Molecular modeling of Momordica cochinchinensis asparagine endopeptidase 2 and its interaction with MCoTI-II peptide

Cyclotides are a large family of plant defense peptides, which display a cyclic backbone. The enzymes responsible for the backbone cyclization of these peptides are called asparagine endopeptidases, and the three-dimensional crystallographic structure of one of these cyclization enzyme has recently been described. The group of David Craik has recently discovered another cyclization enzyme, this time from the plant <em>Momordica cochinchinensis</em>, which is selective for cyclotides belonging to the trypsin inhibitor cyclotide family I have carried out molecular dynamics simulations of this new enzyme in an apo state and in an intermediate state when covalently linked with a substrate peptide. This dataset provides the necessary files to reproduce these molecular dynamics simulations carried out with the software pmemd from the Amber 18 simulation package.