Protein folding by zipping and assembly.

Protein folding by zipping and assembly. Research Abstract Details 

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Protein folding by zipping and assembly. Abstract Text:

S Banu Ozkan,G Albert Wu,John D Chodera,Ken A Dill,

How do proteins fold so quickly? Some denatured proteins fold to their native structures in only microseconds, on average, implying that there is a folding "mechanism," i.e., a particular set of events by which the protein short-circuits a broader conformational search. Predicting protein structures using atomically detailed physical models is currently challenging. The most definitive proof of a putative folding mechanism would be whether it speeds up protein structure prediction in physical models. In the zipping and assembly (ZA) mechanism, local structuring happens first at independent sites along the chain, then those structures either grow (zip) or coalescence (assemble) with other structures. Here, we apply the ZA search mechanism to protein native structure prediction by using the AMBER96 force field with a generalized Born/surface area implicit solvent model and sampling by replica exchange molecular dynamics. Starting from open denatured conformations, our algorithm, called the ZA method, converges to an average of 2.2 A from the Protein Data Bank native structures of eight of nine proteins that we tested, which ranged from 25 to 73 aa in length. In addition, experimental Phi values, where available on these proteins, are consistent with the predicted routes. We conclude that ZA is a viable model for how proteins physically fold. The present work also shows that physics-based force fields are quite good and that physics-based protein structure prediction may be practical, at least for some small proteins.

Protein folding by zipping and assembly. Publishing Authors By Initials

SB Ozkan,GA Wu,JD Chodera,KA Dill,

For similar proteins research abstracts see: proteins research

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Protein folding by zipping and assembly. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Proceedings of the National Academy of Sciences of

VOLUME: 104

Page Numbers: 11987-92

Journal Abbreviation: Proc. Natl. Acad. Sci. U.S.A.

ISSN: 0027-8424

DAY: 9

MONTH: 07

YEAR: 2007

Protein folding by zipping and assembly. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 7505876

Protein folding by zipping and assembly. Keywords Mesh Terms:

KEYWORDS: Proteins

MESH TERMS: metabolism

Chemical & Substance for Abstract: Protein folding by zipping and assembly. Information

Substance Name: Proteins

Registry Number: 0

Grant and Affiliation Information for Protein folding by zipping and assembly.

AFFILIATION: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM34993

ACRONYM: GM

MEDLINETA: Proc Natl Acad Sci U S A

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