{"id":{"repo_id":"gmu","oai_identifier":"oai:MARS:1920/13754"},"canonical_url":"https://search.dev.ndltd.org/etd/gmu/oai:MARS:1920/13754","repository":{"repo_id":"gmu","name":"George Mason University","base_url":"https://mars.gmu.edu/server/oai/request"},"display":{"title":"Interactions of PGLa Peptides with Bacterial Membranes","abstract":"PGLA is an antimicrobial peptide (AMP) isolated from the skin of the Xenopus laevis frog. AMPs are being studied as a potential new source of new antibiotics, which are needed because of problems with drug resistant bacteria. PGLA has been shown to be effective against many bacteria and fungi, but it is also hemolytic in high concentrations. It appears that PGLA works by increasing the permeability of the membrane, although the exact mechanism remains unknown. To gain molecular insights into PGLa cytotoxicity, we used molecular dynamics simulations to probe binding of PGLa peptides to microbial-like membranes. Our objectives were three-fold. First, to determine the best method for sampling peptide-bilayer interactions, we compared replica exchange molecular dynamics with solute tempering (REST) against replica exchange molecular dynamics with hybrid tempering (REHT), which had never before been used for peptide membrane interactions. Specifically, we performed REST and REHT simulations of PGLa monomers binding to a simplified mimic of a bacterial membrane (DMPC-DMPG). We found that REHT was significantly more efficient than standard REST. Although REHT required 66% more replicas (20 vs. 12), we estimated that it would take between 2 and 3 times longer to equilibrate the simulation system using REST compared to REHT (Bowers, Lockhart, and Klimov, 2023). As a result, using the same computer resources, it would require about 50% longer to equilibrate using REST than REHT. Although REST did not equilibrate the system in 400ns, it did map the same bimodal binding mechanism but not in the same weights. REST would eventually generate an equilibrated ensemble of structures after sufficiently long simulation times. Second, using REHT we exhaustively studied the mechanism of PGLa monomer binding to DMPC/DMPG bilayer. These simulations utilized low peptide:lipid (P:L) ratio blocking, by design, PGLa aggregation. We found that the binding free energy landscape identifies two major bound states, a metastable surface bound state and a dominant inserted state. In both states positively charged PGLa amino acids maintain electrostatic interactions with anionic phosphate groups by rotating the PGLa helix around its axis. PGLa binding causes an influx of anionic DMPG and efflux of zwitterionic DMPC lipids from the peptide proximity. PGLa thins the bilayer and disorders the adjacent fatty acid tails. Deep invasion of water wires into the bilayer hydrophobic core is detected in the inserted peptide state. The analysis of charge density distributions indicated that peptide positive charges are nearly compensated by lipid negative charges and water dipole ordering, whereas ions play no role in peptide binding. Thus, electrostatic interactions are the key energetic factor in binding cationic PGLa to anionic DMPC/DMPG bilayer. Third, we used REST to study PGLa binding to a model anionic DMPC/DMPG bilayer at high P:L ratio, which promotes PGLa aggregation. As a reference we used our previous simulations at the low peptide: lipid ratio. We found that the increase in the peptide: lipid ratio suppresses PGLa helical propensity, tilts the bound peptide toward the bilayer hydrophobic core, and forces it deeper into the bilayer. Surprisingly, at the high peptide: lipid ratio PGLa binding induces weaker bilayer thinning, but deeper water permeation. We explain these effects by cross-correlations between lipid shells surrounding PGLa that leads to a much-diminished efflux of DMPC lipids from the peptide proximity at the high P:L ratio. Consistent with the experimental data the propensity for PGLa self-aggregation was found to be weak resulting in coexistence of monomers and dimers with distinctive properties. PGLa dimers assemble via apolar crisscross interface and become partially expelled from the bilayer residing at the bilayer-water boundary. We rationalize their properties by the dimer tendency to preserve favorable electrostatic interactions between lysine groups and phosphate lipid groups as well as to avoid electrostatic repulsion between lysine in the low dielectric environment of the bilayer core. PGLa aggregation was found to be distinct from that involved in PGLa-magainine heterodimers. Taken together, our studies provide molecular level information on the early events of PGLa binding and aggregation in anionic lipid bilayers.","abstract_html":"PGLA is an antimicrobial peptide (AMP) isolated from the skin