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Protein structural homology: a metric approach
International Journal of Peptide and Protein Research
|October 1, 1986
Summary
Protein structure similarity can be found by analyzing virtual bonds between C alpha atoms. This method uses a sequence alignment algorithm to compare protein folds, detecting similarities of 7 or more residues.
Area of Science:
- Structural biology
- Bioinformatics
Background:
- Protein flexibility arises from rotational freedom around main chain bonds involving C alpha atoms.
- The three-dimensional structure of proteins, or their fold, is determined by the arrangement of these bonds.
Purpose of the Study:
- To present a novel method for comparing protein structures.
- To utilize sequence alignment algorithms for structural comparison.
Main Methods:
- Representing protein folds using virtual bonds connecting consecutive C alpha atoms.
- Defining protein folds by the sequence of virtual torsion and bond angles.
- Applying the Needleman & Wünsch algorithm, originally for amino acid sequence comparison, to these virtual bond representations.
Main Results:
- The method successfully represents and compares protein folds based on virtual bond geometry.
- The approach is capable of detecting structural similarities spanning 7 or more residues.
- Illustrative examples demonstrate the method's efficacy.
Conclusions:
- Comparing sequences of virtual bond angles is a viable method for assessing protein structural similarity.
- This bioinformatics approach offers a new perspective on protein structure analysis and comparison.