Conformational characteristics of asparaginyl residues in proteins.
Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed alpha-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi, psi) regions of left-handed alpha-helix right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha L, which seems to be characteristic of non-glycyl residues at that position. In the liners connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha L or alpha R conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein.
Srinivasan
N
N
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
Anuradha
V S
VS
Ramakrishnan
C
C
Sowdhamini
R
R
Balaram
P
P
D001216:Asparagine / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016208:Databases, Factual; D004151:Dipeptides / Q000737:chemistry; D008956:Models, Chemical; D009842:Oligopeptides / Q000737:chemistry; D017433:Protein Structure, Secondary
D004151:Dipeptides; D009842:Oligopeptides; D001216:Asparagine