On alpha-helices terminated by glycine. 2. Recognition by sequence patterns.

Area of Science:

• Structural biology
• Bioinformatics
• Computational chemistry

Background:

• Protein secondary structures, particularly alpha-helices, are fundamental to protein folding and function.
• Helix termini exhibit unique structural features and conformational preferences.
• Specific hydrogen bonding patterns, including three-center hydrogen bonds, influence helix stability and conformation.

Purpose of the Study:

• To develop and validate consensus sequence patterns for identifying characteristic helix ends in proteins.
• To investigate the role of glycine and specific torsion angles in helix termination.
• To assess the efficacy of these patterns in analyzing protein structural databases.

Main Methods:

• Construction of consensus sequence patterns based on characteristic helix end conformations.
• Utilizing three-center hydrogen bond patterns and glycine residues with positive phi torsion angles.
• Application of a clustering procedure to identify patterns within the Brookhaven Protein Data Bank (PDB).

Main Results:

• Six consensus sequence patterns were derived, effectively identifying 501 out of 575 known helix ends.
• The identified patterns demonstrated high specificity, with no false positive segments detected.
• Numerous sequence segments with potential helical characteristics, not previously identified by structural criteria, were recognized.

Conclusions:

• Consensus sequence patterns provide a reliable method for identifying specific helix ends in protein structures.
• The prevalence of glycine with a positive phi torsion angle at helix termini is a significant structural feature.
• This approach enhances the detection of helices, including those not readily apparent through traditional structural analysis.