Analysis of gamma beta, beta gamma, gamma gamma, beta beta multiple turns in proteins

The number of gamma-turns in a representative protein dataset selected from the current Protein Data Bank has increased almost seven times during the past decade. Eighty percent classic gamma-turns and 57% inverse gamma-turns are associated as multiple turns with either another gamma-turn or a beta- turn. We refer to these as multiple turns of the (gamma beta)(1,2,3) or (be ta gamma)(1,2,3) type, depending upon whether the gamma-turn is before or a fter the beta-turn along the protein chain, respectively. However, for mult iple turns involving only gamma-turns, we follow the nomenclature analogous to that proposed earlier for the multiple (or double) beta-turns. Fifty-ei ght per cent beta-turns are associated as multiple turns with another beta- turn. We extracted multiple turns from the protein dataset and classified t hem on the basis of individual gamma- or beta-turn types and the number of overlapping residues. Furthermore, we evaluated the amino acid positional p otentials and determined the statistically significant amino acid preferenc es, hydrogen bond/side-chain interaction preferences in the multiple turns and secondary structure preferences for residues immediately flanking these turns. The results of our analysis would be useful in the modeling, predic tion or design of multiple turns in proteins. The amino acid sequence corre sponding to the multiple turn, position in the protein chain, PDB Code/chai n in which multiple turn is present and the individual turn types constitut ing the multiple turns are available from our website and this information would also be integrated in our Database of Structural Motifs in Proteins ( http://www.cdfd.orq.in/dsmp.html).