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
    StatePublished - 1995

    Fingerprint

    Protein folding
    folding
    Conformations
    proteins
    Mean field theory
    interactions
    Freezing
    Ground state
    Monomers
    frustration
    matrices
    replicas
    freezing
    energy
    monomers
    Proteins
    ground state

    ASJC Scopus subject areas

    • Atomic and Molecular Physics, and Optics

    Cite this

    Pande, V. S., Grosberg, A. Y., & Tanaka, T. (1995). How accurate must potentials be for successful modeling of protein folding? The Journal of chemical physics, 103(21), 9482-9491.

    How accurate must potentials be for successful modeling of protein folding? / Pande, Vijay S.; Grosberg, Alexander Yu; Tanaka, Toyoichi.

    In: The Journal of chemical physics, Vol. 103, No. 21, 1995, p. 9482-9491.

    Research output: Contribution to journalArticle

    Pande, VS, Grosberg, AY & Tanaka, T 1995, 'How accurate must potentials be for successful modeling of protein folding?', The Journal of chemical physics, vol. 103, no. 21, pp. 9482-9491.
    Pande, Vijay S. ; Grosberg, Alexander Yu ; Tanaka, Toyoichi. / How accurate must potentials be for successful modeling of protein folding?. In: The Journal of chemical physics. 1995 ; Vol. 103, No. 21. pp. 9482-9491.
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