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Robert T. Sauer. Grabenstatter, Jonathan Dean Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences. Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences 2016-02-29T15:01:51Z 2016-02-29T15:01:51Z 2015 http://hdl.handle.net/1721.1/101347 938904120 Thesis: Ph. D., Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, 2015. "September 2015." Cataloged from PDF version of thesis. Includes bibliographical references. ATP dependent proteolysis is a process essential for life and is carried out by AAA+ proteases. AAA+ unfoldases use the energy of ATP hydrolysis to power the unfolding and translocation of protein substrates into compartmentalized peptidases for regulated proteolysis. Cdc48 is a highly conserved AAA+ homohexameric unfoldase which is made up of two AAA+ rings. Each ring can, in principle, bind and hydrolyzing ATP, but it is unclear what roles are played by each ring and how they coordinate their activities. A regulatory N domain functions to control the activity of the enzyme and binding to its partner peptidase, the 20S proteasome. In this thesis I present experiments which investigate the role of inter-ring communication in ATP hydrolysis, protein unfolding, and allosteric interactions with the 20S and show how these features affect enzyme function. Experiments also show how the N domain controls D1-D2 interactions that govern ATP hydrolysis and substrate unfolding. Finally, I present experiments that take steps toward developing a system for screening protein substrates of Cdc48-20S and identify several substrates from E. coli lysates. by Jonathan Dean Grabenstatter. Ph.D. 99 pages eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Earth, Atmospheric, and Planetary Sciences. Cooperativity and communication in archaeal Cdc48·20S, an ancient proteolytic machine Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="8c721d58-e5f9-467d-919c-72e1e1471128"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Cooperativity and communication in archaeal Cdc48·20S, an ancient proteolytic machine</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2015</PublicationDate> <Authors> <Author> <DisplayName>Grabenstatter, Jonathan Dean</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Earth, Atmospheric, and Planetary Sciences.</Keyword> <Abstract>ATP dependent proteolysis is a process essential for life and is carried out by AAA+ proteases. AAA+ unfoldases use the energy of ATP hydrolysis to power the unfolding and translocation of protein substrates into compartmentalized peptidases for regulated proteolysis. Cdc48 is a highly conserved AAA+ homohexameric unfoldase which is made up of two AAA+ rings. Each ring can, in principle, bind and hydrolyzing ATP, but it is unclear what roles are played by each ring and how they coordinate their activities. A regulatory N domain functions to control the activity of the enzyme and binding to its partner peptidase, the 20S proteasome. In this thesis I present experiments which investigate the role of inter-ring communication in ATP hydrolysis, protein unfolding, and allosteric interactions with the 20S and show how these features affect enzyme function. Experiments also show how the N domain controls D1-D2 interactions that govern ATP hydrolysis and substrate unfolding. Finally, I present experiments that take steps toward developing a system for screening protein substrates of Cdc48-20S and identify several substrates from E. coli lysates.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>