{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/117622"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/117622","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Role of lipid-protein interactions in modulating the membrane protein function","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","abstract_has_math":false,"creators":["Dehghanighahnaviyeh, Sepehr"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics & Quant Biology","degree_department":null,"school":null,"contributors":["Tajkhorshid, Emad","Shukla, Diwakar","Aksimentiev, Alek","Procko, Eric"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-12","date_published":"2022-12","updated_at":"2026-07-22T22:24:56Z","subjects":["membrane proteins","molecular dynamics simulations","lipid-protein interactions"],"languages":["en","eng"],"rights":["Copyright 2022 Sepehr Dehghanighahnaviyeh"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/117622","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Tajkhorshid, Emad","Shukla, Diwakar","Aksimentiev, Alek","Procko, Eric"]},{"key":"dc:creator","label":"Author","values":["Dehghanighahnaviyeh, Sepehr"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-12","2022-08-25"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics & Quant Biology"]},{"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":["membrane proteins","molecular dynamics simulations","lipid-protein interactions"]}]},{"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 2022 Sepehr Dehghanighahnaviyeh"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/117622"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","The student, Sepehr Dehghanighahnaviyeh, accepted the attached license on 2022-08-20 at 12:32.","The student, Sepehr Dehghanighahnaviyeh, submitted this Dissertation for approval on 2022-08-20 at 12:43.","This Dissertation was approved for publication on 2022-08-25 at 13:41.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18446 on 2023-04-12 at 08:10:15","Biological membranes are recognized as cell armors, protecting them from surrounding, nevertheless at the same time hosting some of the most important cellular processes. Biological membranes are complex assemblies consisting of diverse lipids. They house a broad range of proteins, known as membrane proteins, the functionality of which can be directly modulated by the lipid environment. Membrane proteins mediate different cellular processes that are fundamental for the flourishing of biological cells, such as translocation of ions and other solutes across membrane, signal transduction, and cell-cell recognition/communication. Despite tremendous biophysical/biochemical advances in understanding the detailed structures and functional states of different proteins, the complexity of membrane proteins demands a higher level of investment to decipher their critical roles in cellular processes. Molecular dynamics (MD) simulations have proven to be a powerful technique in shedding light on the dynamics of macromolecular structures and providing an atomic-resolution picture for diverse biological systems, including membrane proteins. The exquisite details/information provided by MD in conjunction with various experimental techniques, e.g., cryo-EM microscopy, X-ray crystallography, NMR, and electrophysiology, can assist us to better tackle complicated biological problems. Here, I have employed MD simulations and advance sampling techniques to study three membrane proteins with the focus of their detailed interactions with lipid molecules: (1) Prestin, a motor protein which functions as the sound amplifier in outer hair cells (OHCs); (2) P-glycoprotien (Pgp), an ATP-binding cassette (ABC) transporter known to cause multi-drug resistance (MDR) in cancer cells, (3) HnSpns, the bacterial homolog of Spns2 known to modulate sphingosine-1-phosphate (S1P) signaling. Exploiting MD simulation in understanding the role of lipids in modulating the functionality of these membrane proteins requires statistically-valid results which only can be achieved if the simulations are replicated. To address this issue, I was involved in the development of a software, known as Membrane Mixer Plugin (MMP), which employs non-equilibrium MD simulations to quickly shuffle lipid molecules in MD generated systems, and therefore, construct membrane/membrane-protein complexes with the same lipid compositions and different lipid configurations. The generated complexes from MMP can be simulated independently, increasing the amount of sampling."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Role of lipid-protein interactions in modulating the membrane protein function"]}]}],"canonical_facts":{"dc:contributor":["Tajkhorshid, Emad","Shukla, Diwakar","Aksimentiev, Alek","Procko, Eric"],"dc:creator":["Dehghanighahnaviyeh, Sepehr"],"dc:date":["2022-12","2022-08-25"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","The student, Sepehr Dehghanighahnaviyeh, accepted the attached license on 2022-08-20 at 12:32.","The student, Sepehr Dehghanighahnaviyeh, submitted this Dissertation for approval on 2022-08-20 at 12:43.","This Dissertation was approved for publication on 2022-08-25 at 13:41.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18446 on 2023-04-12 at 08:10:15","Biological membranes are recognized as cell armors, protecting them from surrounding, nevertheless at the same time hosting some of the most important cellular processes. Biological membranes are complex assemblies consisting of diverse lipids. They house a broad range of proteins, known as membrane proteins, the functionality of which can be directly modulated by the lipid environment. Membrane proteins mediate different cellular processes that are fundamental for the flourishing of biological cells, such as translocation of ions and other solutes across membrane, signal transduction, and cell-cell recognition/communication. Despite tremendous biophysical/biochemical advances in understanding the detailed structures and functional states of different proteins, the complexity of membrane proteins demands a higher level of investment to decipher their critical roles in cellular processes. Molecular dynamics (MD) simulations have proven to be a powerful technique in shedding light on the dynamics of macromolecular structures and providing an atomic-resolution picture for diverse biological systems, including membrane proteins. The exquisite details/information provided by MD in conjunction with various experimental techniques, e.g., cryo-EM microscopy, X-ray crystallography, NMR, and electrophysiology, can assist us to better tackle complicated biological problems. Here, I have employed MD simulations and advance sampling techniques to study three membrane proteins with the focus of their detailed interactions with lipid molecules: (1) Prestin, a motor protein which functions as the sound amplifier in outer hair cells (OHCs); (2) P-glycoprotien (Pgp), an ATP-binding cassette (ABC) transporter known to cause multi-drug resistance (MDR) in cancer cells, (3) HnSpns, the bacterial homolog of Spns2 known to modulate sphingosine-1-phosphate (S1P) signaling. Exploiting MD simulation in understanding the role of lipids in modulating the functionality of these membrane proteins requires statistically-valid results which only can be achieved if the simulations are replicated. To address this issue, I was involved in the development of a software, known as Membrane Mixer Plugin (MMP), which employs non-equilibrium MD simulations to quickly shuffle lipid molecules in MD generated systems, and therefore, construct membrane/membrane-protein complexes with the same lipid compositions and different lipid configurations. The generated complexes from MMP can be simulated independently, increasing the amount of sampling."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/117622"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Sepehr Dehghanighahnaviyeh"],"dc:subject":["membrane proteins","molecular dynamics simulations","lipid-protein interactions"],"dc:title":["Role of lipid-protein interactions in modulating the membrane protein function"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Biophysics & Quant Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:56Z"}