{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/85463"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/85463","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Enforced Large-Scale Motions in Proteins","abstract":"\"Steered molecular dynamics (SMD) simulations are performed on several model biomolecular systems in order to promote large structural changes in each. External forces are applied to molecular dynamics simulations to promote ligand exit from bacteriorhodopsin, unraveling of titin and fibronectin domains, and rotation of the central stalk within an ATP synthase F1 unit. SMD methods employed include linear constant-velocity extension, multiple-trial segmented path creation, and torque application to enforce angular velocities. The synthesis-direction rotation of ATP synthase central stalk led to: (i) several changes consistent with synthesis nearly 100 A away from the area of torque application, (ii) winding of the coiled-coil stalk, and (iii) a multi-step pathway that allows a key residue (\"\"arginine-finger\"\" alphaTPArg-373) to enter the ATP binding pocket, thereby inducing catalysis. Spontaneous motions of isolated ATP synthase catalytic subunits are also examined. The subunits, starting from different experimentally observed conformations, perform a combination of twisting and bending motions as they move toward a common conformation, which suggest specific mechanical roles for the subunits in central stalk rotation.\"","abstract_html":""Steered molecular dynamics (SMD) simulations are performed on several model biomolecular systems in order to promote large structural changes in each. External forces are applied to molecular dynamics simulations to promote ligand exit from bacteriorhodopsin, unraveling of titin and fibronectin domains, and rotation of the central stalk within an ATP synthase F1 unit. SMD methods employed include linear constant-velocity extension, multiple-trial segmented path creation, and torque application to enforce angular velocities. The synthesis-direction rotation of ATP synthase central stalk led to: (i) several changes consistent with synthesis nearly 100 A away from the area of torque application, (ii) winding of the coiled-coil stalk, and (iii) a multi-step pathway that allows a key residue (""arginine-finger"" alphaTPArg-373) to enter the ATP binding pocket, thereby inducing catalysis. Spontaneous motions of isolated ATP synthase catalytic subunits are also examined. The subunits, starting from different experimentally observed conformations, perform a combination of twisting and bending motions as they move toward a common conformation, which suggest specific mechanical roles for the subunits in central stalk rotation."","abstract_has_math":false,"creators":["Isralewitz, Barry"],"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"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-09-25T22:46:10Z","date_published":"2015-09-25T22:46:10Z","updated_at":"2026-07-22T22:26:25Z","subjects":["Biophysics, General"],"languages":["eng"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["(MiAaPQ)AAI3301154"],"render_values":[{"text":"(MiAaPQ)AAI3301154","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/2142/85463","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Schulten, Klaus"]},{"key":"dc:creator","label":"Author","values":["Isralewitz, Barry"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2015-09-25T22:46:10Z","10000-01-01","2007"]},{"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":["Biophysics, General"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/85463","(MiAaPQ)AAI3301154"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["\"Steered molecular dynamics (SMD) simulations are performed on several model biomolecular systems in order to promote large structural changes in each. External forces are applied to molecular dynamics simulations to promote ligand exit from bacteriorhodopsin, unraveling of titin and fibronectin domains, and rotation of the central stalk within an ATP synthase F1 unit. SMD methods employed include linear constant-velocity extension, multiple-trial segmented path creation, and torque application to enforce angular velocities. The synthesis-direction rotation of ATP synthase central stalk led to: (i) several changes consistent with synthesis nearly 100 A away from the area of torque application, (ii) winding of the coiled-coil stalk, and (iii) a multi-step pathway that allows a key residue (\"\"arginine-finger\"\" alphaTPArg-373) to enter the ATP binding pocket, thereby inducing catalysis. Spontaneous motions of isolated ATP synthase catalytic subunits are also examined. The subunits, starting from different experimentally observed conformations, perform a combination of twisting and bending motions as they move toward a common conformation, which suggest specific mechanical roles for the subunits in central stalk rotation.\"","Made available in DSpace on 2015-09-25T22:46:10Z (GMT). No. of bitstreams: 2 license.txt: 4848 bytes, checksum: 96035ab3f5e1c23cc7138a224ce498bd (MD5) 3301154.pdf: 4661579 bytes, checksum: dc0788a6ef4455138e3881fe0c31835d (MD5) Previous issue date: 2007","Embargo set by: Seth Robbins for item 86744 Lift date: Forever Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs","Restricted to the U of I community idenfinitely during batch ingest of legacy ETDs","U of I Only","154 p.","Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007."]},{"key":"dc:title","label":"Title","values":["Enforced Large-Scale Motions in Proteins"]}]}],"canonical_facts":{"dc:contributor":["Schulten, Klaus"],"dc:creator":["Isralewitz, Barry"],"dc:date":["2015-09-25T22:46:10Z","10000-01-01","2007"],"dc:description":["\"Steered molecular dynamics (SMD) simulations are performed on several model biomolecular systems in order to promote large structural changes in each. External forces are applied to molecular dynamics simulations to promote ligand exit from bacteriorhodopsin, unraveling of titin and fibronectin domains, and rotation of the central stalk within an ATP synthase F1 unit. SMD methods employed include linear constant-velocity extension, multiple-trial segmented path creation, and torque application to enforce angular velocities. The synthesis-direction rotation of ATP synthase central stalk led to: (i) several changes consistent with synthesis nearly 100 A away from the area of torque application, (ii) winding of the coiled-coil stalk, and (iii) a multi-step pathway that allows a key residue (\"\"arginine-finger\"\" alphaTPArg-373) to enter the ATP binding pocket, thereby inducing catalysis. Spontaneous motions of isolated ATP synthase catalytic subunits are also examined. The subunits, starting from different experimentally observed conformations, perform a combination of twisting and bending motions as they move toward a common conformation, which suggest specific mechanical roles for the subunits in central stalk rotation.\"","Made available in DSpace on 2015-09-25T22:46:10Z (GMT). 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