Conformational Analysis of Pol-Rfamide II (Glu}^{1}-Trp^{2}-Leu^{3}-Lys^{4}-Gly^{5}-Arg^{6}-Phe^{7}-NH_{2}) Heptapeptide


Abstract: The geometrical structure of the sea anemone and sea pansies neuropeptide Pol-RFamide II Glu^{1}-Trp^{2}-Leu^{3}-Lys^{4}-Gly^{5}-Arg^{6}-Phe^{7}-NH_{2} was carried out by molecular mechanics (MM). The linkage bonds are characterised by the torsional angles \phi, \psi and \omega and the side groups characterised by the torsional angles \chi_{1}, \chi_{2}, \chi_{3},... subsequently. The energy-map for each monopeptide of the Pol-RFamide II was drawn in the range of -180° to 180° with increments of 20°. Conformation facilities for monopeptides were decided from these maps. These results were used in the analysis of the dipeptide Glu^{1}-Trp^{2}. Then, the Glu^{1}-Trp^{2}-Leu^{3} tripeptide was examined by using the calculated results for dipeptide. Conformational analysis of the Glu^{1}-Trp^{2}-Leu^{3}-Lys^{4} tetrapeptide was performed using the low-energy values of the tripeptide. The geometrical structure of Glu^{1}-Trp^{2}-Leu^{3}-Lys^{4}-Gly^{5}-Arg^{6}-Phe^{7}-NH_{2} neuropeptide was determined by rotating the tetrapeptide Glu^{1}-Trp^{2}-Leu^{3}-Lys^{4} and the dipeptide Arg^{6}-Phe^{7}-NH_{2} about the monopeptide Gly^{5} due to the minimisation of energy.


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