Proline/sidechain C–H/O interactions stabilize cis-proline

Abstract

Bioinformatics analysis was conducted on proteins in the PDB to identify local structures that can stabilize the cis-proline conformation. C–H/O interactions were observed between a sidechain oxygen and Pro C–Hα in the cis-proline conformation at Glu–Pro, Asp–Pro, Gln–Pro, Asn–Pro, Ser–Pro, and Thr–Pro sequences. These C–H/O interactions are apparently most stabilizing at Glu–Pro sequences, which have a substantially higher than average frequency of cis-proline (7.1% of all Glu–Pro amide bonds in the PDB). DFT calculations were conducted to understand the bases and geometries of C–H/O interactions in these sequences. Computationally, these residues all exhibit close C–H/O interactions (substantially below the 2.72 Å sum of the van der Waals radii of H and O), with the closest C–H/O interactions observed with the anionic oxygens of Glu and Asp, and with closer interactions for the anionic residues than the neutral carboxamides Gln and Asn. DFT calculations revealed that C–H/O interactions also stabilize cis-proline at phosphoserine–proline and phosphothreonine–proline sequences, with closer C–H/O interactions in the dianionic forms of phosphorylated residues that predominate at physiological pH. These results also provide an explanation for the observed higher activation barrier for amide bond isomerism at phosphoserine–proline and phosphothreonine–proline sequences. Calculations suggested that C–H/O interactions mediated by these residues could also stabilize non-proline cis amide bonds, which are often functionally important when observed.