{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/22296"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/22296","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Molecular dynamics studies of membranes and membrane proteins","abstract":"Properties of phospholipid membrane bilayers and of proteins associating and functioning in the membrane bilayer or at the membrane-water interface are studied by combining molecular dynamics simulations, free energy perturbation theory and continuum electrostatics calculations. Three systems were investigated: (1) The proton pump cycle of the integral membrane protein bacteriorhodopsin: The photoisomerization and subsequent thermal reactions of the protein were studied by molecular dynamics simulations. Internal water molecules were placed in the protein. The studies attribute a key role to the Schiff base-counterion electrostatic interaction in controlling the initial photoreaction and revealed an important role of internal water molecules for the function of bacteriorhodopsin. (2) A dilaurylphosphatidylethanolamine membrane bilayer solvated in excess water: Structural properties of the membrane, electrostatic properties of the membrane-water interface and charge distributions on the membrane surface were characterized. (3) The activation of enzyme human synovial phospholipase A$\\sb2$ at membrane surface was investigated. The activation was attributed to desolvation effects of lipid head groups in a tight enzyme-membrane complex. The electrostatic interactions between the enzyme and the membrane were studied and found to favor the binding of negatively charged lipid molecules to the enzyme-membrane interface.","abstract_html":"Properties of phospholipid membrane bilayers and of proteins associating and functioning in the membrane bilayer or at the membrane-water interface are studied by combining molecular dynamics simulations, free energy perturbation theory and continuum electrostatics calculations. Three systems were investigated: (1) The proton pump cycle of the integral membrane protein bacteriorhodopsin: The photoisomerization and subsequent thermal reactions of the protein were studied by molecular dynamics simulations. Internal water molecules were placed in the protein. The studies attribute a key role to the Schiff base-counterion electrostatic interaction in controlling the initial photoreaction and revealed an important role of internal water molecules for the function of bacteriorhodopsin. (2) A dilaurylphosphatidylethanolamine membrane bilayer solvated in excess water: Structural properties of the membrane, electrostatic properties of the membrane-water interface and charge distributions on the membrane surface were characterized. (3) The activation of enzyme human synovial phospholipase A$\\sb2$ at membrane surface was investigated. The activation was attributed to desolvation effects of lipid head groups in a tight enzyme-membrane complex. The electrostatic interactions between the enzyme and the membrane were studied and found to favor the binding of negatively charged lipid molecules to the enzyme-membrane interface.","abstract_has_math":true,"creators":["Zhou, Feng"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics and Computational Biology","degree_department":null,"school":null,"contributors":["Schulten, Klaus J."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2011,"date_issued":"2011-05-07T13:35:21Z","date_published":"2011-05-07T13:35:21Z","updated_at":"2026-07-22T22:25:19Z","subjects":["Biology, Molecular","Chemistry, Biochemistry","Chemistry, Physical"],"languages":["eng"],"rights":["Copyright 1996 Zhou, Feng"],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["AAI9625221","(UMI)AAI9625221"],"render_values":[{"text":"AAI9625221","href":null,"code":true},{"text":"(UMI)AAI9625221","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/22296","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Schulten, Klaus J."]},{"key":"dc:creator","label":"Author","values":["Zhou, Feng"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2011-05-07T13:35:21Z","10000-01-01","1996"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics and Computational 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":["Biology, Molecular","Chemistry, Biochemistry","Chemistry, Physical"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 1996 Zhou, Feng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["AAI9625221","(UMI)AAI9625221","http://hdl.handle.net/2142/22296"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Properties of phospholipid membrane bilayers and of proteins associating and functioning in the membrane bilayer or at the membrane-water interface are studied by combining molecular dynamics simulations, free energy perturbation theory and continuum electrostatics calculations. 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