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10 results for “quorum quenching”
Common Dynamic Determinants Govern Quorum Quenching Activity in N-terminal Serine Hydrolases
<ul> <li> <p>(File-01) Free enzymes molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ enzymes</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from minimization, equilibration and production runs</p> </li> <li> <p>output files from minimization, equilibration and production runs</p> </li> <li> <p>raw data for analysis and visualization:</p> <ol> <li> <p>protein backbone RMSD evolution</p> </li> <li> <p>binding cavity dynamics analysis</p> </li> <li> <p>principal component analysis of catalytic machinery (with states' representatives in PDF format)</p> </li> </ol> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(File-02) Ligand-enzyme complexes molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from minimization, equilibration and production runs</p> </li> <li> <p>output files from minimization, equilibration and production runs</p> </li> <li> <p>raw data for analysis and visualization:</p> <ol> <li> <p>protein backbone RMSD evolution</p> </li> <li> <p>near-attack-conformation (NAC) stabilization</p> </li> <li> <p>HSLs RMSD evolution</p> </li> <li> <p>MM/PBSA binding energy estimation</p> </li> <li> <p>HSLs heavy atoms RMSF</p> </li> </ol> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(File-03) Michaelis complex ensemble generation molecular dynamics:</p> <ul> <li> <p>input parameters and topologies for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>general input files for MD simulations in AMBER</p> </li> <li> <p>output restart files from ensemble generation production runs</p> </li> <li> <p>output files from ensemble generation production runs</p> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(Files-04-06) Ligand-enzyme QM/MM steered molecular dynamics:</p> <ul> <li> <p>input parameters for aPGA, ecPGA and paPvdQ in complex with C06- and C08-HSL molecules</p> </li> <li> <p>ensemble of input restart files generated in stage 3</p> </li> <li> <p>general input files for QM/MM steered MD simulations in AMBER</p> </li> <li> <p>output restart files from QM/MM MD equilibration simulations and QM/MM steered MD simulations</p> </li> <li> <p>output files and output work from QM/MM steered MD simulations</p> </li> </ul> </li> </ul> <p> </p> <ul> <li> <p>(File-07) Ligand-enzyme QM/MM steered molecular dynamics data for analysis and visualization:</p> <ul> <li> <p>reaction states ensembles (in PDB format) extracted from QM/MM steered MD simulations with crucial distances measured</p> </li> <li> <p>evolution of the reaction coordinate elements in the first and second step of acylation</p> </li> <li> <p>representative states of the reaction stages for visualization (in PDB format)</p> </li> <li> <p>different dynamics of the residues gating access to acyl-binding cavity at TS1</p> </li> <li> <p>different dynamics of the residues gating overall access to active site at TS2a</p> </li> <li> <p>different system-dependent bending of the HSLs at TS1 and TS2a</p> </li> </ul> </li> </ul> <p> </p>
Fig. 7 in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 7. Supervised multivariate analysis of NMR data. A) OPLS score plot using Y-variable of QSI activity. The plot showed the separation of active and non-active samples along OPLS1 (left side active samples). B) The corresponding S-plot significant values for QSI activity without P. lehmanii samples. C) The corresponding Splot significant values for QSI activity without P. cumbalensis samples.
Fig. 6 in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 6. PCA plot: The score plot of the principal component analysis (PCA) of 8 different species of banana passion fruits species shows a separation into four main groups.
Fig. 4 in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 4. UHPLC chromatograms (340 nm) of the butanolic extract of Passiflora species. Bold numbers correspond to identified compounds, and numbers in italics to the m/z of unidentified compounds.
Fig. 2 in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 2. The main differences for Passiflora samples can be observed in the aromatic region, suggesting a different composition of flavonoids and other polyphenolic compounds for each species.
Fig. 1. 1H in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 1. 1H NMR spectrum of Passiflora leave extract showing aliphatic, sugar and aromatic region and some assignments: ascorbic acid (I), proline (II), threonine (III), ethanol (IV), leucine (V) pipecolic acid (VI) and acetic acid (VIII) (A and B). Sugar region ascorbic acid (I) and glucose (X) (B and C). Phenolic region glucose (X), tyrosine (IX), 5-carboxymethyl-2,5-dihydrofuran-2-one (XI) shikimic acid (XII) (D). The whole NMR signals assignation can be consulted at Table 1 supporting information.
Fig. 3 in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 3. Barcoding of primary metabolites for banana passion fruit species.
Quorum Sensing/Quorum Quenching in Acinetobacter baumannii clinical strains
GEO Series GSE87009. Acinetobacter baumannii. 4 samples. Type: Expression profiling by array.
Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification.
GEO Series GSE84969. Nitrobacter winogradskyi. 8 samples. Type: Expression profiling by high throughput sequencing.
Fig. 5 in Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity
Fig. 5. Unreported flavonoids identified as major components from Passiflora lehmannii Apigenin-4′-O-β-glucopyranosyl, 8-C-β-(6″acetyl)-glucopyranoside (1) (A) and Passiflora uribei Apigenin-4-O-β-glucopyranosyl-8-C-β-neohesperidoside (2) (B). Arrows represent key HMBC correlations.
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