The Orientational Order of the α-Helical Backbone of Poly(γ-Benzyl L-Glutamate) – a Molecular Dynamics Simulation

Abstract

For a Poly(γ-benzyl L-glutamate) (PBLG) segment with 30 monomers, molecular dynamics simulation was carry out in the Amber forcefield, by the software package InsightII/Discover. The geometrical structure of the backbone of the model molecule in the minimized energy state is in close agreement with that in the solid polypeptides. In the dynamic equilibrium state, the structure becomes slightly flabby and has a potential ca. 4800kJ/mol higher than that in the minimized energy state for the model molecule. On the average, the α-helical backbone architecture of PBLG remains quite stable during the molecular dynamic process, though the fluctuation of the bond and dihedral angles. The observed D NMR spectra for the quadrupolar splittings are reproduced and the previous architecture analysis was verified by the simulation calculations.