Biology – Quantitative Biology – Biomolecules
Scientific paper
2005-09-07
Biology
Quantitative Biology
Biomolecules
submitted to PNAS 2005-03-16
Scientific paper
10.1073/pnas.0502181102
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systematically applied and consistently produced structure predictions of approximately 3 Angstroms without any knowledge of the native state. To measure and understand the significance of the results, extensive control simulations were conducted. Graph theoretic analysis provides a means for systematically identifying the native fold and provides physical insight, conceptually linking the results to modern theoretical views of protein folding. In addition to presenting a method for prediction of structure and folding mechanism, our model suggests that a accurate all-atom amino acid representation coupled with a physically reasonable atomic interaction potential (that does not require optimization to the test set) and hydrogen bonding are essential features for a realistic protein model.
Deeds Eric J.
Hubner Isaac A.
Shakhnovich Eugene I.
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