{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/21296"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/21296","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Rate-window methods and myoglobin dynamics","abstract":"The problem of protein dynamics is introduced and its significance explained. Properties of the oxygen-storage protein myoglobin (Mb) as a model system for dynamics studies are discussed. Special attention is paid to Mb's physiological role, and the basic quantities that describe the protein's function. Background on ligand binding experiments in Mb is reviewed and appropriate mathematical models established. The specific goal of this work is to determine as many as possible of the model parameters (pre-exponentials and activation enthalpies of intrinsic rate coefficients), with a view towards calculation of one functionally important quantity, the CO affinity at physiological temperatures.","abstract_html":"The problem of protein dynamics is introduced and its significance explained. Properties of the oxygen-storage protein myoglobin (Mb) as a model system for dynamics studies are discussed. Special attention is paid to Mb's physiological role, and the basic quantities that describe the protein's function. Background on ligand binding experiments in Mb is reviewed and appropriate mathematical models established. The specific goal of this work is to determine as many as possible of the model parameters (pre-exponentials and activation enthalpies of intrinsic rate coefficients), with a view towards calculation of one functionally important quantity, the CO affinity at physiological temperatures.","abstract_has_math":false,"creators":["Berendzen, Joel Ray"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics","degree_department":null,"school":null,"contributors":["Frauenfelder, Hans"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2011,"date_issued":"2011-05-07T13:04:30Z","date_published":"2011-05-07T13:04:30Z","updated_at":"2026-07-22T22:25:17Z","subjects":["Chemistry, Biochemistry","Chemistry, Physical","Biophysics, General"],"languages":["eng"],"rights":["Copyright 1990 Berendzen, Joel Ray"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["AAI9026138","(UMI)AAI9026138"],"render_values":[{"text":"AAI9026138","href":null,"code":true},{"text":"(UMI)AAI9026138","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/21296","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Frauenfelder, Hans"]},{"key":"dc:creator","label":"Author","values":["Berendzen, Joel Ray"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2011-05-07T13:04:30Z","10000-01-01","1990"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics"]},{"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":["Chemistry, Biochemistry","Chemistry, Physical","Biophysics, General"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 1990 Berendzen, Joel Ray"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["AAI9026138","(UMI)AAI9026138","http://hdl.handle.net/2142/21296"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The problem of protein dynamics is introduced and its significance explained. Properties of the oxygen-storage protein myoglobin (Mb) as a model system for dynamics studies are discussed. Special attention is paid to Mb's physiological role, and the basic quantities that describe the protein's function. Background on ligand binding experiments in Mb is reviewed and appropriate mathematical models established. The specific goal of this work is to determine as many as possible of the model parameters (pre-exponentials and activation enthalpies of intrinsic rate coefficients), with a view towards calculation of one functionally important quantity, the CO affinity at physiological temperatures.","\"Relaxation spectroscopy is a powerful means for studying dynamics. Different perturbations and observables are considered, and two kinetic methods are introduced: temperature-derivative spectroscopy (TDS), a non-isothermal technique that measures the derivative of a population with respect to temperature; and deep-level transient spectroscopy (DLTS), an isothermal technique that determines the behavior of a small range of rate coefficients as a function of temperature. These \"\"rate-window\"\" methods are shown to be widely applicable and may prove highly advantageous in difficult measurements such as kinetic X-ray crystallography.