A contact scoring matrix for qualitative prediction of change in folding of alpha-helices in globular proteins caused by a mutation
- Resource Type
- Authors
- Wen-Jiun Peng; Thy-Hou Lin; Jin-Jang Lin
- Source
- Biochimica et biophysica acta. 1337(1)
- Subject
- chemistry.chemical_classification
Protein Folding
Databases, Factual
Globular protein
Mutant
Biophysics
computer.file_format
Protein Data Bank
Biochemistry
Qualitative prediction
Protein tertiary structure
Protein Structure, Secondary
Crystallography
chemistry
Models, Chemical
Structural Biology
Mutant protein
Helix
Mutation
Molecular Biology
computer
Sequence Analysis
Alpha helix
Forecasting
- Language
- ISSN
- 0006-3002
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 α-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 α-helices in several mutant proteins are reflected in both the change of the contact scores and the helix geometry calculated.