Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Proteins. 2010 Feb 1;78(2):325-35. doi: 10.1002/prot.22545.
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.
基质金属蛋白酶 (MMPs) 在单一位置切割天然胶原蛋白，尽管胶原蛋白含有多个可切割的键，原则上可以切割。为了使肽键在一个特定的位置水解，MMP 必须 (1) 定位到靠近独特切割键的区域，(2) 结合催化位点形成切割键的残基，以及 (3) 水解相应的肽键。先前的研究表明，对于某些类型的胶原蛋白，非催化 MMP 结构域与真正切割位点附近氨基酸序列的结合有助于胶原酶的定位。在本研究中，我们的目标是确定与催化位点的结合是否也在确定 MMP 特异性方面发挥作用。为了研究这个问题，我们计算了 III 型胶原蛋白在每个潜在切割位点的构象自由能景观。自由能图谱表明，尽管所有潜在的切割位点在相对较低的温度下都能采样到展开状态，但真正的切割位点采样到的结构与催化位点互补。相比之下，未被切割的潜在切割位点采样到的状态与 MMP 活性位点相对不兼容。此外，我们的研究结果表明，精氨酸残基在调节胶原蛋白酶切割位点附近胶原蛋白的结构稳定性方面具有特定的作用。这些数据表明，III 型胶原蛋白中局部展开的潜在切割位点采样到不同的展开集合，而真正的胶原酶切割位点附近的区域采样到与 MMP 活性位点最互补的状态。
