{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/14593"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/14593","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"The study of aa3-type cytochrome c oxidase in Rhodobacter sphaeroides","abstract":"Cytochrome c oxidase is the final electron acceptor in the respiratory chain and catalyzes the highly exergonic oxygen reduction reaction to water and forms a transmembrane electrochemical proton gradient. This transmembrane gradient is used by ATP synthase to produce ATP. The oxygen chemistry reaction of the enzyme is coupled to a proton pump, which substantially contributes to the transmembrane electrochemical gradient. Two proton entry pathways, D pathway and K pathway, have been resolved in X-ray crystal structures. But the exit pathway for the pumped proton and its mechanism is not well understood. The work in this thesis presents extensive studies in proton translocation in both the D-pathway and putative exit pathway. The mutations in the highly conserved R481 confirmed that the residue itself and the hydrogen bonds it forms with the heme propionates are not critical for proton pumping ability and the environmental changes of the hemes were detected on the R481 mutant oxidases. The putative exit pathway is very complicated to define due to the network of many water molecules and hydrophilic residues in the area. But clearly, changing the charge status in some of the residues in putative exit pathway affected the function of the oxidases and the environment of hemes. The D-pathway proton translocation study reveals that the waters do not necessarily need to be hydrogen-bonded to conserved serines in the middle of the pathway. However, the serine mutations caused changes in the pKa of E286 (branch point for substrate proton and pumped proton), which led to the conclusion that the pKa of E286 is not directly related to proton pumping ability.","abstract_html":"Cytochrome c oxidase is the final electron acceptor in the respiratory chain and catalyzes the highly exergonic oxygen reduction reaction to water and forms a transmembrane electrochemical proton gradient. This transmembrane gradient is used by ATP synthase to produce ATP. The oxygen chemistry reaction of the enzyme is coupled to a proton pump, which substantially contributes to the transmembrane electrochemical gradient. Two proton entry pathways, D pathway and K pathway, have been resolved in X-ray crystal structures. But the exit pathway for the pumped proton and its mechanism is not well understood. The work in this thesis presents extensive studies in proton translocation in both the D-pathway and putative exit pathway. The mutations in the highly conserved R481 confirmed that the residue itself and the hydrogen bonds it forms with the heme propionates are not critical for proton pumping ability and the environmental changes of the hemes were detected on the R481 mutant oxidases. The putative exit pathway is very complicated to define due to the network of many water molecules and hydrophilic residues in the area. But clearly, changing the charge status in some of the residues in putative exit pathway affected the function of the oxidases and the environment of hemes. The D-pathway proton translocation study reveals that the waters do not necessarily need to be hydrogen-bonded to conserved serines in the middle of the pathway. However, the serine mutations caused changes in the pKa of E286 (branch point for substrate proton and pumped proton), which led to the conclusion that the pKa of E286 is not directly related to proton pumping ability.","abstract_has_math":false,"creators":["Lee, Hyun Ju"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biochemistry","degree_department":null,"school":null,"contributors":["Gennis, Robert B.","Nair, Satish K.","Rienstra, Chad M.","Spies, Maria"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2010,"date_issued":"2010-01-06T16:13:35Z","date_published":"2010-01-06T16:13:35Z","updated_at":"2026-07-22T22:25:07Z","subjects":["Cytochrome c oxidase","adenosine triphosphate (ATP)","proton pump"],"languages":["en"],"rights":["Copyright 2009 Hyun Ju Lee"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/14593","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gennis, Robert B.","Nair, Satish K.","Rienstra, Chad M.","Spies, Maria"]},{"key":"dc:creator","label":"Author","values":["Lee, Hyun Ju"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2010-01-06T16:13:35Z","2009-12"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biochemistry"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Cytochrome c oxidase","adenosine triphosphate (ATP)","proton pump"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2009 Hyun Ju Lee"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/14593"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Cytochrome c oxidase is the final electron acceptor in the respiratory chain and catalyzes the highly exergonic