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Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank
1Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, China.
Journal of Protein Chemistry
|October 1, 1996
Summary
Researchers analyzed short peptide connections in 240 proteins, identifying 11 common supersecondary structure motifs. These findings reveal limited patterns and conformations, aiding protein structure prediction and folding studies.
Area of Science:
- Structural biology
- Protein structure analysis
Background:
- Short peptides link secondary structures (alpha-helices and beta-strands) in proteins.
- Understanding these connecting loops is crucial for deciphering protein architecture.
Purpose of the Study:
- To classify and characterize short connecting peptides (loops) in proteins.
- To identify commonly occurring supersecondary structure motifs formed by these loops.
Main Methods:
- Analysis of 240 protein structures refined at high resolution (≤0.25 nm).
- Classification of connecting peptides (1-5 residues) into four types: alpha alpha, alpha beta, beta alpha, and beta beta.
- Definition of secondary structures based on hydrogen bonds and conformational angles.
- Identification of 34 supersecondary motif classes occurring ≥5 times, using five residue conformation classes.
Main Results:
- Identified 34 classes of supersecondary motifs.
- Found 11 classes that occur frequently (≥25 times), representing common supersecondary structure motifs.
- Characterized the patterns and conformations of these 11 common motifs.
- Demonstrated that the adopted patterns and conformations are limited.
Conclusions:
- Supersecondary structure motifs formed by short connecting peptides exhibit limited diversity in patterns and conformations.
- These findings are relevant for improving protein structure prediction and comparative modeling.
- Understanding these motifs contributes to insights into the protein folding process.