{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/127165"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/127165","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Probing human disease through protein-ligand and protein-lipid interactions via molecular simulation","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-03-28 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-03-28 without embargo terms","abstract_has_math":false,"creators":["Sinclair, Matt"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biochemistry","degree_department":null,"school":null,"contributors":["Tajkhorshid, Emad","Stadtmueller, Beth","Cronan, John","Zhang, Kai"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-11-12","date_published":"2024-11-12","updated_at":"2026-07-22T22:25:03Z","subjects":["Molecular Dynamics","Biophysics","Antibiotics","Drug Design","Simulation","Abc Transporters"],"languages":["en","eng"],"rights":["Copyright 2024 Matt Sinclair"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/127165","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Tajkhorshid, Emad","Stadtmueller, Beth","Cronan, John","Zhang, Kai"]},{"key":"dc:creator","label":"Author","values":["Sinclair, Matt"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2024-11-12","2024-12"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biochemistry"]},{"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":["Molecular Dynamics","Biophysics","Antibiotics","Drug Design","Simulation","Abc Transporters"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2024 Matt Sinclair"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/127165"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-03-28 without embargo terms","The student, Matt Sinclair, accepted the attached license on 2024-10-23 at 12:32.","The student, Matt Sinclair, submitted this Dissertation for approval on 2024-10-23 at 12:57.","This Dissertation was approved for publication on 2024-11-12 at 12:52.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21270 on 2025-03-28 at 14:25:12","The role proteins play in both healthy, steady-state metabolism, and in dysfunction is a complex interplay that remains elusive. As we continue to probe these import interactions more fully, the broader impact of perturbations in protein biology is slowly being resolved. As the role of human health in our understanding of protein biology is brought more into focus, there is a continued need for probing molecular interactions at an atomic level. More specifically, the part that a protein's local chemical environment plays in both its structure and dynamics is of increasing interest in recent years. To address this in a specific light, I have sought to understand how proteins interact with their environment in several human health-related systems. The first lens through with which I probe this question is how the landscape of clinical point mutants give rise to enzymatic dysfunction in the glucose-6-phosphatase system. The next facet that I probed is multidrug resistance, which threatens our ability to stave off pathogenic bacteria. To address this problem I examined two model systems: (i) the B. subtilis type IV ABC transporter, BmrCD, and its interactions with the phospholipid membrane in which it is situated and (ii) characterizing a novel inhibitor of the Gram-negative type VII ABC transporter, LolCDE. To address the above problems, I primarily rely on molecular dynamics (MD) to perform physics-based simulation of biomolecules. In addition to MD, I use other common biophysical, cheminformatics and bioinformatics techniques as well as data analysis strategies to examine these systems more holistically. Where possible I also sought to develop custom analysis and tools, including integrating a machine learning approach to measure membrane curvature into open source projects (SVMem/MDAnalysis) and modeling lipids from incomplete EM densities (CryoLipids). My work on the G6Pase systems highlights not only previously unreported disease-causing point mutants but also mechanistic insights into how these point mutants lead to enzyme dysfunction. Enzyme activity is attenuated by a variety of means including electrostatic over/understabilization of the native substrate, active site remodelling and simply abolishing the ability of the enzyme to be folded. Beyond point mutants my collaborators and I also demonstrated the ability of cholesterol to attenuate activity in biologically-relevant concentrations. Simulations of BmrCD elucidated the role that phospholipids play in stabilizing the various metastable conformations that demarcate different phases of the transport cycle. In the inward-facing conformation lipids are more strongly coordinated by basic residues which sit along the phosphate plane of both leaflets leading to a longer-lived IF state. Of particular note are lipids which are recruited by the elbow helix region of the protein. Through a series of rigorous steps involving molecular docking and simulation, I was able to characterize the key molecular interactions of novel inhibitor Lolamicin, with its target LolCDE. These findings corroborated experimental mutagenesis data as well as clarifying the role of activity recovery mutants which resist inhibitor activity. Taken together, this collaboration demonstrates the power of joint experimental and computational efforts towards designing next generation drugs. Characterizing the various interactions that proteins participate in with their local environments is increasingly important in understanding the atomistic details of disease-state mechanisms. My efforts to further our understanding of this interplay highlight several opportunities for future therapeutic intervention. By probing these basic science questions I hope to contribute to a meaningful body of science that dovetails nicely with probing human health and drug development."