Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation.

Allsopp R, Pavlova A, Cline T, Salyapongse AM, Gillilan RE, Di YP, Deslouches B, Klauda JB, Gumbart JC, Tristram-Nagle S
J Phys Chem B (2022 Sep 6)

PMID: 36067064 doi: 10.1021/acs.jpcb.2c03193

Submitted to SASBDB: 2022 Jan 18 Published in SASBDB: 2022 Sep 10

SASDNU4 – Di[3-deoxy-D-manno-octulosonyl]-lipid A ammonium salt deposited onto silicon wafer (oriented sample anisotropic scattering, KDO2 control) Sample: Di[3-deoxy-D-manno-octulosonyl]-lipid A (ammonium salt), unidentified lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Apr 1

SASDNV4 – Di[3-deoxy-D-manno-octulosonyl]-lipid A ammonium salt deposited onto silicon wafer in the presence of antimicrobial peptide WLBU2 (oriented sample anisotropic scattering, KDO2-WLBU2) Sample: Di[3-deoxy-D-manno-octulosonyl]-lipid A (ammonium salt) plus WLBU2, unidentified lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Apr 1

SASDNW4 – Gram-negative bacteria lipid membrane mimic deposited onto silicon wafer (oriented sample anisotropic scattering) Sample: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(10-rac-glycerol) sodium salt, 10,30-bis-[1,2-dioleoyl-sn-glycero-3-phospho]-sn-glycerol (7:2:1), lipid Buffer: water, pH: 7 Experiment: SAXS data collected at ID7A1 BioSAXS / HP-Bio Beamline, Cornell High Energy Synchrotron Source (CHESS) on 2021 Jun 23

SASDNX4 – Gram-negative bacteria lipid membrane mimic deposited onto silicon wafer in the presence of antimicrobial peptide WLBU2 (oriented sample anisotropic scattering) Sample: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanol, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(10-rac-glycerol) sodium salt, 10,30-bis-[1,2-dioleoyl-sn-glycero-3-phospho]-sn-glycerol sodium salt, WLBU2, synthetic construct lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Apr 1

SASDNY4 – Gram-positive bacteria lipid membrane mimic deposited onto silicon wafer (oriented sample anisotropic scattering) Sample: 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(10-rac-glycerol), 1,2-dioleoyl-3-trimethylammonium-propane, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 10,30-bis-[1,2-dioleoyl-sn-glycero-3-phos, lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Apr 1

SASDNZ4 – Gram-positive bacteria lipid membrane mimic deposited onto silicon wafer in the presence of antimicrobial peptide WLBU2 (oriented sample anisotropic scattering) Sample: 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(10-rac-glycerol), 1,2-dioleoyl-3-trimethylammonium-propane, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 10,30-bis-[1,2-dioleoyl-sn-glycero-3-phos, synthetic construct lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Apr 1

SASDN25 – Lipopolysaccharide outer membrane of the Gram-negative bacteria Pseudomonas aeruginosa deposited onto silicon wafer (oriented sample anisotropic scattering, LPS control) Sample: Lipopolysaccharide, Pseudomonas aeruginosa lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Jun 1

SASDN35 – Lipopolysaccharide outer membrane of the Gram-negative bacteria Pseudomonas aeruginosa deposited onto silicon wafer in the presence of antimicrobial peptide WLBU2 (LPS-WLBU2, oriented sample anisotropic scattering) Sample: Lipopolysaccharide plus WLBU2 dimer, Pseudomonas aeruginosa lipid Buffer: water, pH: 7 Experiment: SAXS data collected at G1, Cornell High Energy Synchrotron Source (CHESS) on 2018 Jun 1