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 Momordica cochinchinensis, 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.