{"id":{"repo_id":"brock","oai_identifier":"oai:brocku.scholaris.ca:10464/20290"},"canonical_url":"https://search.dev.ndltd.org/etd/brock/oai:brocku.scholaris.ca:10464/20290","repository":{"repo_id":"brock","name":"Brock University","base_url":"https://brocku.scholaris.ca/server/oai/request"},"display":{"title":"Investigating Lipase Stability in Hydrophobic Solvent at Extreme Temperatures: A Molecular Dynamics Study of Candida Antarctica Lipase B in Polydimethylsiloxane","abstract":"Molecular dynamics (MD) simulations were employed to investigate the effects of using polydimethylsiloxane (PDMS) as a reaction solvent on the structural stability and conformational dynamics of a well known enzyme, Candida Antarctica Lipase B (CALB). In a previous study, CALB was utilized as the catalyst for the polymerization reaction of disiloxane-containing polyesters. The results demonstrated a remarkable thermal tolerance of CALB, with peak catalytic efficiency achieved at 130°C and a high level of activity maintained at 100°C after ten 24 hour reaction cycles. To investigate these results in further detail, adaptations were made to the parameterizations of a PDMS force field to enable use with the GROMACS software and were subsequently combined with the CHARMM36 biomolecular force field. Validation of the force field adaptions showed excellent agreement with the experimental results and the original force field validation. MD simulations of CALB solvated in water, glycerol and PDMS were then performed at multiple temperatures. Simulation results revealed that CALB did not experience thermal denaturation in PDMS at extreme temperatures and structural analysis showed that CALB became more rigid and compact in PDMS compared to the other solvents. The results suggest that the improved thermostability of CALB is a product of interactions between the protein and the extremely hydrophobic, non-polar PDMS. Umbrella sampling of CALB was then performed across a water-PDMS interfacial system. The free energy profile revealed a significant increase in the change in free energy from CALB solvated in water to CALB solvated in PDMS. The free energy profile also demonstrated a thermodynamic preference for the enzyme's active site residues being absorbed onto the water-PDMS interface. Analysis of an extended simulation at the interface revealed that CALB adopts and maintains an open conformation at the interface, which was not observed in either bulk water or bulk PDMS. These results provide support for the atypical interfacial activation that has been previously proposed for CALB.","abstract_html":"Molecular dynamics (MD) simulations were employed to investigate the effects of using polydimethylsiloxane (PDMS) as a reaction solvent on the structural stability and conformational dynamics of a well known enzyme, Candida Antarctica Lipase B (CALB). In a previous study, CALB was utilized as the catalyst for the polymerization reaction of disiloxane-containing polyesters. The results demonstrated a remarkable thermal tolerance of CALB, with peak catalytic efficiency achieved at 130°C and a high level of activity maintained at 100°C after ten 24 hour reaction cycles. To investigate these results in further detail, adaptations were made to the parameterizations of a PDMS force field to enable use with the GROMACS software and were subsequently combined with the CHARMM36 biomolecular force field. Validation of the force field adaptions showed excellent agreement with the experimental results and the original force field validation. MD simulations of CALB solvated in water, glycerol and PDMS were then performed at multiple temperatures. Simulation results revealed that CALB did not experience thermal denaturation in PDMS at extreme temperatures and structural analysis showed that CALB became more rigid and compact in PDMS compared to the other solvents. The results suggest that the improved thermostability of CALB is a product of interactions between the protein and the extremely hydrophobic, non-polar PDMS. Umbrella sampling of CALB was then performed across a water-PDMS interfacial system. The free energy profile revealed a significant increase in the change in free energy from CALB solvated in water to CALB solvated in PDMS. The free energy profile also demonstrated a thermodynamic preference for the enzyme's active site residues being absorbed onto the water-PDMS interface. Analysis of an extended simulation at the interface revealed that CALB adopts and maintains an open conformation at the interface, which was not observed in either bulk water or bulk PDMS. These results provide support for the atypical interfacial activation that has been previously proposed for CALB.","abstract_has_math":false,"creators":["Holditch, Nicholas Edwin Michael"],"institution":"Brock University","degree_name":"M.Sc. Physics","degree_level":"Master","degree_discipline":"Faculty of Mathematics and Science","degree_department":"Department of Physics","school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2026,"date_issued":"2026-05-01","date_published":"2026-05-01","updated_at":"2026-07-24T01:23:18Z","subjects":["Candida Antarctica Lipase B","Polydimethylsiloxane","Protein Thermal Stability","Molecular Dynamics Simulations","NATURAL SCIENCES::Physics::Atomic and molecular physics::Molecular physics"],"languages":["eng"],"rights":["Attribution-ShareAlike 4.0 International"],"rights_urls":["http://creativecommons.org/licenses/by-sa/4.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10464/20290","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.department","label":"Department","values":["Department of Physics"]},{"key":"dc:creator","label":"Author","values":["Holditch, Nicholas Edwin Michael"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2026-05-08T11:49:25Z"]},{"key":"dc:date.issued","label":"Date","values":["2026-05-01"]},{"key":"dc:publisher","label":"Institution","values":["Brock University"]},{"key":"dc:type","label":"Dc Type","values":["Electronic Thesis or Dissertation"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Faculty of Mathematics and Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Master"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.Sc. Physics"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Candida Antarctica Lipase B","Polydimethylsiloxane","Protein Thermal Stability","Molecular Dynamics Simulations","NATURAL SCIENCES::Physics::Atomic and molecular physics::Molecular physics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Attribution-ShareAlike 4.0 International"]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://creativecommons.org/licenses/by-sa/4.