Cracking the code of cathepsin S: Structural determinants of specificity switching
| dc.contributor.author | DeHority, Riley Ambrose | en |
| dc.contributor.committeechair | Zhang, Chenming | en |
| dc.contributor.committeemember | Li, Liwu | en |
| dc.contributor.committeemember | Luo, Xin | en |
| dc.contributor.committeemember | Wright, Robert Clay | en |
| dc.contributor.department | Biological Systems Engineering | en |
| dc.date.accessioned | 2025-01-10T09:00:18Z | en |
| dc.date.available | 2025-01-10T09:00:18Z | en |
| dc.date.issued | 2025-01-09 | en |
| dc.description.abstract | Cathepsin S is a cysteine protease in the papain family that digests antigens as part of the adaptive immune response, activates receptors, and is associated with extracellular matrix degradation in autoimmune diseases and cancer. A comprehensive review of the literature revealed potential pH- and redox-dependent specificity switches in the proteolytic specificity of cathepsin S. These were investigated through the digestion of peptides across a variety of pH and redox conditions. These experiments confirmed both pH- and redox-dependent patterns of proteolytic specificity, with narrowed specificity in alkaline and oxidizing conditions. An analysis of publicly available structures of cathepsin S identified a lysine residue which descends into the S3 pocket of the active site above pH 7.0, acting as a pH-dependent gate. Energy minimization of crystal structures show disorder in the loops which make up the active site of the protein, which increases in disorder when the disulfide bonds on the surface of cathepsin S are reduced. This is explored as a potential mechanism for the redox-dependent specificity identified in the digest experiments. These specificity switches may contribute to pathological structural damage attributed to cathepsin S, as pH and redox dysregulation are features of several cathepsin S-associated diseases. | en |
| dc.description.abstractgeneral | Proteases are protein enzymes that break the bonds of other proteins, cleaving them into pieces. Cathepsin S is a protease that has many important roles in the body. If you have ever become immune to something, it is thanks to cathepsin S. Proteases can't cleave every protein: they are limited to specific sequences, and this is called proteolytic specificity. It is usually determined by the shape and charge of the active site of the enzyme. The purpose of this set of experiments was to find out whether two environmental factors change the specificity of cathepsin S: pH (the balance of proton donors and acceptors), and redox state (the balance of electron donors and acceptors). By combining cathepsin S with short proteins of varying sequences in different pH and redox conditions, we found that both of these conditions impact which sequences cathepsin S can cleave most easily. We identified areas of the structure of cathepsin S that are likely responsible for these specificity switches. The pH-dependence can be explained by an amino acid that bends down into the active site of cathepsin S at high pH, closing off part of the pocket and limiting what protein sequences can fit into it. The redox-dependence may be explained by bonds on the surface of cathepsin S being broken in some environments, making the active site more flexible and able to accept more protein sequences. These specificity switches may explain the destructive behavior of cathepsin S in a variety of diseases, since in many of these diseases, pH and redox states get out of balance. | en |
| dc.description.degree | Doctor of Philosophy | en |
| dc.format.medium | ETD | en |
| dc.identifier.other | vt_gsexam:42290 | en |
| dc.identifier.uri | https://hdl.handle.net/10919/124078 | en |
| dc.language.iso | en | en |
| dc.publisher | Virginia Tech | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | cathepsin S | en |
| dc.subject | proteases | en |
| dc.subject | specificity | en |
| dc.title | Cracking the code of cathepsin S: Structural determinants of specificity switching | en |
| dc.type | Dissertation | en |
| thesis.degree.discipline | Biological Systems Engineering | en |
| thesis.degree.grantor | Virginia Polytechnic Institute and State University | en |
| thesis.degree.level | doctoral | en |
| thesis.degree.name | Doctor of Philosophy | en |
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