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Probing human disease through protein-ligand and protein-lipid interactions via molecular simulation"]}]}],"canonical_facts":{"dc:contributor":["Tajkhorshid, Emad","Stadtmueller, Beth","Cronan, John","Zhang, Kai"],"dc:creator":["Sinclair, Matt"],"dc:date":["2024-11-12","2024-12"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-03-28 without embargo terms","The student, Matt Sinclair, accepted the attached license on 2024-10-23 at 12:32.","The student, Matt Sinclair, submitted this Dissertation for approval on 2024-10-23 at 12:57.","This Dissertation was approved for publication on 2024-11-12 at 12:52.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21270 on 2025-03-28 at 14:25:12","The role proteins play in both healthy, steady-state metabolism, and in dysfunction is a complex interplay that remains elusive. As we continue to probe these import interactions more fully, the broader impact of perturbations in protein biology is slowly being resolved. As the role of human health in our understanding of protein biology is brought more into focus, there is a continued need for probing molecular interactions at an atomic level. More specifically, the part that a protein's local chemical environment plays in both its structure and dynamics is of increasing interest in recent years. To address this in a specific light, I have sought to understand how proteins interact with their environment in several human health-related systems. The first lens through with which I probe this question is how the landscape of clinical point mutants give rise to enzymatic dysfunction in the glucose-6-phosphatase system. The next facet that I probed is multidrug resistance, which threatens our ability to stave off pathogenic bacteria. To address this problem I examined two model systems: (i) the B. subtilis type IV ABC transporter, BmrCD, and its interactions with the phospholipid membrane in which it is situated and (ii) characterizing a novel inhibitor of the Gram-negative type VII ABC transporter, LolCDE. To address the above problems, I primarily rely on molecular dynamics (MD) to perform physics-based simulation of biomolecules. In addition to MD, I use other common biophysical, cheminformatics and bioinformatics techniques as well as data analysis strategies to examine these systems more holistically. Where possible I also sought to develop custom analysis and tools, including integrating a machine learning approach to measure membrane curvature into open source projects (SVMem/MDAnalysis) and modeling lipids from incomplete EM densities (CryoLipids). My work on the G6Pase systems highlights not only previously unreported disease-causing point mutants but also mechanistic insights into how these point mutants lead to enzyme dysfunction. Enzyme activity is attenuated by a variety of means including electrostatic over/understabilization of the native substrate, active site remodelling and simply abolishing the ability of the enzyme to be folded. Beyond point mutants my collaborators and I also demonstrated the ability of cholesterol to attenuate activity in biologically-relevant concentrations. Simulations of BmrCD elucidated the role that phospholipids play in stabilizing the various metastable conformations that demarcate different phases of the transport cycle. In the inward-facing conformation lipids are more strongly coordinated by basic residues which sit along the phosphate plane of both leaflets leading to a longer-lived IF state. Of particular note are lipids which are recruited by the elbow helix region of the protein. Through a series of rigorous steps involving molecular docking and simulation, I was able to characterize the key molecular interactions of novel inhibitor Lolamicin, with its target LolCDE. These findings corroborated experimental mutagenesis data as well as clarifying the role of activity recovery mutants which resist inhibitor activity. Taken together, this collaboration demonstrates the power of joint experimental and computational efforts towards designing next generation drugs. Characterizing the various interactions that proteins participate in with their local environments is increasingly important in understanding the atomistic details of disease-state mechanisms. My efforts to further our understanding of this interplay highlight several opportunities for future therapeutic intervention. By probing these basic science questions I hope to contribute to a meaningful body of science that dovetails nicely with probing human health and drug development."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/127165"],"dc:language":["en","eng"],"dc:rights":["Copyright 2024 Matt Sinclair"],"dc:subject":["Molecular Dynamics","Biophysics","Antibiotics","Drug Design","Simulation","Abc Transporters"],"dc:title":["Probing human disease through protein-ligand and protein-lipid interactions via molecular simulation"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Biochemistry"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:03Z"}