Stabilization of local structures by π-CH and aromatic-backbone amide interactions involving prolyl and aromatic residues

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-BN) and CHn of aliphatic groups (pi -CH) are known to form local structures and to stabilize secondary structure in peptides and proteins. To investigate the existence of these interactions and to explore their possible role in constraining the structures of Pro-Xaa and Xaa-Pro fragments in proteins, a database search was performed in a nonredundant set of proteins from the Brookheaven Protein Data Bank for 7 pi -CH and Ar-HN interactions in Pro-Xaa and Xaa-Pro fragments (where Xaa is either Phe, Tyr or Trp). In Xaa-Pro fragments, the percentage of pi -CH interactions and Ar-HN interactions, respectively, was 20.6 and 3.2%, in Pro-Xaa fragments 26.8, 8.6 and 4.0% of the Pro-Xaa fragments contained both interactions, while no Xaa-Pro fragments had both. The protein fragments containing Ar-HN and/or pi -CH interactions were clustered on the basis of similarity of selected torsion angles. The clustering resulted in well defined clusters. Thus, pi -CH and Ar(i)-HN(i) interactions were able to constrain individual conformations of the Pro-Xaa and Xaa-Pro fragments. These local structures were found to be independent of the secondary structure of the polypeptide chains in which the fragments were found.