{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/46668"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/46668","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Temperature- and pressure-induced protein dynamics from microseconds to minutes","abstract":"For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. This thesis describes recent experiments (and simulations) of fast protein folding ranging from microseconds to minutes using temperature and pressure as perturbation variables. Chapter 1 compares recent progress in the field of fast protein folding from experimental and computational sides. Chapters 2--5 are dedicated to unveiling the mechanism of folding of a model protein called lambda-repressor fragment 6-85. Specifically, Chapter 2 describes an effort to identify the rate-limiting step of lambda-repressor folding, Chapter 3 discusses potential origins of the slow (millisecond) phase in the folding of some lambda-repressor mutants, Chapter 4 deals with lambda-repressor refolding after a large ultrafast pressure jump, and Chapter 5 investigates the mechanism of lambda-repressor folding monitored using multiple fluorescent probes to achieve better structural resolution of the folding process. Chapter 5 also compares lambda-repressor folding triggered by temperature and pressure perturbations. Chapter 6 explores how the pressure-temperature phase-diagram of phosphoglycerate kinase is influenced by macromolecular crowding. In Chapter 7, an outreach project is described where simple mechanical and computer models of protein folding were used to teach students at the high school and undergraduate levels about scientific modeling and other basic concepts in physical chemistry and statistics. The ultimate goal of these endeavors is to map out the energy landscapes of proteins and to generate ''molecular movies'', which reveal protein (mis)folding dynamics in atomistic detail. To this end, I have been striving to refine experiments (and guide simulations) to provide better mechanistic detail and tackle the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.","abstract_html":"For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. This thesis describes recent experiments (and simulations) of fast protein folding ranging from microseconds to minutes using temperature and pressure as perturbation variables. Chapter 1 compares recent progress in the field of fast protein folding from experimental and computational sides. Chapters 2--5 are dedicated to unveiling the mechanism of folding of a model protein called lambda-repressor fragment 6-85. Specifically, Chapter 2 describes an effort to identify the rate-limiting step of lambda-repressor folding, Chapter 3 discusses potential origins of the slow (millisecond) phase in the folding of some lambda-repressor mutants, Chapter 4 deals with lambda-repressor refolding after a large ultrafast pressure jump, and Chapter 5 investigates the mechanism of lambda-repressor folding monitored using multiple fluorescent probes to achieve better structural resolution of the folding process. Chapter 5 also compares lambda-repressor folding triggered by temperature and pressure perturbations. Chapter 6 explores how the pressure-temperature phase-diagram of phosphoglycerate kinase is influenced by macromolecular crowding. In Chapter 7, an outreach project is described where simple mechanical and computer models of protein folding were used to teach students at the high school and undergraduate levels about scientific modeling and other basic concepts in physical chemistry and statistics. The ultimate goal of these endeavors is to map out the energy landscapes of proteins and to generate ''molecular movies'', which reveal protein (mis)folding dynamics in atomistic detail. To this end, I have been striving to refine experiments (and guide simulations) to provide better mechanistic detail and tackle the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.","abstract_has_math":false,"creators":["Prigozhin, Maxim"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Chemical Physics","degree_department":null,"school":null,"contributors":["Gruebele, Martin","Martin Gruebele","Murphy, Catherine J.","Luthey-Schulten, Zaida A.","Chemla, Yann R."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-01-16T17:58:26Z","date_published":"2014-01-16T17:58:26Z","updated_at":"2026-07-22T22:25:36Z","subjects":["biophysics","molecular biology","protein biochemistry","fast protein folding","downhill folding","fluorescence spectroscopy","temperature jump","pressure jump","molecular kinetics","molecular dynamics simulations","infrared spectroscopy","circular dichroism spectroscopy","Outreach","scientific modelling"],"languages":["en"],"rights":["Copyright 2013 Maxim Prigozhin"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/46668","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gruebele, Martin","Martin Gruebele","Murphy, Catherine J.","Luthey-Schulten, Zaida A.","Chemla, Yann R."]