovich, E 1999, 'On the role of conformational geometry in protein folding', Journal of Chemical Physics, vol. 111, no. 22, pp. 10375-10380.
    Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich E. On the role of conformational geometry in protein folding. Journal of Chemical Physics. 1999 Dec 8;111(22):10375-10380.
    Du, Rose ; Pande, Vijay S. ; Grosberg, Alexander Yu ; Tanaka, Toyoichi ; Shakhnovich, Eugene. / On the role of conformational geometry in protein folding. In: Journal of Chemical Physics. 1999 ; Vol. 111, No. 22. pp. 10375-10380.
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