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10464/20290"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Molecular dynamics (MD) simulations were employed to investigate the effects of using polydimethylsiloxane (PDMS) as a reaction solvent on the structural stability and conformational dynamics of a well known enzyme, Candida Antarctica Lipase B (CALB). In a previous study, CALB was utilized as the catalyst for the polymerization reaction of disiloxane-containing polyesters. The results demonstrated a remarkable thermal tolerance of CALB, with peak catalytic efficiency achieved at 130°C and a high level of activity maintained at 100°C after ten 24 hour reaction cycles. To investigate these results in further detail, adaptations were made to the parameterizations of a PDMS force field to enable use with the GROMACS software and were subsequently combined with the CHARMM36 biomolecular force field. Validation of the force field adaptions showed excellent agreement with the experimental results and the original force field validation. MD simulations of CALB solvated in water, glycerol and PDMS were then performed at multiple temperatures. Simulation results revealed that CALB did not experience thermal denaturation in PDMS at extreme temperatures and structural analysis showed that CALB became more rigid and compact in PDMS compared to the other solvents. The results suggest that the improved thermostability of CALB is a product of interactions between the protein and the extremely hydrophobic, non-polar PDMS. Umbrella sampling of CALB was then performed across a water-PDMS interfacial system. The free energy profile revealed a significant increase in the change in free energy from CALB solvated in water to CALB solvated in PDMS. The free energy profile also demonstrated a thermodynamic preference for the enzyme's active site residues being absorbed onto the water-PDMS interface. Analysis of an extended simulation at the interface revealed that CALB adopts and maintains an open conformation at the interface, which was not observed in either bulk water or bulk PDMS. These results provide support for the atypical interfacial activation that has been previously proposed for CALB."]},{"key":"dc:title","label":"Title","values":["Investigating Lipase Stability in Hydrophobic Solvent at Extreme Temperatures: A Molecular Dynamics Study of Candida Antarctica Lipase B in Polydimethylsiloxane"]}]}],"canonical_facts":{"dc:contributor.department":["Department of Physics"],"dc:creator":["Holditch, Nicholas Edwin Michael"],"dc:date.accessioned":["2026-05-08T11:49:25Z"],"dc:date.issued":["2026-05-01"],"dc:description.abstract":["Molecular dynamics (MD) simulations were employed to investigate the effects of using polydimethylsiloxane (PDMS) as a reaction solvent on the structural stability and conformational dynamics of a well known enzyme, Candida Antarctica Lipase B (CALB). In a previous study, CALB was utilized as the catalyst for the polymerization reaction of disiloxane-containing polyesters. The results demonstrated a remarkable thermal tolerance of CALB, with peak catalytic efficiency achieved at 130°C and a high level of activity maintained at 100°C after ten 24 hour reaction cycles. To investigate these results in further detail, adaptations were made to the parameterizations of a PDMS force field to enable use with the GROMACS software and were subsequently combined with the CHARMM36 biomolecular force field. Validation of the force field adaptions showed excellent agreement with the experimental results and the original force field validation. MD simulations of CALB solvated in water, glycerol and PDMS were then performed at multiple temperatures. Simulation results revealed that CALB did not experience thermal denaturation in PDMS at extreme temperatures and structural analysis showed that CALB became more rigid and compact in PDMS compared to the other solvents. The results suggest that the improved thermostability of CALB is a product of interactions between the protein and the extremely hydrophobic, non-polar PDMS. Umbrella sampling of CALB was then performed across a water-PDMS interfacial system. The free energy profile revealed a significant increase in the change in free energy from CALB solvated in water to CALB solvated in PDMS. The free energy profile also demonstrated a thermodynamic preference for the enzyme's active site residues being absorbed onto the water-PDMS interface. Analysis of an extended simulation at the interface revealed that CALB adopts and maintains an open conformation at the interface, which was not observed in either bulk water or bulk PDMS. These results provide support for the atypical interfacial activation that has been previously proposed for CALB."],"dc:identifier.uri":["https://hdl.handle.net/10464/20290"],"dc:language.iso":["eng"],"dc:publisher":["Brock University"],"dc:rights":["Attribution-ShareAlike 4.0 International"],"dc:rights.uri":["http://creativecommons.org/licenses/by-sa/4.0/"],"dc:subject":["Candida Antarctica Lipase B","Polydimethylsiloxane","Protein Thermal Stability","Molecular Dynamics Simulations","NATURAL SCIENCES::Physics::Atomic and molecular physics::Molecular physics"],"dc:title":["Investigating Lipase Stability in Hydrophobic Solvent at Extreme Temperatures: A Molecular Dynamics Study of Candida Antarctica Lipase B in Polydimethylsiloxane"],"dc:type":["Electronic Thesis or Dissertation"],"thesis:degree_discipline":["Faculty of Mathematics and Science"],"thesis:degree_level":["Master"],"thesis:degree_name":["M.Sc. Physics"]},"updated_at":"2026-07-24T01:23:18Z"}