of the Xenopus laevis frog. AMPs are being studied as a potential new source of new antibiotics, which are needed because of problems with drug resistant bacteria. PGLA has been shown to be effective against many bacteria and fungi, but it is also hemolytic in high concentrations. It appears that PGLA works by increasing the permeability of the membrane, although the exact mechanism remains unknown. To gain molecular insights into PGLa cytotoxicity, we used molecular dynamics simulations to probe binding of PGLa peptides to microbial-like membranes. Our objectives were three-fold. First, to determine the best method for sampling peptide-bilayer interactions, we compared replica exchange molecular dynamics with solute tempering (REST) against replica exchange molecular dynamics with hybrid tempering (REHT), which had never before been used for peptide membrane interactions. Specifically, we performed REST and REHT simulations of PGLa monomers binding to a simplified mimic of a bacterial membrane (DMPC-DMPG). We found that REHT was significantly more efficient than standard REST. Although REHT required 66% more replicas (20 vs. 12), we estimated that it would take between 2 and 3 times longer to equilibrate the simulation system using REST compared to REHT (Bowers, Lockhart, and Klimov, 2023). As a result, using the same computer resources, it would require about 50% longer to equilibrate using REST than REHT. Although REST did not equilibrate the system in 400ns, it did map the same bimodal binding mechanism but not in the same weights. REST would eventually generate an equilibrated ensemble of structures after sufficiently long simulation times. Second, using REHT we exhaustively studied the mechanism of PGLa monomer binding to DMPC/DMPG bilayer. These simulations utilized low peptide:lipid (P:L) ratio blocking, by design, PGLa aggregation. We found that the binding free energy landscape identifies two major bound states, a metastable surface bound state and a dominant inserted state. In both states positively charged PGLa amino acids maintain electrostatic interactions with anionic phosphate groups by rotating the PGLa helix around its axis. PGLa binding causes an influx of anionic DMPG and efflux of zwitterionic DMPC lipids from the peptide proximity. PGLa thins the bilayer and disorders the adjacent fatty acid tails. Deep invasion of water wires into the bilayer hydrophobic core is detected in the inserted peptide state. The analysis of charge density distributions indicated that peptide positive charges are nearly compensated by lipid negative charges and water dipole ordering, whereas ions play no role in peptide binding. Thus, electrostatic interactions are the key energetic factor in binding cationic PGLa to anionic DMPC/DMPG bilayer. Third, we used REST to study PGLa binding to a model anionic DMPC/DMPG bilayer at high P:L ratio, which promotes PGLa aggregation. As a reference we used our previous simulations at the low peptide: lipid ratio. We found that the increase in the peptide: lipid ratio suppresses PGLa helical propensity, tilts the bound peptide toward the bilayer hydrophobic core, and forces it deeper into the bilayer. Surprisingly, at the high peptide: lipid ratio PGLa binding induces weaker bilayer thinning, but deeper water permeation. We explain these effects by cross-correlations between lipid shells surrounding PGLa that leads to a much-diminished efflux of DMPC lipids from the peptide proximity at the high P:L ratio. Consistent with the experimental data the propensity for PGLa self-aggregation was found to be weak resulting in coexistence of monomers and dimers with distinctive properties. PGLa dimers assemble via apolar crisscross interface and become partially expelled from the bilayer residing at the bilayer-water boundary. We rationalize their properties by the dimer tendency to preserve favorable electrostatic interactions between lysine groups and phosphate lipid groups as well as to avoid electrostatic repulsion between lysine in the low dielectric environment of the bilayer core. PGLa aggregation was found to be distinct from that involved in PGLa-magainine heterodimers. Taken together, our studies provide molecular level information on the early events of PGLa binding and aggregation in anionic lipid bilayers.","abstract_has_math":false,"creators":["Bowers, Steven R"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023","date_published":"2023","updated_at":"2026-07-27T19:51:56Z","subjects":["Antimicrobial peptide","PGLa","REHT","Replica Exchange","REST"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["hdl:1920/13754"],"render_values":[{"text":"hdl:1920/13754","href":null,"code":true}]}]},"links":{"outbound_url":null,"outbound_label":null,"outbound_source":null},"metadata_groups":[{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2023"]},{"key":"dc:type","label":"Dc