},{"key":"dc:creator","label":"Author","values":["Prigozhin, Maxim"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2014-01-16T17:58:26Z","2013-12"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemical Physics"]},{"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":["biophysics","molecular biology","protein biochemistry","fast protein folding","downhill folding","fluorescence spectroscopy","temperature jump","pressure jump","molecular kinetics","molecular dynamics simulations","infrared spectroscopy","circular dichroism spectroscopy","Outreach","scientific modelling"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2013 Maxim Prigozhin"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/46668"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. This thesis describes recent experiments (and simulations) of fast protein folding ranging from microseconds to minutes using temperature and pressure as perturbation variables. Chapter 1 compares recent progress in the field of fast protein folding from experimental and computational sides. Chapters 2--5 are dedicated to unveiling the mechanism of folding of a model protein called lambda-repressor fragment 6-85. Specifically, Chapter 2 describes an effort to identify the rate-limiting step of lambda-repressor folding, Chapter 3 discusses potential origins of the slow (millisecond) phase in the folding of some lambda-repressor mutants, Chapter 4 deals with lambda-repressor refolding after a large ultrafast pressure jump, and Chapter 5 investigates the mechanism of lambda-repressor folding monitored using multiple fluorescent probes to achieve better structural resolution of the folding process. Chapter 5 also compares lambda-repressor folding triggered by temperature and pressure perturbations. Chapter 6 explores how the pressure-temperature phase-diagram of phosphoglycerate kinase is influenced by macromolecular crowding. In Chapter 7, an outreach project is described where simple mechanical and computer models of protein folding were used to teach students at the high school and undergraduate levels about scientific modeling and other basic concepts in physical chemistry and statistics. The ultimate goal of these endeavors is to map out the energy landscapes of proteins and to generate ''molecular movies'', which reveal protein (mis)folding dynamics in atomistic detail. To this end, I have been striving to refine experiments (and guide simulations) to provide better mechanistic detail and tackle the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.","Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2013-12-05T21:23:40Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Prigozhin_Maxim.pdf: 48630707 bytes, checksum: a49c12131fc45fd544cbbf5752485f6a (MD5)","Made available in DSpace on 2014-01-16T17:58:26Z (GMT). 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Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. This thesis describes recent experiments (and simulations) of fast protein folding ranging from microseconds to minutes using temperature and pressure as perturbation variables. Chapter 1 compares recent progress in the field of fast protein folding from experimental and computational sides. Chapters 2--5 are dedicated to unveiling the mechanism of folding of a model protein called lambda-repressor fragment 6-85. Specifically, Chapter 2 describes an effort to identify the rate-limiting step of lambda-repressor folding, Chapter 3 discusses potential origins of the slow (millisecond) phase in the folding of some lambda-repressor mutants, Chapter 4 deals with lambda-repressor refolding after a large ultrafast pressure jump, and Chapter 5 investigates the mechanism of lambda-repressor folding monitored using multiple fluorescent probes to achieve better structural resolution of the folding process. Chapter 5 also compares lambda-repressor folding triggered by temperature and pressure perturbations. Chapter 6 explores how the pressure-temperature phase-diagram of phosphoglycerate kinase is influenced by macromolecular crowding. In Chapter 7, an outreach project is described where simple mechanical and computer models of protein folding were used to teach students at the high school and undergraduate levels about scientific modeling and other basic concepts in physical chemistry and statistics. The ultimate goal of these endeavors is to map out the energy landscapes of proteins and to generate ''molecular movies'', which reveal protein (mis)folding dynamics in atomistic detail. To this end, I have been striving to refine experiments (and guide simulations) to provide better mechanistic detail and tackle the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.","Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2013-12-05T21:23:40Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 1 Prigozhin_Maxim.pdf: 48630707 bytes, checksum: a49c12131fc45fd544cbbf5752485f6a (MD5)","Made available in DSpace on 2014-01-16T17:58:26Z (GMT). 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