tlr4 md 2 agonists  (Molecular Dynamics Inc)

Journal: bioRxiv

Article Title: Interrogating the genus Yersinia to define the rules of lipopolysaccharide lipid A structure associated with pathogenicity

doi: 10.1101/2025.03.03.641127

Figure Lengend Snippet: (A) Initial snapshot of the (TLR4/MD-2) 2 complex bound to m/z 1768 (left). Final snapshots of each one side of the (TLR4/MD-2) 2 complex bound to m/z 1768 (right). Labelled basic amino acid residues observed to make significant hydrogen-bonding interactions with m/z 1768 are shown in licorice format, coloured in blue. (B) Root mean square deviation (RMSD) of TLR4 dimer backbone atoms. (C) Buried solvent accessible surface area (SASA) between MD-2-lipid A species and TLR4. (D) Contacts between lipid A species and (TLR4/MD-2) 2 . (E) Overlaid every 200 ns simulation snapshots of F126 side chain and its orientation with respect to the MD-2:lipid A species. The pseudo trajectory was made of two aligned MD-2:lipid monomer frames for each system. The F126 side chain is shown in licorice representation and coloured according to simulation time (red-white-blue for 0 to 2,000 ns). (F) RMSD of MD-2 backbone loop region after alignment on the entire MD-2 backbone. (G) Porcupine plot of TLR4 dimer alpha carbons corresponding to the most dominant motion (PCA1). The colours corresponds to distances as labelled inset. In panel (A) and (E) protein is shown in cartoon representation: TLR monomers in violet and red, MD-2 dimers shown in grey. Lipid A species and side chains are shown in licorice representation (cyan – carbon, red – oxygen, blue – nitrogen, brown – phosphorus). All values in panels (B)-(D) and (F) were averaged over last 200 ns and across both dimers.

Article Snippet: To gain insights into the potential of the different lipid A molecular species as TLR4/MD-2 agonists, we used explicitly solvated atomic-resolution molecular dynamics (MD) simulations to assess the interaction between the lipid A molecular species and the TLR4 2 /MD-2 2 complex, and with the F126 residues within the MD-2 loop encompassing 120 to 129 residues.

Techniques: Solvent

Journal: bioRxiv

Article Title: Interrogating the genus Yersinia to define the rules of lipopolysaccharide lipid A structure associated with pathogenicity

doi: 10.1101/2025.03.03.641127

Figure Lengend Snippet: (A) Surface expression of TLR4 as measured by mean fluorescence intensity (MFI) on iBMDMs non-infected (ni) or exposed to live E. coli , pathogenic yersiniae, YeO8 and YeO3, and non- pathogenic yersiniae , 1A strain 0902, Y. aldovae, Y. nurmii , grown at 21°C (denoted as 21) and 37°C (denoted as 37). (B)) Surface expression of TLR4 as measured by MFI on iBMDMs non-infected (ni) or exposed to live YeO8, chimeric YeO8 strain expressing a non-pathogenic lipid A, strain YeO8NPL, and YeO8 lpxR mutant (Δ lpxR , strain YeO8-Δ lpxR ) grown at 21°C (denoted as 21) and 37°C (denoted as 37). (C) TNFα secretion by infected iBMDMs with YeO8,and YeO8NPL.“c” denotes bacteria without the virulence plasmid. Strains were grown at 21°C (denoted as 21) and 37°C (denoted as 37). (D) TNFα secretion by iBMDMs challenge with 10 ng/ml of repurified LPS from YeO8, YeO8NPL, and YeO8 lpxR mutant (Δ lpxR , strain YeO8-Δ lpxR ) grown at 37°C. Data are presented as mean ± SD (n□=□3). In panels A and B, **** P □≤□0.0001; ns, P □>□0.05 for the comparisons against non-infected cells, and # P □≤□0.0001 for the comparisons against YeO8 grown at 37°C using One□way ANOVA with Bonferroni contrast for multiple comparisons test. In panels C and D, **** P □≤□0.0001; ns, P □>□0.05 for the indicated comparisons using One□way ANOVA Dunnett’s multiple comparisons test.

Article Snippet: To gain insights into the potential of the different lipid A molecular species as TLR4/MD-2 agonists, we used explicitly solvated atomic-resolution molecular dynamics (MD) simulations to assess the interaction between the lipid A molecular species and the TLR4 2 /MD-2 2 complex, and with the F126 residues within the MD-2 loop encompassing 120 to 129 residues.

Techniques: Expressing, Fluorescence, Infection, Mutagenesis, Bacteria, Plasmid Preparation