{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/157629"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/157629","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Specificity and structural characterization of the PDZ domain from DegS, an extracytoplasmic E. coli protease","abstract":"DegS is a membrane-bound bacterial protease that is involved in the extracytoplasmic-stress response. The C-terminal domain has limited homology to PDZ domains and was thought to be involved in regulation or substrate recognition. A model of this PDZ domain was generated from NMR solution studies and homology modeling. Peptide selection studies identified the sequence Tyr-Tyr-Phe (YYF) as a C-terminal motif that binds to the PDZ domain. Possible targets were identified including many of the outer-membrane proteins (OMPs), which contain both a conserved terminal YxF and internal YYF sequences. The binding of the DegS PDZ domain to a YYF peptide and OMP derivatives were confirmed using microcalorimetry. Because stress signaling can be triggered by over-expression of some of the outer-membrane proteins, I propose that DegS may receive a signal from unassembled OMPs and transmit it to the aE transcription factor by increasing proteolysis of RseA.","abstract_html":"DegS is a membrane-bound bacterial protease that is involved in the extracytoplasmic-stress response. The C-terminal domain has limited homology to PDZ domains and was thought to be involved in regulation or substrate recognition. A model of this PDZ domain was generated from NMR solution studies and homology modeling. Peptide selection studies identified the sequence Tyr-Tyr-Phe (YYF) as a C-terminal motif that binds to the PDZ domain. Possible targets were identified including many of the outer-membrane proteins (OMPs), which contain both a conserved terminal YxF and internal YYF sequences. The binding of the DegS PDZ domain to a YYF peptide and OMP derivatives were confirmed using microcalorimetry. Because stress signaling can be triggered by over-expression of some of the outer-membrane proteins, I propose that DegS may receive a signal from unassembled OMPs and transmit it to the aE transcription factor by increasing proteolysis of RseA.","abstract_has_math":false,"creators":["Walsh, Nathan P. (Nathan Peter), 1973-"],"institution":"Massachusetts Institute of Technology","degree_name":"Doctoral","degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Biology","school":null,"contributors":[],"advisors":["Robert T. Sauer."],"committee_chairs":[],"committee_members":[],"year":2002,"date_issued":"February 2002","date_published":"February 2002","updated_at":"2026-07-22T22:21:40Z","subjects":["Biology."],"languages":[],"rights":["MIT theses may be protected by copyright. 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Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1721.1/157629"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, February 2002","Includes bibliographical references (p. 87-95)."]},{"key":"dc:description.abstract","label":"Abstract","values":["DegS is a membrane-bound bacterial protease that is involved in the extracytoplasmic-stress response. The C-terminal domain has limited homology to PDZ domains and was thought to be involved in regulation or substrate recognition. A model of this PDZ domain was generated from NMR solution studies and homology modeling. Peptide selection studies identified the sequence Tyr-Tyr-Phe (YYF) as a C-terminal motif that binds to the PDZ domain. Possible targets were identified including many of the outer-membrane proteins (OMPs), which contain both a conserved terminal YxF and internal YYF sequences. The binding of the DegS PDZ domain to a YYF peptide and OMP derivatives were confirmed using microcalorimetry. Because stress signaling can be triggered by over-expression of some of the outer-membrane proteins, I propose that DegS may receive a signal from unassembled OMPs and transmit it to the aE transcription factor by increasing proteolysis of RseA."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Ph. D."]},{"key":"dc:title","label":"Title","values":["Specificity and structural characterization of the PDZ domain from DegS, an extracytoplasmic E. coli protease"]}]}],"canonical_facts":{"dc:contributor.advisor":["Robert T. Sauer."],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Biology"],"dc:contributor.other":["Massachusetts Institute of Technology. Department of Biology."],"dc:creator":["Walsh, Nathan P. (Nathan Peter), 1973-"],"dc:date.accessioned":["2024-11-21T17:34:31Z"],"dc:date.available":["2024-11-21T17:34:31Z"],"dc:date.issued":["February 2002"],"dc:description":["Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, February 2002","Includes bibliographical references (p. 87-95)."],"dc:description.abstract":["DegS is a membrane-bound bacterial protease that is involved in the extracytoplasmic-stress response. The C-terminal domain has limited homology to PDZ domains and was thought to be involved in regulation or substrate recognition. A model of this PDZ domain was generated from NMR solution studies and homology modeling. Peptide selection studies identified the sequence Tyr-Tyr-Phe (YYF) as a C-terminal motif that binds to the PDZ domain. Possible targets were identified including many of the outer-membrane proteins (OMPs), which contain both a conserved terminal YxF and internal YYF sequences. The binding of the DegS PDZ domain to a YYF peptide and OMP derivatives were confirmed using microcalorimetry. Because stress signaling can be triggered by over-expression of some of the outer-membrane proteins, I propose that DegS may receive a signal from unassembled OMPs and transmit it to the aE transcription factor by increasing proteolysis of RseA."],"dc:description.degree":["Ph. D."],"dc:identifier.uri":["https://hdl.handle.net/1721.1/157629"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Biology."],"dc:title":["Specificity and structural characterization of the PDZ domain from DegS, an extracytoplasmic E. coli protease"],"dc:type":["Academic theses.","Thesis"],"thesis:degree_name":["Doctoral"]},"updated_at":"2026-07-22T22:21:40Z"}