A contact scoring matrix for qualitative prediction of change in folding of alpha-helices in globular proteins caused by a mutation.
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.
Lin
T H
TH
Department of Life Science, National Tsing Hua University, Taiwan, ROC. thlin@biom.nthu.edu.tw
Peng
W J
WJ
Lin
J J
JJ
D016208:Databases, Factual; D005544:Forecasting; D008956:Models, Chemical; D009154:Mutation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017421:Sequence Analysis / Q000379:methods*