Designing of amino acids and their interactions in to unique tripeptide conformations for developing new peptide pharmaceuticals using Ramachandran plot

Summary The Ramachandran plot displays the main chain conformational angles (Phi and Psi) of the polypeptide chain of a protein molecule. The amino acid conformations of 13 tripeptide template analogue sets were analyzed with Ramchandran plots. Several of these amino acids are predicted to fold in to unique tripeptide conformations such as alpha helix, beta sheets and gamma turns. All the tripeptides (Thr-Phe-Arg; Thr-TrpLys; Thr-Phe-Lys; Thr-Tyr-His; Thr-His-Arg; Thr-Arg-Asn; Phe-Trp-Lys; Phe-Lys-Gln; Phe-His-Arg; Phe-Arg-Asn; Glu-Trp-Lys; Glu-His-Arg and Thr-Lys-Gln) showed most favourable allowed regions of alpha helix in lower left quadrant of plot thereby satisfied with ideal phi values (–57°) and psi values (–47°). Similarly, the above all templates have shown most favourable allowed regions of beta sheets in upper left quadrant by satisfying the ideal phi values (–80%) and psi values (+150°). In addition, all the subjected templates have shown less favourable generously allowed regions of gamma turns in upper left quadrant by fulfilling the phi and psi values (–80°; +80°). Among all the inbuilt templates tested for conformational analysis, we found that PheLys-Gln; Phe-Arg-Asn; Glu-Trp-Lys and Glu-His-Arg have shown maximum percentage of low energy allowed regions (15.5%; 16%; 16%; 15.5%) as the most stable conformations in developing a new peptide based pharmaceuticals.