Computational study of the conformational flexibility of the amphibian tachykinin neuropeptides

Abstract

The conformational flexibility of some amphibian tachykinin neuropeptides have been investigated by computer modeling with molecular dynamics method in the different conditions. At the first stage the conformational changes of these peptides were studied in vacuum, but in the second stage they were surrounded by water molecules with the periodic boundary conditions. All molecules were observed in vacuum and in water with large flexibility of the N-terminal parts of its aminoacid sequences. It is shown that C-terminal backbone parts of these molecules save a alpha-helix conformation, but their side chains may exist in more than one orientations in all conditions.