Sparsely populated residue conformations in protein structures: revisiting "experimental" Ramachandran maps.
The Ramachandran map clearly delineates the regions of accessible conformational (φ-ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely "arid", fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ-ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II' β turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II' β turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in β hairpins. The β strand-helix motif with the Type II' β turn as a connecting element was also found in as many as 57 examples.
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India.
Neha V
NV
Kalmankar
C
C
Ramakrishnan
P
P
Balaram
D000596:Amino Acids / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins
Ramachandran map; Type II′ β turn; amino acid conformational propensities; protein conformation; secondary structural motifs