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Funnel sculpting for in silico assembly of secondary structure elements of proteins.

ABSTRACT: We present a method for designing a funnel-shaped free-energy surface that reproducibly assembles secondary structure elements of proteins into their native conformations from a random extended configuration. Assuming a priori knowledge of secondary structure, our method can design a funnel-shaped surface for folding of alpha, beta, and alphabeta structures individually. We design energy surfaces that fold up to five unrelated sequences with the same energy parameters. We develop a measure of the foldability of an energy landscape in silico and present an alternative way to view energy landscapes.

SUBMITTER: Fain B

PROVIDER: S-EPMC293046 | biostudies-literature | 2003 Sep

REPOSITORIES: biostudies-literature

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Funnel sculpting for in silico assembly of secondary structure elements of proteins.

Fain Boris B Levitt Michael M

Proceedings of the National Academy of Sciences of the United States of America 20030818 19

We present a method for designing a funnel-shaped free-energy surface that reproducibly assembles secondary structure elements of proteins into their native conformations from a random extended configuration. Assuming a priori knowledge of secondary structure, our method can design a funnel-shaped surface for folding of alpha, beta, and alphabeta structures individually. We design energy surfaces that fold up to five unrelated sequences with the same energy parameters. We develop a measure of th ...[more]

PMID: 12925740

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