Molecular dynamics simulation of spatial structure of rat/mouse hemokinin-1

Molecular dynamics simulations were performed for rat/mouse hemokinin-1, mammalian tachykinin peptide. A single rat/mouse hemokinin-1 was modeled in vacuum as well as in water. In the latter case it was surrounded by 264 SPC water molecules and a periodic boundary condition was applied. A large flexibility of the Arg¹-Thr⁴ amino acids sequence was observed in vacuum in contrast to water simulation. The Arg⁵- Tyr⁸ backbone can adopt only a limited number of conformations, while the side chains may populate all three major rotamers.