Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid

Abstract

Asparagine and aspartate are known to adopt conformations in the left-handed α-helical region and other partially allowed regions of the Ramachandran plot more readily than any other non-glycyl amino acids. The reason for this preference has not been established. An examination of the local environments of asparagine and aspartic acid in protein structures with a resolution better than 1.5 Å revealed that their side-chain carbonyls are frequently within 4 Å of their own backbone carbonyl or the backbone carbonyl of the previous residue. Calculations using protein structures with a resolution better than 1.8 Å reveal that this close contact occurs in more than 80% of cases. This carbonyl-carbonyl interaction offers an energetic sabilization for the partially allowed conformations of asparagine and aspartic acid with respect to all other non-glycyl amino acids. The non-covalent attractive interactions between the dipoles of two carbonyls has recently been calculated to have an energy comparable to that of a hydrogen bond. The preponderance of asparagine in the left-handed α-helical region, and in general of aspartic acid and asparagine in the partially allowed regions of the Ramachandran plot, may be a consequence of this carbonyl-carbonyl stacking interaction.