{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/97595"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/97595","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Automated protein NMR data analysis and its application to a-synuclein fibrils","abstract":"In principle, nuclear magnetic resonance (NMR) spectroscopy provides structural and conformational information with sub-Angstrom precision and the ability to measure dynamics with timescales ranging from femtoseconds to years, all with atomic specificity. However, due to the relatively low sensitivity of NMR, fundamental limits on spectral resolution, and the complexity of the quantum mechanical phenomena NMR exploits, that wealth of information often remains out of reach. The highly varied presentation of molecular information in NMR spectra and the difficulty of numerical simulation of non-trivial systems has lead the majority of data analysis to be performed by trained experts, and because of its time-intensive nature, that analysis is rarely replicated by a third party or validated in an objective manner. In this dissertation I report my efforts to automate NMR data analysis in an objective and replicable manner and to provide tools for validation of resulting three-dimensional structures by direct comparison to raw spectral data. The first method, COMPASS, attempts to extract as much information as possible from a single 13C-13C two-dimensional spectrum for the determination of protein structure and successfully identified the true structure of 15 test proteins. The second method, GPS, predicts features of data that would be expected given a set of chemical shift assignments and possibly a three-dimensional structure and uses the presence or absence of those features in experimental spectra to refine or validate a given structure. I then report my application of these computational methods to the problems of refining an a-synuclein fibril structure with proton-detected NMR data, the analysis and characterization of a pair of interrelated a-synuclein fibril strains with distinct pathological properties, and to the general question of fibril polymorphism, a phenomenon that presents a substantial challenge to forming consistent conclusions about fibril properties and interactions across samples and research groups.","abstract_html":"In principle, nuclear magnetic resonance (NMR) spectroscopy provides structural and conformational information with sub-Angstrom precision and the ability to measure dynamics with timescales ranging from femtoseconds to years, all with atomic specificity. However, due to the relatively low sensitivity of NMR, fundamental limits on spectral resolution, and the complexity of the quantum mechanical phenomena NMR exploits, that wealth of information often remains out of reach. The highly varied presentation of molecular information in NMR spectra and the difficulty of numerical simulation of non-trivial systems has lead the majority of data analysis to be performed by trained experts, and because of its time-intensive nature, that analysis is rarely replicated by a third party or validated in an objective manner. In this dissertation I report my efforts to automate NMR data analysis in an objective and replicable manner and to provide tools for validation of resulting three-dimensional structures by direct comparison to raw spectral data. The first method, COMPASS, attempts to extract as much information as possible from a single 13C-13C two-dimensional spectrum for the determination of protein structure and successfully identified the true structure of 15 test proteins. The second method, GPS, predicts features of data that would be expected given a set of chemical shift assignments and possibly a three-dimensional structure and uses the presence or absence of those features in experimental spectra to refine or validate a given structure. I then report my application of these computational methods to the problems of refining an a-synuclein fibril structure with proton-detected NMR data, the analysis and characterization of a pair of interrelated a-synuclein fibril strains with distinct pathological properties, and to the general question of fibril polymorphism, a phenomenon that presents a substantial challenge to forming consistent conclusions about fibril properties and interactions across samples and research groups.","abstract_has_math":false,"creators":["Courtney, Joseph M"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Chemistry","degree_department":null,"school":null,"contributors":["Rienstra, Chad M.","Gruebele, Martin","Hammes-Schiffer, Sharon","Oldfield, Eric"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017-08-10T19:52:10Z","date_published":"2017-08-10T19:52:10Z","updated_at":"2026-07-22T22:24:34Z","subjects":["Alpha-synuclein","Magic-angle spinning (MAS)","Solid-state nuclear magnetic resonance (SSNMR)"],"languages":["en"],"rights":["Copyright 2017 Joseph Courtney"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/97595","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Rienstra, Chad M.","Gruebele, Martin","Hammes-Schiffer, Sharon","Oldfield, Eric"]},{"key":"dc:creator","label":"Author","values":["Courtney, Joseph M"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2017-08-10T19:52:10Z","2019-08-11T09:15:21Z","2017-04-19","2017-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Chemistry"]},{"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":["Alpha-synuclein","Magic-angle spinning (MAS)","Solid-state nuclear magnetic resonance (SSNMR)"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2017 Joseph Courtney"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/97595"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["In principle, nuclear magnetic resonance (NMR) spectroscopy provides structural and conformational information with sub-Angstrom precision and the ability to measure dynamics with timescales ranging from femtoseconds to years, all with atomic specificity. However, due to the relatively low sensitivity of NMR, fundamental limits on spectral resolution, and the complexity of the quantum mechanical phenomena NMR exploits, that wealth of information often remains out of reach. The highly varied presentation of molecular information in NMR spectra and the difficulty of numerical simulation of non-trivial systems has lead the majority of data analysis to be performed by trained experts, and because of its time-intensive nature, that analysis is rarely replicated by a third party or validated in an objective manner. In this dissertation I report my efforts to automate NMR data analysis in an objective and replicable manner and to provide tools for validation of resulting three-dimensional structures by direct comparison to raw spectral data. The first method, COMPASS, attempts to extract as much information as possible from a single 13C-13C two-dimensional spectrum for the determination of protein structure and successfully identified the true structure of 15 test proteins. The second method, GPS, predicts features of data that would be expected given a set of chemical shift assignments and possibly a three-dimensional structure and uses the presence or absence of those features in experimental spectra to refine or validate a given structure. I then report my application of these computational methods to the problems of refining an a-synuclein fibril structure with proton-detected NMR data, the analysis and characterization of a pair of interrelated a-synuclein fibril strains with distinct pathological properties, and to the general question of fibril polymorphism, a phenomenon that presents a substantial challenge to forming consistent conclusions about fibril properties and interactions across samples and research groups.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-05-01","The student, Joseph Courtney, accepted the attached license on 2017-04-18 at 13:24.","The student, Joseph Courtney, submitted this Dissertation for approval on 2017-04-18 at 13:29.","This Dissertation was approved for publication on 2017-04-19 at 08:43.","DSpace SAF Submission Ingestion Package generated from Vireo submission #10859 on 2017-08-10 at 14:31:38","Made available in DSpace on 2017-08-10T19:52:10Z (GMT). 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The first method, COMPASS, attempts to extract as much information as possible from a single 13C-13C two-dimensional spectrum for the determination of protein structure and successfully identified the true structure of 15 test proteins. The second method, GPS, predicts features of data that would be expected given a set of chemical shift assignments and possibly a three-dimensional structure and uses the presence or absence of those features in experimental spectra to refine or validate a given structure. I then report my application of these computational methods to the problems of refining an a-synuclein fibril structure with proton-detected NMR data, the analysis and characterization of a pair of interrelated a-synuclein fibril strains with distinct pathological properties, and to the general question of fibril polymorphism, a phenomenon that presents a substantial challenge to forming consistent conclusions about fibril properties and interactions across samples and research groups.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2019-05-01","The student, Joseph Courtney, accepted the attached license on 2017-04-18 at 13:24.","The student, Joseph Courtney, submitted this Dissertation for approval on 2017-04-18 at 13:29.","This Dissertation was approved for publication on 2017-04-19 at 08:43.","DSpace SAF Submission Ingestion Package generated from Vireo submission #10859 on 2017-08-10 at 14:31:38","Made available in DSpace on 2017-08-10T19:52:10Z (GMT). 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