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Pi-turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence
1Department of Physics, Indian Institute of Science, Bangalore, India.
Summary
The study identifies two new types of protein structures called pi alpha L-turns and pi alpha R-turns. These findings offer insights into protein folding and design.
Area of Science:
- Protein structure and conformation analysis
- Structural bioinformatics
- Molecular biology
Background:
- The i + 5-->i hydrogen bonded turn conformation (pi-turn) is often found at helix C-termini and considered a helix termination signal.
- Previous studies focused on pi-turns specifically at helix C-termini.
Purpose of the Study:
- To analyze the occurrence and characteristics of pi-turns at any general position within protein structures.
- To identify novel pi-turn conformations and their sequence preferences.
Main Methods:
- Analysis of 228 protein crystal structures (resolution < 2.5 A).
- Identification and classification of pi-turn conformations based on the (i+4)th residue's conformation (alpha L, alpha R, or beta).
Main Results:
- Identified 486 pi-turns, classifying them into pi alpha L-turns (367 instances) and pi alpha R-turns (111 instances).
- Discovered pi alpha R-turns as novel distortions within alpha-helices, not just at termini.
- Characterized distinct amino acid preferences for pi alpha L and pi alpha R-turns, including preferences for Pro, Gly, Asn, His, Tyr, and avoidance of Ala in specific positions.
- Observed four pi alpha L'-turns (mirror images) and four pi beta-turns within beta-hairpin bends.
Conclusions:
- Pi-turns are more diverse than previously thought, with pi alpha R-turns representing a novel structural motif in alpha-helices.
- Amino acid preferences differ significantly between pi alpha L and pi alpha R-turns, providing sequence-based identification clues.
- Findings are crucial for protein structure prediction, modeling, and de novo protein design.