[[pi]]-TURNS IN PROTEINS AND PEPTIDES; CLASSIFICATION, OCCURRENCE, SEQUENCE AND HYDRATION: A PROTEIN DATA BANK ANALYSIS S. Ramakumar, K. R. Rajashankar, Department of Physics, Indian Institute of Science, Bangalore-560012, India
This paper describes the conformational features of 61 hydrogen bonded turns ([[pi]]-turns) observed in proteins and peptides. The polypeptide conformations under the constraint of 61 hydrogen bond were selected 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 2.5 Å resolution. Totally 486 [[pi]]-turns were located. 367 [[pi]]-Turns were found to have 5th residue in left handed a-helical(aL) region of Ramachandrans map and were classified as [[pi]]aL-turns. These turns are generally observed at the C-terminal end of helices, a result in harmony with previous observations. 286 [[pi]]aL-Turns define `Schellman motif' (61 & 52 hydrogen bond). 111 [[pi]]-Turns had 5th residue in R region, a novel finding and were referred by the name [[pi]]aR-turns. [[pi]]aR-Turns generally occur in a-helices as a distortion. Four [[pi]]-turns were seen to be mirror images of [[pi]]aL-turns and hence were termed as [[pi]]aL'-turns. The 5th residue in rest of the four [[pi]]-turns were seen to adopt ß-conformation, hence these four were named as [[pi]]ß-turns. The former two classes of [[pi]]-Turns ([[pi]]aL & [[pi]]aR) form major classes. Nine [[pi]]-turns observed so far in oligopeptides share the features of [[pi]]aL-turns. Sequence analysis shows that hydrophilic residues are preferred at position 2,3 and 4 of [[pi]]aL-turns while position 1 and 6 prefer hydrophobic residues. Residue 5 (aL) is mainly Gly and less often Asn. A high preference for Pro after the C-termini is observed in both the major classes. Poor a-helix formers like His, Tyr and Asn were found to be preferred for [[pi]]aR -turns, where as good a-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.
(K.R.R. thanks CSIR(India) for a fellowship)