Type","values":["Dissertation"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Antimicrobial peptide","PGLa","REHT","Replica Exchange","REST"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["hdl:1920/13754"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.other","label":"Dc Description Other","values":["PGLA is an antimicrobial peptide (AMP) isolated from the skin of the Xenopus laevis frog. AMPs are being studied as a potential new source of new antibiotics, which are needed because of problems with drug resistant bacteria. PGLA has been shown to be effective against many bacteria and fungi, but it is also hemolytic in high concentrations. It appears that PGLA works by increasing the permeability of the membrane, although the exact mechanism remains unknown. To gain molecular insights into PGLa cytotoxicity, we used molecular dynamics simulations to probe binding of PGLa peptides to microbial-like membranes. Our objectives were three-fold. First, to determine the best method for sampling peptide-bilayer interactions, we compared replica exchange molecular dynamics with solute tempering (REST) against replica exchange molecular dynamics with hybrid tempering (REHT), which had never before been used for peptide membrane interactions. Specifically, we performed REST and REHT simulations of PGLa monomers binding to a simplified mimic of a bacterial membrane (DMPC-DMPG). We found that REHT was significantly more efficient than standard REST. Although REHT required 66% more replicas (20 vs. 12), we estimated that it would take between 2 and 3 times longer to equilibrate the simulation system using REST compared to REHT (Bowers, Lockhart, and Klimov, 2023). As a result, using the same computer resources, it would require about 50% longer to equilibrate using REST than REHT. Although REST did not equilibrate the system in 400ns, it did map the same bimodal binding mechanism but not in the same weights. REST would eventually generate an equilibrated ensemble of structures after sufficiently long simulation times. Second, using REHT we exhaustively studied the mechanism of PGLa monomer binding to DMPC/DMPG bilayer. These simulations utilized low peptide:lipid (P:L) ratio blocking, by design, PGLa aggregation. We found that the binding free energy landscape identifies two major bound states, a metastable surface bound state and a dominant inserted state. In both states positively charged PGLa amino acids maintain electrostatic interactions with anionic phosphate groups by rotating the PGLa helix around its axis. PGLa binding causes an influx of anionic DMPG and efflux of zwitterionic DMPC lipids from the peptide proximity. PGLa thins the bilayer and disorders the adjacent fatty acid tails. Deep invasion of water wires into the bilayer hydrophobic core is detected in the inserted peptide state. The analysis of charge density distributions indicated that peptide positive charges are nearly compensated by lipid negative charges and water dipole ordering, whereas ions play no role in peptide binding. Thus, electrostatic interactions are the key energetic factor in binding cationic PGLa to anionic DMPC/DMPG bilayer. Third, we used REST to study PGLa binding to a model anionic DMPC/DMPG bilayer at high P:L ratio, which promotes PGLa aggregation. As a reference we used our previous simulations at the low peptide: lipid ratio. We found that the increase in the peptide: lipid ratio suppresses PGLa helical propensity, tilts the bound peptide toward the bilayer hydrophobic core, and forces it deeper into the bilayer. Surprisingly, at the high peptide: lipid ratio PGLa binding induces weaker bilayer thinning, but deeper water permeation. We explain these effects by cross-correlations between lipid shells surrounding PGLa that leads to a much-diminished efflux of DMPC lipids from the peptide proximity at the high P:L ratio. Consistent with the experimental data the propensity for PGLa self-aggregation was found to be weak resulting in coexistence of monomers and dimers with distinctive properties. PGLa dimers assemble via apolar crisscross interface and become partially expelled from the bilayer residing at the bilayer-water boundary. We rationalize their properties by the dimer tendency to preserve favorable electrostatic interactions between lysine groups and phosphate lipid groups as well as to avoid electrostatic repulsion between lysine in the low dielectric environment of the bilayer core. PGLa aggregation was found to be distinct from that involved in PGLa-magainine heterodimers. Taken together, our studies provide molecular level information on the early events of PGLa binding and aggregation in anionic lipid bilayers."]