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A structure-based method for derivation of all-atom potentials for protein folding.

ABSTRACT: A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a C(alpha) distance rms from the native structure of less than 2 A. Similar results were obtained for the hairpin and helices by using different potentials. We derived potentials for several different proteins and found a high correlation between the derived parameters, suggesting that a potential of this form eventually could be found that folds multiple, unrelated proteins at the atomic level of detail.

SUBMITTER: Kussell E

PROVIDER: S-EPMC122771 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature

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A structure-based method for derivation of all-atom potentials for protein folding.

Kussell Edo E Shimada Jun J Shakhnovich Eugene I EI

Proceedings of the National Academy of Sciences of the United States of America 20020409 8

A method for deriving all-atom protein folding potentials is presented and tested on a three-helix bundle protein, as well as on hairpin and helical sequences. The potentials obtained are composed of a contact term between pairs of atoms, and a local density term for each atom, mimicking solvent exposure preferences. Using this potential in an all-atom protein folding simulation, we repeatedly folded the three-helix bundle, with the lowest energy conformations having a C(alpha) distance rms from ...[more]

PMID: 11943859

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