Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts

Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal COmiddotmiddotmiddotCO interactions that extend over the whole PPII helical region. Interestingly, the COmiddotmiddotmiddotCO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger COmiddotmiddotmiddotCO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (-0.9 kcalmiddotmol-1) nO -> Sigma*C alpha-C beta interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (Sigma*) of their C alpha-C beta bonds. As the nO -> Sigma*C alpha-C beta interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual nN(amide) -> Sigma*C-N interaction (-0.3 kcalmiddotmol-1) was observed between the peptidic nitrogen lone pair (nN) and the antibonding orbital (Sigma*C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.