{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/23914"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/23914","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"FTIR study of carboxylic acids and tyrosines in bacteriorhodopsin","abstract":"High quality infrared difference spectra of bacteriorhodopsin (bR) were obtained in order to study its photoreaction at the molecular level. The noise level was near 10-5 in the spectral regions where amino acid residues are monitored. The excellent signal to noise ratio allowed detection of absorption changes of single amino acids during the photoreaction. Aspartic acids and glutamic acids in bR were monitored by 13C labeling. Tyrosines were monitored by both 2H and nitrate substitution. Some of the amino acid band regions were decomposed by curve fitting. Alteration of absorption bands among individual bR states were found for aspartic acids and tyrosines, but were not found for glutamic acids. These changes are interpreted as a change in protonation of at least two aspartic acids and one tyrosine. In addition one aspartic acid and one tyrosine were subject to environmental perturbation. Nitration of tyrosines indicates that none of the tyrosine spectral changes occurring during the photoreaction cycle can be attributed to tyrosine-26 or tyrosine-64. A model based on intramolecular interaction is built to elucidate the spectral change observed during the cycle. This model places the three aspartic acids and the two tyrosines near the chromophore of bR. One aspartic acid and one tyrosine, together with a hypothetical positive charge, are postulated to form the primary environment around the Schiff base of the chromophore. These residues adjust conformation during the photoreaction. Another aspartic acid interacts with the Schiff base after the chromophore 13-cia isomerization. The nature of the environmental perturbation is discussed for individual residues. Also discussed in the thesis are the quality control in FTIR spectroscopy, prospective experiments, the present finding's implication to the mechanism of the color regulation and proton pumping of bR, and the general structure-function relationship of opsins.","abstract_html":"High quality infrared difference spectra of bacteriorhodopsin (bR) were obtained in order to study its photoreaction at the molecular level. The noise level was near 10-5 in the spectral regions where amino acid residues are monitored. The excellent signal to noise ratio allowed detection of absorption changes of single amino acids during the photoreaction. Aspartic acids and glutamic acids in bR were monitored by 13C labeling. Tyrosines were monitored by both 2H and nitrate substitution. Some of the amino acid band regions were decomposed by curve fitting. Alteration of absorption bands among individual bR states were found for aspartic acids and tyrosines, but were not found for glutamic acids. These changes are interpreted as a change in protonation of at least two aspartic acids and one tyrosine. In addition one aspartic acid and one tyrosine were subject to environmental perturbation. Nitration of tyrosines indicates that none of the tyrosine spectral changes occurring during the photoreaction cycle can be attributed to tyrosine-26 or tyrosine-64. A model based on intramolecular interaction is built to elucidate the spectral change observed during the cycle. This model places the three aspartic acids and the two tyrosines near the chromophore of bR. One aspartic acid and one tyrosine, together with a hypothetical positive charge, are postulated to form the primary environment around the Schiff base of the chromophore. These residues adjust conformation during the photoreaction. Another aspartic acid interacts with the Schiff base after the chromophore 13-cia isomerization. The nature of the environmental perturbation is discussed for individual residues. Also discussed in the thesis are the quality control in FTIR spectroscopy, prospective experiments, the present finding's implication to the mechanism of the color regulation and proton pumping of bR, and the general structure-function relationship of opsins.","abstract_has_math":false,"creators":["Lin, Shuo-Liang"],"institution":null,"degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Physics","degree_department":null,"school":null,"contributors":["Gratton, E."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2011,"date_issued":"2011-05-17T15:44:16Z","date_published":"2011-05-17T15:44:16Z","updated_at":"2026-07-22T22:25:22Z","subjects":["FTIR study","carboxylic acids","tyrosines","bacteriorhodopsin","infrared spectra","photoreaction","amino acid residues"],"languages":["en"],"rights":["1988 Shuo-Liang Lin"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["3476389"],"render_values":[{"text":"3476389","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/23914","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gratton, E."]},{"key":"dc:creator","label":"Author","values":["Lin, Shuo-Liang"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2011-05-17T15:44:16Z","10000-01-01","1988"]},{"key":"dc:type","label":"Dc Type","values":["Dissertation / Thesis","text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Physics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["FTIR study","carboxylic acids","tyrosines","bacteriorhodopsin","infrared spectra","photoreaction","amino acid residues"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["1988 Shuo-Liang Lin"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["3476389","http://hdl.handle.net/2142/23914"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["High quality infrared difference spectra of bacteriorhodopsin (bR) were obtained in order to study its photoreaction at the molecular level. The noise level was near 10-5 in the spectral