{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/30806"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/30806","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Mesoscopic modeling of protein conformational changes","abstract":"\"The conformational changes of proteins are studied theoretically with the help of coarsegrained mesoscopic models of protein structure. The models explicitly incorporate the effects of the polarity of the peptide backbone and of the specificity of hydrophobic interactions. These two features are found essential to give a realistic phase diagram of a coiled-coil peptide without producing spurious hydrophobically collapsed \"\"molten-globule\"\" states. The model is simple enough to allow the computational simulation of protein folding events occurring in millisecond time scales. We use the model to analyze the behavior of proteins under the perturbation due to external forces. Force induced folding/refolding transitions show a significant hysteresis in the millisecond time scale. We find that, in general, proteins do not deform continuously as elastic bodies do, but exhibit abrupt unfolding transitions, instead.\"","abstract_html":""The conformational changes of proteins are studied theoretically with the help of coarsegrained mesoscopic models of protein structure. The models explicitly incorporate the effects of the polarity of the peptide backbone and of the specificity of hydrophobic interactions. These two features are found essential to give a realistic phase diagram of a coiled-coil peptide without producing spurious hydrophobically collapsed ""molten-globule"" states. The model is simple enough to allow the computational simulation of protein folding events occurring in millisecond time scales. We use the model to analyze the behavior of proteins under the perturbation due to external forces. Force induced folding/refolding transitions show a significant hysteresis in the millisecond time scale. We find that, in general, proteins do not deform continuously as elastic bodies do, but exhibit abrupt unfolding transitions, instead."","abstract_has_math":false,"creators":["Balsera, Manuel-Angel"],"institution":null,"degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Physics","degree_department":null,"school":null,"contributors":["Oono, Yoshitsugu"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2012,"date_issued":"2012-05-05T17:53:18Z","date_published":"2012-05-05T17:53:18Z","updated_at":"2026-07-22T22:25:29Z","subjects":["protein folding, peptides, physics"],"languages":["en"],"rights":["©1998 Manuel-Angel Balsera"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["4224054"],"render_values":[{"text":"4224054","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/30806","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Oono, Yoshitsugu"]},{"key":"dc:creator","label":"Author","values":["Balsera, Manuel-Angel"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2012-05-05T17:53:18Z","10000-01-01","1998"]},{"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":["protein folding, peptides, physics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["©1998 Manuel-Angel Balsera"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["4224054","http://hdl.handle.net/2142/30806"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["\"The conformational changes of proteins are studied theoretically with the help of coarsegrained mesoscopic models of protein structure. The models explicitly incorporate the effects of the polarity of the peptide backbone and of the specificity of hydrophobic interactions. These two features are found essential to give a realistic phase diagram of a coiled-coil peptide without producing spurious hydrophobically collapsed \"\"molten-globule\"\" states. The model is simple enough to allow the computational simulation of protein folding events occurring in millisecond time scales. We use the model to analyze the behavior of proteins under the perturbation due to external forces. Force induced folding/refolding transitions show a significant hysteresis in the millisecond time scale. We find that, in general, proteins do not deform continuously as elastic bodies do, but exhibit abrupt unfolding transitions, instead.\"","Submitted by Jesse Garrison (jagarris@illinois.edu) on 2012-05-05T17:53:17Z No. of bitstreams: 1 1998_balsera.pdf: 5621877 bytes, checksum: 6ee52487bde48badf0bbea488f18c210 (MD5)","Made available in DSpace on 2012-05-05T17:53:18Z (GMT). No. of bitstreams: 1 1998_balsera.pdf: 5621877 bytes, checksum: 6ee52487bde48badf0bbea488f18c210 (MD5) Previous issue date: 1998","Restriction data tranferred 2014-07-01T11:10:36-05:00 Original Data Group with Access UIUC Users [automated] Release Date: none Reason: thesis","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Jesse Garrison (jagarris@illinois.edu) on 2012-05-05T17:53:18Z Item is restricted indefinitely.","thesis","U of I Only"]},{"key":"dc:title","label":"Title","values":["Mesoscopic modeling of protein conformational changes"]}]}],"canonical_facts":{"dc:contributor":["Oono, Yoshitsugu"],"dc:creator":["Balsera, Manuel-Angel"],"dc:date":["2012-05-05T17:53:18Z","10000-01-01","1998"],"dc:description":["\"The conformational changes of proteins are studied theoretically with the help of coarsegrained mesoscopic models of protein structure. The models explicitly incorporate the effects of the polarity of the peptide backbone and of the specificity of hydrophobic interactions. These two features are found essential to give a realistic phase diagram of a coiled-coil peptide without producing spurious hydrophobically collapsed \"\"molten-globule\"\" states. The model is simple enough to allow the computational simulation of protein folding events occurring in millisecond time scales. We use the model to analyze the behavior of proteins under the perturbation due to external forces. Force induced folding/refolding transitions show a significant hysteresis in the millisecond time scale. We find that, in general, proteins do not deform continuously as elastic bodies do, but exhibit abrupt unfolding transitions, instead.\"","Submitted by Jesse Garrison (jagarris@illinois.edu) on 2012-05-05T17:53:17Z No. of bitstreams: 1 1998_balsera.pdf: 5621877 bytes, checksum: 6ee52487bde48badf0bbea488f18c210 (MD5)","Made available in DSpace on 2012-05-05T17:53:18Z (GMT). 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