oxygen reduction reaction to water and forms a transmembrane electrochemical proton gradient. This transmembrane gradient is used by ATP synthase to produce ATP. The oxygen chemistry reaction of the enzyme is coupled to a proton pump, which substantially contributes to the transmembrane electrochemical gradient. Two proton entry pathways, D pathway and K pathway, have been resolved in X-ray crystal structures. But the exit pathway for the pumped proton and its mechanism is not well understood. The work in this thesis presents extensive studies in proton translocation in both the D-pathway and putative exit pathway. The mutations in the highly conserved R481 confirmed that the residue itself and the hydrogen bonds it forms with the heme propionates are not critical for proton pumping ability and the environmental changes of the hemes were detected on the R481 mutant oxidases. The putative exit pathway is very complicated to define due to the network of many water molecules and hydrophilic residues in the area. But clearly, changing the charge status in some of the residues in putative exit pathway affected the function of the oxidases and the environment of hemes. The D-pathway proton translocation study reveals that the waters do not necessarily need to be hydrogen-bonded to conserved serines in the middle of the pathway. However, the serine mutations caused changes in the pKa of E286 (branch point for substrate proton and pumped proton), which led to the conclusion that the pKa of E286 is not directly related to proton pumping ability.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2009-11-11T20:22:30Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Lee_Hyun Ju.pdf: 6350318 bytes, checksum: 089d4faee500615af975f45e049386e1 (MD5)","Made available in DSpace on 2010-01-06T16:13:35Z (GMT). No. of bitstreams: 3 license.txt: 4056 bytes, checksum: 4f1e848861302e169cc77850da123093 (MD5) Lee_Hyun Ju.pdf: 6350318 bytes, checksum: 089d4faee500615af975f45e049386e1 (MD5) 1_Lee_Hyun Ju.pdf: 6350248 bytes, checksum: b2c305610ed62dbc3b9feba09d8b7819 (MD5)"]},{"key":"dc:title","label":"Title","values":["The study of aa3-type cytochrome c oxidase in Rhodobacter sphaeroides"]}]}],"canonical_facts":{"dc:contributor":["Gennis, Robert B.","Nair, Satish K.","Rienstra, Chad M.","Spies, Maria"],"dc:creator":["Lee, Hyun Ju"],"dc:date":["2010-01-06T16:13:35Z","2009-12"],"dc:description":["Cytochrome c oxidase is the final electron acceptor in the respiratory chain and catalyzes the highly exergonic oxygen reduction reaction to water and forms a transmembrane electrochemical proton gradient. This transmembrane gradient is used by ATP synthase to produce ATP. The oxygen chemistry reaction of the enzyme is coupled to a proton pump, which substantially contributes to the transmembrane electrochemical gradient. Two proton entry pathways, D pathway and K pathway, have been resolved in X-ray crystal structures. But the exit pathway for the pumped proton and its mechanism is not well understood. The work in this thesis presents extensive studies in proton translocation in both the D-pathway and putative exit pathway. The mutations in the highly conserved R481 confirmed that the residue itself and the hydrogen bonds it forms with the heme propionates are not critical for proton pumping ability and the environmental changes of the hemes were detected on the R481 mutant oxidases. The putative exit pathway is very complicated to define due to the network of many water molecules and hydrophilic residues in the area. But clearly, changing the charge status in some of the residues in putative exit pathway affected the function of the oxidases and the environment of hemes. The D-pathway proton translocation study reveals that the waters do not necessarily need to be hydrogen-bonded to conserved serines in the middle of the pathway. However, the serine mutations caused changes in the pKa of E286 (branch point for substrate proton and pumped proton), which led to the conclusion that the pKa of E286 is not directly related to proton pumping ability.","Item withdrawn by Mark Zulauf (zulauf@illinois.edu) on 2009-11-11T20:22:30Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Lee_Hyun Ju.pdf: 6350318 bytes, checksum: 089d4faee500615af975f45e049386e1 (MD5)","Made available in DSpace on 2010-01-06T16:13:35Z (GMT). No. of bitstreams: 3 license.txt: 4056 bytes, checksum: 4f1e848861302e169cc77850da123093 (MD5) Lee_Hyun Ju.pdf: 6350318 bytes, checksum: 089d4faee500615af975f45e049386e1 (MD5) 1_Lee_Hyun Ju.pdf: 6350248 bytes, checksum: b2c305610ed62dbc3b9feba09d8b7819 (MD5)"],"dc:identifier":["http://hdl.handle.net/2142/14593"],"dc:language":["en"],"dc:rights":["Copyright 2009 Hyun Ju Lee"],"dc:subject":["Cytochrome c oxidase","adenosine triphosphate (ATP)","proton pump"],"dc:title":["The study of aa3-type cytochrome c oxidase in Rhodobacter sphaeroides"],"thesis:degree_discipline":["Biochemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:07Z"}