Molecular dynamics simulation provides a possible structure for substance P-like peptides in aqueous solution

A hypothetical conformation of the undecapeptide Substance P in aqueous solution is generated by molecular dynamics simulation for 284 ps. The conformation takes explicit solvent interactions into account as well as entropic effects to the extent that phase space is sampled in simulation. The initial conformation is taken from energy minimization studies and modified. In spite of fluctuations through 180 degrees in some backbone dihedral angles, the peptide settles with all backbone dihedrals within +/- 60 degrees from the initial values. In 130 ps, the radius of gyration decreases from 6.2 A to 5.5 A, whereas only fluctuation (+/- .2 A) is observed during the last 150 ps. The root-mean-square deviation at optimal superposition for a pair of conformations from the last 150 ps is 0.6 A, based on backbone atoms. The final structure is close-knit, nearly globular, and stabilized by several long-lived hydrogen bonds. The simulation conformation agrees with the scarce experimental data including a large number of structure-activity relationships. Thus, the simulation conformation is a likely candidate for one of the several conformations, the existence of which has been deduced from nuclear magnetic resonance data. Simulation results and experimental modification studies suggest that Phe 8 and Leu 10 are involved in the primary binding of SP to its receptors.