Conformational analysis of a cyclic heptapeptide, pseudostellarin D by molecular dynamics and Monte Carlo simulations

Restrained molecular dynamics calculation in vacuo using AMBER force field implemented in MacroModel/Batchmin showed a major solution conformation in dimethyl sulfoxide-d6 of pseudostellarin D, cyclo(Gly-Tyr-Gly-Pro-Leu-Ile-Leu-). This is a cyclic heptapeptide isolated from Pseudostellaria heterophylla possessing characteristics of a beta-bulge motif with three intramolecular hydrogen bonds, two beta-turns (one type I at Pro4 and Leu5 residues, and one type II at Leu7 and Gly1 residues) and all trans amide bonds. The solution form of pseudostellarin D, which was homologous to that observed in the solid state, was also supported by Monte Carlo simulation study.