title: A contact scoring matrix for qualitative prediction of change in folding of alpha-helices in globular proteins caused by a mutation.
abstract: The atomic pairs in contact for atoms from pairs of amino-acid residues on pairs of helices in a protein database consisting of 48 proteins of known tertiary structure from the Brookhaven Protein Data Bank are searched and counted to construct a primary scoring system. Each score in the primary scoring system is weighted further with the possibility of occurrence of each residue pair in the protein database to give a final scoring matrix. Scores for predicting change in folding of alpha-helices in a mutant protein are calculated by assuming that every pair of helices in the protein can closely interact with each other. It is shown that the change in folding of alpha-helices in several mutant proteins are reflected in both the change of the contact scores and the helix geometry calculated.
authors.affiliation: Department of Life Science, National Tsing Hua University, Taiwan, ROC. thlin@biom.nthu.edu.tw
authors.forename: T H
authors.initials: TH
authors.lastname: Lin
authors.forename: W J
authors.initials: WJ
authors.lastname: Peng
authors.forename: J J
authors.initials: JJ
authors.lastname: Lin
mesh_terms: D016208:Databases, Factual; D005544:Forecasting; D008956:Models, Chemical; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017421:Sequence Analysis / Q000379:methods*