Conformational analysis of linear peptide ($Glu^1-Leu^2-Leu^3-Gly^4-Gly^5-Arg^6-Phe^7NH_2$)

Abstract

Conformational energy-minimization of the Sea Anemone and Sea Pansy neuropeptide Pol-RFamide ($Glu^1-Leu^2-Leu^3-Gly^4-Gly^5-Arg^6-Phe^7-NH_2$) was carried out by molecular mechanics (MM). The linkage bonds were characterized by the torsion angles $Theta$, $Psi$ and $Omega$ and the side groups were characterized by the torsion angles $chi_1$, $chi_2$, $chi_3$... The energy-map for each monopeptide of the Pol-RFamide I was drawn in the range of -180° to 180° with increments of 20°. Conformation facilities for monopeptides were determined from these maps. These results were used in the analysis of the dipeptide ($Glu^1-Leu^2$). Then, the ($Glu^1-Leu^2-Leu^3$) tripeptide was examined using the calculated results for the dipeptide. Conformational analysis of the ($Glu^1-Leu^2-Leu^3-Gly^4$) tetrapeptide was performed using the low-energy values for the tripeptide. The space structure of the ($Glu^1-Leu^2-Leu^3-Gly^4-Gly^5-Arg^6-Phe^7-NH_2$) neuropeptide was found as a result of minimization of energies by rotating the tetrapeptide ($Glu^1-Leu^2-Leu^3-Gly^4) and the dipeptide ($Arg^6-Phe^7-NH_2$) about the monopeptide ($Gly^5$).