ppII

PPII stands for polyproline II helix, a type of protein secondary structure that commonly occurs in proline-rich regions of proteins. It is an extended, left-handed helix with three residues per turn and a rise per residue of about 3.0 Å, giving a pitch of roughly 9 Å. The backbone dihedral angles are typically around phi minus 75 degrees and psi around 145 degrees. Although proline favors this geometry, PPII can be adopted by sequences that include residues other than proline. Unlike canonical alpha helices and beta sheets, PPII is not stabilized primarily by a network of regular intramolecular hydrogen bonds along the backbone; its conformation is driven by the intrinsic conformational preferences of the amino acids and solvent interactions.

Functional and structural role: PPII is often found in intrinsically disordered regions and in proline-rich motifs that mediate protein–protein interactions. Segments adopting a PPII geometry can serve as binding motifs for interaction domains such as SH3, WW, and profilin, enabling signaling, cytoskeletal regulation, and other cellular processes. The geometry of PPII provides a recognizable, extended surface that can interact with partner proteins and nucleic acids in a manner distinct from more compact secondary structures.

Detection and relevance: PPII can be characterized by experimental techniques such as nuclear magnetic resonance spectroscopy and circular dichroism, as well as by computational prediction based on sequence context and structural data. It contributes to the diversity of protein conformations and is an important consideration in studies of protein folding, dynamics, and interactions.