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) Europe PMC

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)

Lipopolysaccharide plus WLBU2
Temperature 37.0
log I(s)
Lipopolysaccharide plus WLBU2 small angle scattering data  s, nm-1
Lipopolysaccharide plus WLBU2 Kratky plot 0 s

Data validation

Fits and models

log I(s)
 s, nm-1
Lipopolysaccharide plus WLBU2 OTHER [STATIC IMAGE] model
Lipopolysaccharide plus WLBU2 OTHER model

Anisotropic synchrotron SAXS data from the lipopolysaccharide outer membrane of the Gram-negative bacteria Pseudomonas aeruginosa in the presence of antimicrobial peptide WLBU2 and deposited onto silicon wafer fully hydrated with water, pH 7 were collected on the G1 beam line at the Cornell High Energy Synchrotron Source (CHESS) storage ring (Ithaca, NY, USA) using a Finger Lakes CCD detector at a sample-detector distance of 0.35 m and at a wavelength of λ = 0.118 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The sample temperature was maintained at 37°C. Two successive 30 second frames were collected and the 2D data analysed along the principle s-z axis.

The sample is 4 mg of LPS plus WLBU2 oriented onto a silicon wafer, hydrated fully through the vapor. The area/lipid is 1.789 +/- 0.011 sq. nm. The lipid is deposited using the rock and roll procedure where the lipid (and peptide if present) is solubilized in two organic solvents - one to dissolve the lipid and the other to spread the lipid solution onto the silicon wafer. All of the organic solvent is removed under vacuum for at least two hours, after the lipid is initially dry. The sample is trimmed to a thin strip (5 mm wide) in the center of the silicon wafer. The width of the wafer is 1.5 cm and its length is 3 cm. It is 1 mm thick. The sample is fully hydrated in a thick-walled hydration chamber. The sample is rotated in the x-ray beam during the data acquisition. For more detail regarding this kind of sample please see: Kučerka, N., Liu, Y. F., Chu, N. J., Petrache, H. I., Tristram-Nagle, S. & Nagle, J. F. (2005). Structure of fully hydrated fluid phase DMPC and DLPC lipid bilayers using X-ray scattering from oriented multilamellar arrays and from unilamellar vesicles. Biophys J 88, 2626-2637. The data analysis uses liquid-crystal theory to obtain the bending modulus and the compressibility modulus. These are needed to obtain the structure factor. The form factor is then obtained as described in: Lyatskaya, Y., Liu, Y., Tristram-Nagle, S., Katsaras, J. & Nagle, J. F. (2001). Method for obtaining structure and interactions from oriented lipid bilayers. Phys Rev E Stat Nonlin Soft Matter Phys 63, 011907. The sample consists of lipopolysaccharide and the RRWVRRVRRWVRRVVRVVRRWVRR peptide in a 75:1 lipid:peptide molar ratio.

Tags: softmatter
Lipopolysaccharide plus WLBU2 (LPS)
Mol. type   Lipid
Organism   Pseudomonas aeruginosa
Olig. state   Monomers
Chemical formula