| Summary: | Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2010. === This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. === Cataloged from student-submitted PDF version of thesis. === Includes bibliographical references. === Excessive collagen degradation (collagenolysis) has been implicated in a series of diseases such as tumor metastasis, atherosclerosis and arthritis. There are still several unresolved questions about the mechanism of collagenolysis. First, the prototypical structure of the collagen triple helix does not fit into the active site of collagenases, the enzymes responsible of cleaving collagen. Moreover, the scissile bond that is degraded during collagenolysis is hidden from solvent. Therefore it is widely agreed that collagen unfolding must occur in order for collagenolysis to proceed. Some proposed mechanisms suggest that collagenases actively unfold collagen in order to expose the cleavage site, but no direct evidence of such mechanisms has been provided. Second, while several potential cleavage sites exist in the sequence of collagen, only one is cleaved in triple helical collagen. The hypothesis of this work is that locally unfolded states exist in collagen in the absence of collagenases. They occur as a result of the natural thermal fluctuations in the structure of collagen. Collagenolysis occurs when collagenases bind and cleave these unfolded states. In this work, a combination of computational and experimental methods is presented in order to test this hypothesis. Initially, computational results suggest that locally unfolded states are ubiquitous along the structure of collagen. However, it is shown that not all unfolded states are created equal, and that the precise sequence in the vicinity of the true collagenase cleavage site in type III collagen allows collagen to sample locally unfolded states that are complimentary to the collagenase active site. Therefore, it is hypothesized that cleavage site specificity is encoded in the nature of the unfolded states. Next, it is shown that types I and III collagen can be bound and cleaved at the actual cleavage site by just the catalytic domain of collagenases, a finding in apparent contradiction with previous work in this field. These results are interpreted in light of a novel conformational selection mechanism in which collagenases only cleave locally unfolded, vulnerable states. Finally, based on the new mechanism of collagenolysis presented here, new strategies to regulate collagenolysis are proposed. === by Ramon Salsas Escat. === Ph.D.
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