Department of Physics, Indian Institute of Science, Bangalore-560012, India
rshankar@physics.iisc.ernet.in
Conformational features and classification of 6-->1 hydrogen bonded turns (pi-turns) observed in proteins and peptides are described. The polypeptide conformations under the constraint of 6-->1 hydrogen bonds were detected in the crystal structures of proteins from Brookhaven Protein Data Bank (PDB) using a FORTRAN program developed in our laboratory. The data set consisted of the co-ordinates of 228 non-homologous protein chains, determined by X-ray crystallography to better than 2.5Å resolution. Totally 486 pi-turns were located. 367 Pi-turns of these were found to have the 5th residue in left handed alpha-helical region of Ramachandran's map and were classified as Pi-alpha-L-turns. These turns are generally observed at the C-terminal end of helices. 286 Pi-alpha-L-Turns define Schellman motif (6-->1 & 5-->2 hydrogen bond). 111 Pi-Turns had 5th residue in alpha-R region, a novel finding and were referred by the name Pi-alpha-R-turns. Pi-alpha-R-Turns generally occur in alpha-helices as a distortion. Four Pi-turns were seen to be mirror images of Pi-alpha-turns and hence were termed as Pi-alpha-L'-turns. The 5th residue in rest of the four pi-turns were seen to adopt beta-conformation, hence these four were named as Pi-beta-turns.
The former two classes of pi-turns (pi-alpha-L and R) form major classes. Nine pi-turns observed so far in oligopeptides share the features of pi-alpha-L-turns. Sequence analysis shows that hydrophilic residues are preferred at position 2,3 and 4 of pi-alpha-L-turns while position 1 and 6 prefer hydrophobic residues. Residue 5 (left-handed alpha) is mainly Gly and less often Asn. A high preference for Pro after the C-termini is observed in both the major classes. Poor alpha-helix formers like His, Tyr and Asn were found to be preferred for pi-alpha-R-turns, where as good alpha-helix former Ala is not preferred. The discussion will include the details of classification, context of occurrence, sequence and hydration of pi-turns in proteins and peptides.
(KRR thanks CSIR, India for a fellowship. Funding from DST, India is acknowledged).