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

Feng Ding; Sergey V. Buldyrev; Nikolay V. Dokholyan

doi:10.1529/biophysj.104.046375

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

Feng Ding·Sergey V. Buldyrev·Nikolay V. Dokholyan

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Abstract

We develop a coarse-grained protein model with a simplified amino acid interaction potential. 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 2angstrom backbone root-mean-square distance (RMSD) from the corresponding NMR structures. The minimum RMSD of Trp-cage conformations in the simulation can be smaller than 1.00angstrom. Our findings suggest that, at least for the case of Trp-cage, a detailed all-atom protein model with a physical molecular mechanics force field is not necessary to reach the native state of a protein. Our results also suggest that the success folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulations studies may be mainly due to the special stabilizing features specific to this miniprotein.

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physics.bio-ph cond-mat.other cond-mat.soft cond-mat.stat-mech physics.comp-ph q-bio.OT

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Feng Ding, Sergey V. Buldyrev, Nikolay V. Dokholyan. 2004-05-25. Folding Trp-cage to NMR resolution native structure using a coarse-grained model. https://doi.org/10.1529/biophysj.104.046375

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