regions where amino acid residues are monitored. The excellent signal to noise ratio allowed detection of absorption changes of single amino acids during the photoreaction. Aspartic acids and glutamic acids in bR were monitored by 13C labeling. Tyrosines were monitored by both 2H and nitrate substitution. Some of the amino acid band regions were decomposed by curve fitting. Alteration of absorption bands among individual bR states were found for aspartic acids and tyrosines, but were not found for glutamic acids. These changes are interpreted as a change in protonation of at least two aspartic acids and one tyrosine. In addition one aspartic acid and one tyrosine were subject to environmental perturbation. Nitration of tyrosines indicates that none of the tyrosine spectral changes occurring during the photoreaction cycle can be attributed to tyrosine-26 or tyrosine-64. A model based on intramolecular interaction is built to elucidate the spectral change observed during the cycle. This model places the three aspartic acids and the two tyrosines near the chromophore of bR. One aspartic acid and one tyrosine, together with a hypothetical positive charge, are postulated to form the primary environment around the Schiff base of the chromophore. These residues adjust conformation during the photoreaction. Another aspartic acid interacts with the Schiff base after the chromophore 13-cia isomerization. The nature of the environmental perturbation is discussed for individual residues. Also discussed in the thesis are the quality control in FTIR spectroscopy, prospective experiments, the present finding's implication to the mechanism of the color regulation and proton pumping of bR, and the general structure-function relationship of opsins.","Submitted by Carolyn Mead (cmead2@illinois.edu) on 2011-05-17T15:44:16Z No. of bitstreams: 1 1988_lin.pdf: 6990244 bytes, checksum: 344c286712c187b87aaae45639b6a4c6 (MD5)","Made available in DSpace on 2011-05-17T15:44:16Z (GMT). No. of bitstreams: 1 1988_lin.pdf: 6990244 bytes, checksum: 344c286712c187b87aaae45639b6a4c6 (MD5) Previous issue date: 1988","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Carolyn Mead (cmead2@illinois.edu) on 2011-05-17T15:44:16Z Item is restricted indefinitely.","Restriction data tranferred 2014-07-01T11:13:58-05:00 Original Data Group with Access UIUC Users [automated] Release Date: none Reason: Thesis","Thesis","U of I Only"]},{"key":"dc:title","label":"Title","values":["FTIR study of carboxylic acids and tyrosines in bacteriorhodopsin"]}]}],"canonical_facts":{"dc:contributor":["Gratton, E."],"dc:creator":["Lin, Shuo-Liang"],"dc:date":["2011-05-17T15:44:16Z","10000-01-01","1988"],"dc:description":["High quality infrared difference spectra of bacteriorhodopsin (bR) were obtained in order to study its photoreaction at the molecular level. The noise level was near 10-5 in the spectral regions where amino acid residues are monitored. The excellent signal to noise ratio allowed detection of absorption changes of single amino acids during the photoreaction. Aspartic acids and glutamic acids in bR were monitored by 13C labeling. Tyrosines were monitored by both 2H and nitrate substitution. Some of the amino acid band regions were decomposed by curve fitting. Alteration of absorption bands among individual bR states were found for aspartic acids and tyrosines, but were not found for glutamic acids. These changes are interpreted as a change in protonation of at least two aspartic acids and one tyrosine. In addition one aspartic acid and one tyrosine were subject to environmental perturbation. Nitration of tyrosines indicates that none of the tyrosine spectral changes occurring during the photoreaction cycle can be attributed to tyrosine-26 or tyrosine-64. A model based on intramolecular interaction is built to elucidate the spectral change observed during the cycle. This model places the three aspartic acids and the two tyrosines near the chromophore of bR. One aspartic acid and one tyrosine, together with a hypothetical positive charge, are postulated to form the primary environment around the Schiff base of the chromophore. These residues adjust conformation during the photoreaction. Another aspartic acid interacts with the Schiff base after the chromophore 13-cia isomerization. The nature of the environmental perturbation is discussed for individual residues. Also discussed in the thesis are the quality control in FTIR spectroscopy, prospective experiments, the present finding's implication to the mechanism of the color regulation and proton pumping of bR, and the general structure-function relationship of opsins.","Submitted by Carolyn Mead (cmead2@illinois.edu) on 2011-05-17T15:44:16Z No. of bitstreams: 1 1988_lin.pdf: 6990244 bytes, checksum: 344c286712c187b87aaae45639b6a4c6 (MD5)","Made available in DSpace on 2011-05-17T15:44:16Z (GMT). No. of bitstreams: 1 1988_lin.pdf: 6990244 bytes, checksum: 344c286712c187b87aaae45639b6a4c6 (MD5) Previous issue date: 1988","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Carolyn Mead (cmead2@illinois.edu) on 2011-05-17T15:44:16Z Item is restricted indefinitely.","Restriction data tranferred 2014-07-01T11:13:58-05:00 Original Data Group with Access UIUC Users [automated] Release Date: none Reason: Thesis","Thesis","U of I Only"],"dc:identifier":["3476389","http://hdl.handle.net/2142/23914"],"dc:language":["en"],"dc:rights":["1988 Shuo-Liang Lin"],"dc:subject":["FTIR study","carboxylic acids","tyrosines","bacteriorhodopsin","infrared spectra","photoreaction","amino acid residues"],"dc:title":["FTIR study of carboxylic acids and tyrosines in bacteriorhodopsin"],"dc:type":["Dissertation / Thesis","text"],"thesis:degree_discipline":["Physics"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."]},"updated_at":"2026-07-22T22:25:22Z"}