Journal: RSC Medicinal Chemistry

Article Title: Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection †

doi: 10.1039/d3md00724c

Figure Lengend Snippet: a) BLI sensogram of fragment hit 1 binding to PaFabF C164A. The dashed red line indicates the start of the dissociation step. b) Steady-state plot fitted to the responses of three independent experiments using exclusively repurchased material of fragment hit 1.

Article Snippet: The DNA sequence coding for Pa FabF C164A was synthesized and cloned into pET-28a-TEV vectors by Genscript (New Jersey).

Techniques: Binding Assay

Journal: RSC Medicinal Chemistry

Article Title: Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection †

doi: 10.1039/d3md00724c

Figure Lengend Snippet: Binding of fragment hit 1 (EOS102727, yellow) to Pa FabF C164A (PDB ID 8PJ0 ). a) | F o − F c | omit map of 1 binding to Pa FabF C164A, contoured at 3.0 sigma. b) Solvent accessible surface using residues 4 Å from ligand 1. c) Interactions between 1 (yellow) and Pa FabF C164A (green). Putative hydrogen bonds and π–π interactions are displayed as yellow dotted lines. d) Binding modes of 1 overlayed with the binding modes of platensimycin (magenta), PDB ID 7OC1 , and cerulenin (teal), PDB ID 4LS8 .

Article Snippet: The DNA sequence coding for Pa FabF C164A was synthesized and cloned into pET-28a-TEV vectors by Genscript (New Jersey).

Techniques: Binding Assay, Solvent

Journal: RSC Medicinal Chemistry

Article Title: Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection †

doi: 10.1039/d3md00724c

Figure Lengend Snippet: Dissociation constants and ligand efficiency of EFSL hit 1 and ECBL compounds 2 and 3

Article Snippet: The DNA sequence coding for Pa FabF C164A was synthesized and cloned into pET-28a-TEV vectors by Genscript (New Jersey).

Techniques:

Journal: RSC Medicinal Chemistry

Article Title: Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection †

doi: 10.1039/d3md00724c

Figure Lengend Snippet: Binding of ECBL compounds 2 and 3 to Pa FabF C164A (PDB ID 8R0I and 8R1V , respectively). a) | F o − F c | omit map of 2 (top) and 3 (bottom) binding to Pa FabF C164A contoured at 3.0 sigma. b) Alignment of binding modes of 1 (yellow), 2 (magenta) and 3 (cyan) together with solvent accessible surface of the binding site using residues 6 Å from ligand 3. For clarity, only selected interacting residues from the complex Pa FabF C164A-1 are shown (green). c) Interactions between 2 (magenta) and Pa FabF C164A (green). Putative hydrogen bonds and π–π interactions are displayed as yellow dotted lines. d) Binding mode of 3 (cyan) together with three water molecules that were found in the complexes with 1 and 2 but displaced by 3 (HOH392, 145 and 163, numbering from Pa FabF C164A-1).

Article Snippet: The DNA sequence coding for Pa FabF C164A was synthesized and cloned into pET-28a-TEV vectors by Genscript (New Jersey).

Techniques: Binding Assay, Solvent

Journal: Biomolecular NMR assignments

Article Title: Backbone NMR resonance assignments for the C terminal domain of the Streptococcus mutans adhesin P1

doi: 10.1007/s12104-023-10158-y

Figure Lengend Snippet: (a) Annotated 2D 1H,15N TROSY spectrum of Adhesin P1 C3 domain (BMRB 52097) collected in an 800 MHz spectrometer at 25 °C in phosphate buffer pH 6. Resonance assignments are shown with black labels; (b) Alphafold structural model for the new, longer C3 construct with the amino acid residues that are currently assigned shown in blue; (c) C3 domain structure (PDB 3QE5) with the residues assigned using the previous, shorter C3 construct (BMRB 27935) shown in red; (d) comparison of 2D 1H,15N TROSY spectra for the previous, shorter C3 construct (red) and the new, longer construct for the AlphaFold-predicted C3 domain (blue). Disordered, poorly resolved resonances observed for the prior C3 construct are now well resolved for the new C3 construct by addition of the seven C-terminal amino acids.

