computer modeling in molecular biology.pdf

3 Molecular Dynamics Simulations of Peptides 47one is illustrated in Figure 3-1. Additional molecular dynamics simulations startingfrom the conformation with a P-turn at residues 5-8 resulted in higher energy conformations.Similar studies were carried out on other antagonists cyclised throughthe side chains of residues 5 and 8. A total of 1.5 nanoseconds of MD simulationswere carried out, starting from different initial conformations as suggested from con-Figure 3-1. Results of a conformational search and molecular dynamics study of an LHRHantagonist. The backbone of the peptide is denoted by the filled bonds. Snapshots of conformationscaptured in this figure show the evolution of a /3-turn, /%sheet conformation at 50 psfrom a fairly extended conformation at 18 ps. The final conformation (lower right hand corner)was found to fold into a 3-6 type I /3-turn which included the Glu-Lys sidechain cyclisationresidues.