Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid.
Asparagine and aspartate are known to adopt conformations in the left-handed alpha-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 A revealed that their side-chain carbonyls are frequently within 4 A of their own backbone carbonyl or the backbone carbonyl of the previous residue. Calculations using protein structures with a resolution better than 1.8 A 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 alpha-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.
Deane
C M
CM
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK.
Allen
F H
FH
Taylor
R
R
Blundell
T L
TL
D000596:Amino Acids / Q000737:chemistry; D001216:Asparagine / Q000737:chemistry*; D001224:Aspartic Acid / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008968:Molecular Conformation; D017433:Protein Structure, Secondary
D000596:Amino Acids; D001224:Aspartic Acid; D001216:Asparagine