Localized unfolding of collagen explains collagenase cleavage near imino-poor sites.

Collagenases cleave all three chains of type III collagen at specific sites characterized by a Gly-Leu or a Gly-Ile bond that is upstream from an imino acid-poor region. Molecular dynamics trajectories were used to calculate the free energy of unfolding for collagen-like model peptides. The free energy profiles suggest that such imino-poor regions can adopt a low-energy, partially unfolded state where one of the peptide chains forms a solvent-exposed loop. The results are consistent with a model for collagenase cleavage where partial unfolding of imino-poor regions enables collagenases to gain access to their cleavage sites.