PPII helices have been found in a large number of proteins using protein crystal structure database analysis, and experimental methods (CD, X-ray crystallography, NMR).
Often found on the surface of globular proteins, being a flexible, hydrophilic structural element, with only few main-chain hydrogen bonds to other parts of the protein, and play an important role in protein-protein interaction (with SH3 domains in intercellular cohesion or enzyme activation), serve (followed by a turn) as a site for proline hydroxilation, linking other structural elements in domain formation.
Here is a short list of a few peptides, proteins or protein families which have this structural element:
Proteins which need PPII helix as substrate:
SH3 domains consist of approximately 60 amino acids, and have a sequence similarity. These domains have the same overall topology: two three stranded antiparallel beta-sheets packed against each other, with two loops. SH3 domains bind proline rich sequences, but have a preference to arginine and leucine residues too. Two classes of substrates were identified : Class I has Arg-x-q-Pro-x-q-Pro, Class II has q-Pro-x-q-Pro-x-Arg (x: any residue; q: any hydrophobic residue, often Pro) sequences and both is in the PPII conformation. They bind in reverse orientation (it depends on at which end is Arg holding a positive charge, which is also needed for the interaction).
by Zoltan Szabo , 1997