Structural and functional analyses of PolyProline-II helices in globular proteins

Area of Science:

• Structural biology
• Protein bioinformatics

Background:

• PolyProline-II (PPII) helices are a type of protein secondary structure characterized by specific backbone torsion angles and an extended left-handed helical conformation.
• While less common than alpha-helices and beta-strands, PPII helices are frequently observed in protein structures.

Purpose of the Study:

• To analyze the structural and functional roles of PPII helices using an expanded database.
• To determine amino acid propensities within and around PPII helices.

Main Methods:

• Utilized the ASSP (a method for identifying regular secondary structures using Cα trace) to identify 3597 PPII helices in 3582 protein chains.
• Analyzed the structural characteristics, amino acid composition, and occurrence in conjunction with other secondary structures.

Main Results:

• Identified a significant number of PPII helices, revealing that proline is not essential for their formation (approx. 40% lacked proline).
• Found that aromatic amino acids are generally avoided within PPII helices, while Gly, Asn, and Asp residues are preferred in flanking regions.
• PPII helices range from 3 to 13 residues, with specific average twist and rise values, and frequently act as linkers between alpha-helices and beta-strands.

Conclusions:

• PPII helices are integral to protein three-dimensional structure and are important components of binding motifs.
• Their frequent association with other secondary structures highlights their role as versatile linkers in protein architecture.
• The study provides insights into the formation and properties of PPII helices, expanding our understanding of protein secondary structures.