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Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.

ABSTRACT: We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2-angstroms backbone root-mean-square distance from the corresponding NMR structures. The minimum root-mean-square distance of Trp-cage conformations in simulations can be <1 angstroms. Our findings suggest that, at least in the case of Trp-cage, a detailed all-atom protein model with a molecular mechanics force field is not necessary to reach the native state of a protein. Our results also suggest that the success of folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulation studies may be mainly due to the special stabilizing features specific to this miniprotein.

SUBMITTER: Ding F

PROVIDER: S-EPMC1304993 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature

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Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model.

Ding Feng F Buldyrev Sergey V SV Dokholyan Nikolay V NV

Biophysical journal 20041108 1

We develop a coarse-grained protein model with a simplified amino acid interaction potential. Using this model, we perform discrete molecular dynamics folding simulations of a small 20-residue protein--Trp-cage--from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2-angstroms backbone root-mean-square distance from the corresponding NMR structures. The minimum root-mean-square distance of Trp-cage conformations in simulat ...[more]

PMID: 15533926

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