\"","TDS and DLTS were used to study the rebinding of CO to sperm whale Mb after photolysis. FTIR measurements of geminate rebinding in the CO-stretch bands show distributed activation enthalpies with different distributions for each band, crossing between two bands that correspond to photolyzed ligands, and kinetic hole-burning. The distributions of activation enthalpies are well described by gaussians; the results match and complement those of traditional multi-rate methods. Further experiments determined the barriers to entry to and escape from the heme pocket for two of the bands. Information about barriers to different kinds of conformational changes were also obtained.","The kinetic differences among different protein conformations provide a mechanism by which the affinity of Mb might be modified in response to physiological demands. It is shown that this effect could be larger than that of the R- to T-state change in hemoglobin. Findings from the physiological and biochemical literature consistent with this possibility are pointed out, and specific tests are proposed.","Made available in DSpace on 2011-05-07T13:04:30Z (GMT). No. of bitstreams: 2 license.txt: 4922 bytes, checksum: 910b249b4beec47e7ab768910c8f966f (MD5) 9026138.pdf: 3686381 bytes, checksum: bb801f0c724edf6810bd716efca5f87f (MD5) Previous issue date: 1990","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Howard Ding (hding2@illinois.edu) on 2011-05-07T14:49:49Z Item is restricted indefinitely.","Restriction data tranferred 2014-07-01T11:22:42-05:00 Original Data Group with Access UIUC Users [automated] Release Date: none Reason: ETDs are only available to UIUC Users without author permission","ETDs are only available to UIUC Users without author permission","U of I Only"]},{"key":"dc:title","label":"Title","values":["Rate-window methods and myoglobin dynamics"]}]}],"canonical_facts":{"dc:contributor":["Frauenfelder, Hans"],"dc:creator":["Berendzen, Joel Ray"],"dc:date":["2011-05-07T13:04:30Z","10000-01-01","1990"],"dc:description":["The problem of protein dynamics is introduced and its significance explained. Properties of the oxygen-storage protein myoglobin (Mb) as a model system for dynamics studies are discussed. Special attention is paid to Mb's physiological role, and the basic quantities that describe the protein's function. Background on ligand binding experiments in Mb is reviewed and appropriate mathematical models established. The specific goal of this work is to determine as many as possible of the model parameters (pre-exponentials and activation enthalpies of intrinsic rate coefficients), with a view towards calculation of one functionally important quantity, the CO affinity at physiological temperatures.","\"Relaxation spectroscopy is a powerful means for studying dynamics. Different perturbations and observables are considered, and two kinetic methods are introduced: temperature-derivative spectroscopy (TDS), a non-isothermal technique that measures the derivative of a population with respect to temperature; and deep-level transient spectroscopy (DLTS), an isothermal technique that determines the behavior of a small range of rate coefficients as a function of temperature. These \"\"rate-window\"\" methods are shown to be widely applicable and may prove highly advantageous in difficult measurements such as kinetic X-ray crystallography.\"","TDS and DLTS were used to study the rebinding of CO to sperm whale Mb after photolysis. FTIR measurements of geminate rebinding in the CO-stretch bands show distributed activation enthalpies with different distributions for each band, crossing between two bands that correspond to photolyzed ligands, and kinetic hole-burning. The distributions of activation enthalpies are well described by gaussians; the results match and complement those of traditional multi-rate methods. Further experiments determined the barriers to entry to and escape from the heme pocket for two of the bands. Information about barriers to different kinds of conformational changes were also obtained.","The kinetic differences among different protein conformations provide a mechanism by which the affinity of Mb might be modified in response to physiological demands. It is shown that this effect could be larger than that of the R- to T-state change in hemoglobin. Findings from the physiological and biochemical literature consistent with this possibility are pointed out, and specific tests are proposed.","Made available in DSpace on 2011-05-07T13:04:30Z (GMT). No. of bitstreams: 2 license.txt: 4922 bytes, checksum: 910b249b4beec47e7ab768910c8f966f (MD5) 9026138.pdf: 3686381 bytes, checksum: bb801f0c724edf6810bd716efca5f87f (MD5) Previous issue date: 1990","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Howard Ding (hding2@illinois.edu) on 2011-05-07T14:49:49Z Item is restricted indefinitely.","Restriction data tranferred 2014-07-01T11:22:42-05:00 Original Data Group with Access UIUC Users [automated] Release Date: none Reason: ETDs are only available to UIUC Users without author permission","ETDs are only available to UIUC Users without author permission","U of I Only"],"dc:identifier":["AAI9026138","(UMI)AAI9026138","http://hdl.handle.net/2142/21296"],"dc:language":["eng"],"dc:rights":["Copyright 1990 Berendzen, Joel Ray"],"dc:subject":["Chemistry, Biochemistry","Chemistry, Physical","Biophysics, General"],"dc:title":["Rate-window methods and myoglobin dynamics"],"dc:type":["text"],"thesis:degree_discipline":["Biophysics"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:17Z"}