Conformational selection and collagenolysis in Type III collagen

Abstract

Matrix metalloproteases (MMPs) cleave native collagen at a single site despite the fact that collagen contains more than one scissile bond that can, in principle, be cleaved. For peptide bond hydrolysis to occur at one specific site, MMPs must (1) localize to a region near the unique scissile bond, (2) bind residues at the catalytic site that form the scissile bond, and (3) hydrolyze the corresponding peptide bond. Prior studies suggest that for some types of collagen, binding of noncatalytic MMP domains to amino acid sequences in the vicinity of the true cleavage site facilitates the localization of collagenases. In the present study, our goal was to determine whether binding to the catalytic site also plays a role in determining MMP specificity. To investigate this, we computed the conformational free energy landscape of Type III collagen at each potential cleavage site. The free energy profiles suggest that although all potential cleavage sites sample unfolded states at relatively low temperatures, the true cleavage site samples structures that are complementary to the catalytic site. By contrast, potential cleavage sites that are not cleaved sample states that are relatively incompatible with the MMP active site. Furthermore, our findings point to a specific role for arginine residues in modulating the structural stability of collagen near the collagenase cleavage site. These data imply that locally unfolded potential cleavage sites in Type III collagen sample distinct unfolded ensembles, and that the region about the true collagenase cleavage site samples states that are most complementary to the MMP active site.

Local Conformation and Dynamics of Isoleucine in the Collagenase Cleavage Site Provide a Recognition Signal for Matrix Metalloproteinases*

“…Similarly, type I collagen heterotrimer has a conserved Pro at the P 3 subsite suggesting that one chain may have more flexibility at the Ile/Leu site than the other two chains. These data support the studies that have shown that only a single chain of collagen can be incorporated into the active site cleft of MMPs and that type I collagen is cleaved by MMPs one chain after the other (32,34).…”

“…NMR studies of an unlabeled heteromeric triple helical peptide containing the cleavage site of type I collagen indicate that the cleavage site region has less ordered structure than the ends with GPO repeating triplets (62). Recent simulations of type III collagen have shown that the whole cleavage site is relatively exposed to solvent, and it samples structures that are more complementary to the MMP active site (34).…”

“…It was proposed that the triple helix needs to unwind locally so that a single chain can enter into the active site of MMPs or the active site of MMPs undergoes large conformational changes (32,33). Computational simulations of type I collagen also indicated that the ␣2 chain is locally unfolded with disrupted hydrogen bonds N-terminal to the cleavage sites and simulations of peptide models of type III collagen show that the real cleavage site is more exposed to solvent and more flexible than the other four potential cleavage sites (33,34). Taken together, these studies suggest that the conformation and dynamics at the collagenase cleavage site is critical for collagen recognition by MMPs.…”

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

“…MD simulations were used by Salsas-Escat and Stultz (2010) to generate ensembles of type III collagen that describe its conformational heterogeneity. They observed that collagen could adopt in the free state the configuration that it adopts in the active site of proteolytic enzyme CMMP8 that cleaves disordered peptides.…”

The Recognition of Collagen and Triple-helical Toolkit Peptides by MMP-13

“…Several G-[I/L]-[A/L] triplets are present in native collagen, indicating that, in principle, other scissile bonds may exist. However, with the exception of MMP-13, most MMPs primarily cleave the collagen helix at a single location, reflecting the importance of the unique sequence which surrounds the cleavage site (13, 14). …”