},{"key":"dc:title","label":"Title","values":["Interactions of PGLa Peptides with Bacterial Membranes"]}]}],"canonical_facts":{"dc:date.issued":["2023"],"dc:description.other":["PGLA is an antimicrobial peptide (AMP) isolated from the skin of the Xenopus laevis frog. AMPs are being studied as a potential new source of new antibiotics, which are needed because of problems with drug resistant bacteria. PGLA has been shown to be effective against many bacteria and fungi, but it is also hemolytic in high concentrations. It appears that PGLA works by increasing the permeability of the membrane, although the exact mechanism remains unknown. To gain molecular insights into PGLa cytotoxicity, we used molecular dynamics simulations to probe binding of PGLa peptides to microbial-like membranes. Our objectives were three-fold. First, to determine the best method for sampling peptide-bilayer interactions, we compared replica exchange molecular dynamics with solute tempering (REST) against replica exchange molecular dynamics with hybrid tempering (REHT), which had never before been used for peptide membrane interactions. Specifically, we performed REST and REHT simulations of PGLa monomers binding to a simplified mimic of a bacterial membrane (DMPC-DMPG). We found that REHT was significantly more efficient than standard REST. Although REHT required 66% more replicas (20 vs. 12), we estimated that it would take between 2 and 3 times longer to equilibrate the simulation system using REST compared to REHT (Bowers, Lockhart, and Klimov, 2023). As a result, using the same computer resources, it would require about 50% longer to equilibrate using REST than REHT. Although REST did not equilibrate the system in 400ns, it did map the same bimodal binding mechanism but not in the same weights. REST would eventually generate an equilibrated ensemble of structures after sufficiently long simulation times. Second, using REHT we exhaustively studied the mechanism of PGLa monomer binding to DMPC/DMPG bilayer. These simulations utilized low peptide:lipid (P:L) ratio blocking, by design, PGLa aggregation. We found that the binding free energy landscape identifies two major bound states, a metastable surface bound state and a dominant inserted state. In both states positively charged PGLa amino acids maintain electrostatic interactions with anionic phosphate groups by rotating the PGLa helix around its axis. PGLa binding causes an influx of anionic DMPG and efflux of zwitterionic DMPC lipids from the peptide proximity. PGLa thins the bilayer and disorders the adjacent fatty acid tails. Deep invasion of water wires into the bilayer hydrophobic core is detected in the inserted peptide state. The analysis of charge density distributions indicated that peptide positive charges are nearly compensated by lipid negative charges and water dipole ordering, whereas ions play no role in peptide binding. Thus, electrostatic interactions are the key energetic factor in binding cationic PGLa to anionic DMPC/DMPG bilayer. Third, we used REST to study PGLa binding to a model anionic DMPC/DMPG bilayer at high P:L ratio, which promotes PGLa aggregation. As a reference we used our previous simulations at the low peptide: lipid ratio. We found that the increase in the peptide: lipid ratio suppresses PGLa helical propensity, tilts the bound peptide toward the bilayer hydrophobic core, and forces it deeper into the bilayer. Surprisingly, at the high peptide: lipid ratio PGLa binding induces weaker bilayer thinning, but deeper water permeation. We explain these effects by cross-correlations between lipid shells surrounding PGLa that leads to a much-diminished efflux of DMPC lipids from the peptide proximity at the high P:L ratio. Consistent with the experimental data the propensity for PGLa self-aggregation was found to be weak resulting in coexistence of monomers and dimers with distinctive properties. PGLa dimers assemble via apolar crisscross interface and become partially expelled from the bilayer residing at the bilayer-water boundary. We rationalize their properties by the dimer tendency to preserve favorable electrostatic interactions between lysine groups and phosphate lipid groups as well as to avoid electrostatic repulsion between lysine in the low dielectric environment of the bilayer core. PGLa aggregation was found to be distinct from that involved in PGLa-magainine heterodimers. Taken together, our studies provide molecular level information on the early events of PGLa binding and aggregation in anionic lipid bilayers."],"dc:identifier":["hdl:1920/13754"],"dc:subject":["Antimicrobial peptide","PGLa","REHT","Replica Exchange","REST"],"dc:title":["Interactions of PGLa Peptides with Bacterial Membranes"],"dc:type":["Dissertation"]},"updated_at":"2026-07-27T19:51:56Z"}