Conformational analysis of pol-RFamide II $(Glu^1-Trp^2-Leu^3-Lys^4-Gly^5-Arg^6-Phe^7-NH_2)$ heptapeptide

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 $mathcal{X}_1$, $mathcal{X}_2$, $mathcal{X}_3$,... 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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