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Assembly of protein tertiary structures from secondary structures using optimized potentials.

Trinh Xuan Hoang·Flavio Seno·Jayanth R Banavar·Marek Cieplak·Amos Maritan
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Abstract

We present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 A in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 A and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 A.

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Amino AcidsHydrogen BondingModels, MolecularMolecular StructurePlant ProteinsProtein FoldingProtein Structure, SecondaryProtein Structure, TertiaryProteinsRibosomal ProteinsEvaluation StudyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, Non-P.H.S.

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Trinh Xuan Hoang, Flavio Seno, Jayanth R Banavar, Marek Cieplak, Amos Maritan. 2003-08-01. Assembly of protein tertiary structures from secondary structures using optimized potentials.. https://doi.org/10.1002/prot.10372

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