How accurate must potentials be for successful modeling of protein folding?

Vijay S. Pande, Alexander Yu Grosberg, Toyoichi Tanaka

    Research output: Contribution to journalArticle

    Abstract

    Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as "minimal frustration," or "optimal energy," of the desirable target conformation over all possible sequences, such that the "design" of the sequence is governed by the interactions between monomers. With replica mean field theory, we examine the possibility to reconstruct the renaturation, or freezing transition, of the "designed" heteropolymer given the inevitable errors in the determination of interaction energies, that is, the difference between sets (matrices) of interactions governing chain design and conformations, respectively. We find that the possibility of folding to the designed conformation is controlled by the correlations of the elements of the design and renaturation interaction matrices; unlike random heteropolymers, the ground state of designed heteropolymers is sufficiently stable, such that even a substantial error in the interaction energy should still yield correct renaturation.

    Original languageEnglish (US)
    Pages (from-to)9482-9491
    Number of pages10
    JournalThe Journal of Chemical Physics
    Volume103
    Issue number21
    DOIs
    StatePublished - Jan 1 1995

    ASJC Scopus subject areas

    • Physics and Astronomy(all)
    • Physical and Theoretical Chemistry

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