Assembly of protein tertiary structures from secondary structures using optimized potentials.
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.
Hoang
Trinh Xuan
TX
The Abdus Salam International Center for Theoretical Physics (ICTP), Trieste, Italy. hoang@sissa.it
Seno
Flavio
F
Banavar
Jayanth R
JR
Cieplak
Marek
M
Maritan
Amos
A
D000596:Amino Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D010940:Plant Proteins / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D012269:Ribosomal Proteins / Q000737:chemistry
D000596:Amino Acids; D010940:Plant Proteins; D011506:Proteins; D012269:Ribosomal Proteins; C024934:crambin protein, Crambe abyssinica