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Universality classes in folding times of proteins.

ABSTRACT: Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes that are correlated with the types of structure: the alpha-, alpha-beta-, and beta- proteins have the scaling exponents of approximately 1.7, 2.5, and 3.2, respectively. The three classes merge into one when the contact range is truncated at a reasonable value. We elucidate the role of the potential associated with the chirality of a protein.

SUBMITTER: Cieplak M

PROVIDER: S-EPMC1302628 | biostudies-literature | 2003 Jan

REPOSITORIES: biostudies-literature

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Universality classes in folding times of proteins.

Cieplak Marek M Hoang Trinh Xuan TX

Biophysical journal 20030101 1

Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes that are correlated with the types of structure: the alpha-, alpha-beta-, ...[more]

PMID: 12524300

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