Article Snippet: The DNA sequence coding for the C3 domain of adhesin P1 (residues 1328–1490; Uniprot accession number P23504) was synthesized, with codon optimization for E. coli , by Genescript and inserted into pET21a(+) plasmid to yield the pET21a-C3-His 6 plasmid with a C-terminal His tag.

Techniques: Construct, Comparison

Journal: Virology Journal

Article Title: Development of a fluorescent probe-based recombinase polymerase amplification assay for rapid detection of Orf virus

doi: 10.1186/s12985-015-0440-z

Figure Lengend Snippet: Performance of the ORFV exo RPA assay. a Amplification curve of ORFV exo RPA assay over time using a dilution range of 10 6 to 10 1 copies/reaction of ORFV. NC represent negative control. b Reproducibility of the ORFV exo RPA assay. The threshold time is represented as the mean ± standard deviation (SD). The standard regression line was generated based on 8 data sets ( c ) Probit regression analysis using Statistics software was done on data from the eight runs of ORFV exo RPA assay. The limit of detection at 95 % probability is depicted by a triangle

Article Snippet: All ORFV DNA polymerase gene coding sequence genes were retrieved from GenBank and multiple sequence alignment of the gene sequences were manually designed based on the ORFV DNA polymerase gene recommendation by TwistDx (Cambridge, UK).

Techniques: Amplification, Negative Control, Standard Deviation, Generated, Software

Journal: Virology Journal

Article Title: Development of a fluorescent probe-based recombinase polymerase amplification assay for rapid detection of Orf virus

doi: 10.1186/s12985-015-0440-z

Figure Lengend Snippet: Evaluation of the specificity of ORFV exo PRA assay

Article Snippet: All ORFV DNA polymerase gene coding sequence genes were retrieved from GenBank and multiple sequence alignment of the gene sequences were manually designed based on the ORFV DNA polymerase gene recommendation by TwistDx (Cambridge, UK).

Techniques: Virus

Journal: Virology Journal

Article Title: Development of a fluorescent probe-based recombinase polymerase amplification assay for rapid detection of Orf virus

doi: 10.1186/s12985-015-0440-z

Figure Lengend Snippet: Comparison between performances of ORFV exo RPA assay and real-time ORFV qPCR assay on samples of ORFV-infected cells ( n = 15) and spiked tissues lysates ( n = 24). Linear regression analysis of the exo RPA threshold time (y axis) and qPCR cycle threshold (CT) values (x axis) were determined by Excel software

Article Snippet: All ORFV DNA polymerase gene coding sequence genes were retrieved from GenBank and multiple sequence alignment of the gene sequences were manually designed based on the ORFV DNA polymerase gene recommendation by TwistDx (Cambridge, UK).

Techniques: Comparison, Infection, Software

Journal: Virology Journal

Article Title: Development of a fluorescent probe-based recombinase polymerase amplification assay for rapid detection of Orf virus

doi: 10.1186/s12985-015-0440-z

Figure Lengend Snippet: Comparison of ORFV exo RPA assay with qPCR assay on clinical samples a

Article Snippet: All ORFV DNA polymerase gene coding sequence genes were retrieved from GenBank and multiple sequence alignment of the gene sequences were manually designed based on the ORFV DNA polymerase gene recommendation by TwistDx (Cambridge, UK).

Techniques: Comparison

Journal: Virology Journal

Article Title: Development of a fluorescent probe-based recombinase polymerase amplification assay for rapid detection of Orf virus

doi: 10.1186/s12985-015-0440-z

Figure Lengend Snippet: RPA primers and probes designed in this study

Article Snippet: All ORFV DNA polymerase gene coding sequence genes were retrieved from GenBank and multiple sequence alignment of the gene sequences were manually designed based on the ORFV DNA polymerase gene recommendation by TwistDx (Cambridge, UK).

Techniques: Sequencing