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Predicting helical segments in proteins by a helix‐coil transition theory with parameters derived from a structural database of proteins
Author(s) -
Misra Gauri P.,
Wong Chung F.
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199707)28:3<344::aid-prot5>3.0.co;2-c
Subject(s) - helix (gastropod) , protein folding , protein structure , protein secondary structure , sequence (biology) , folding (dsp implementation) , protein structure prediction , protein design , electromagnetic coil , computer science , chemistry , crystallography , physics , biology , biochemistry , engineering , structural engineering , ecology , quantum mechanics , snail
A novel helix‐coil transition theory has been developed. This new theory contains more types of interactions than similar theories developed earlier. The parameters of the models were obtained from a database of 351 nonhomologous proteins. No manual adjustment of the parameters was performed. The interaction parameters obtained in this manner were found to be physically meaningful, consistent with current understanding of helix stabilizing/destabilizing interactions. Novel insights into helix stabilizing/destabilizing interactions have also emerged from this analysis. The theory developed here worked well in sorting out helical residues from amino acid sequences. If the theory was forced to make prediction on every residue of a given amino acid sequence, its performance was the best among ten other secondary structural prediction algorithms in distinguishing helical residues from nonhelical ones. The theory worked even better if one only required it to make prediction on residues that were “predictable” (identifiable by the theory); >90% predictive reliability could be achieved. The helical residues or segments identified by the helix‐coil transition theory can be used as secondary structural contraints to speed up the prediction of the three‐dimensional structure of a protein by reducing the dimension of a computational protein folding problem. Possible further improvements of this helix‐coil transition theory are also discussed. Proteins 28:344–359, 1997. © 1997 Wiley‐Liss, Inc.