Journal: Cell Host & Microbe

Article Title: Poxviruses and paramyxoviruses use a conserved mechanism of STAT1 antagonism to inhibit interferon signaling

doi: 10.1016/j.chom.2022.01.014

Figure Lengend Snippet:

Article Snippet: 018 21-mer peptide (Ac-MWSVFIHGHD GSNKGSKTYTS-NH2) , Genosphere Biotechnologies , https://www.genosphere-biotech.com/.

Techniques: Virus, Subcloning, Western Blot, Construct, Recombinant, Modification, Protease Inhibitor, Electron Microscopy, Lysis, Luciferase, Expressing, Plasmid Preparation, Bicinchoninic Acid Protein Assay, Mutagenesis, SYBR Green Assay, Cell Culture, Sequencing, Software

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Modular organization of human ErbB4 and YAP2 proteins. (a) ErbB4 contains the canonical ECD-TM-ICD receptor tyrosine kinase modular cassette, where the central single-helical transmembrane (TM) domain is flanked between an N-terminal extracellular domain (ECD) and a C-terminal intracellular domain (ICD). The three PPXY motifs (designated PY1, PY2 and PY3) within the ICD are located at the extreme C-terminus. Note that the amino acid sequence of 12-mer peptides containing the PPXY motifs and flanking residues are provided. The numerals indicate the nomenclature used in this study to distinguish residues within and flanking the PPXY motifs relative to the first consensus proline, which is arbitrarily assigned zero. (b) YAP2 is comprised of a tandem copy of WW domains, designated WW1 and WW2, located N-terminal to the trans-activation (TA) domain.

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Sequencing, Activation Assay

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Representative ITC isotherms for the binding of WW1 domain of YAP2 to ErbB4_PY1 (a), ErbB4_PY2 (b) and ErbB4_PY3 (c) peptides. The upper panels show the raw ITC data expressed as change in thermal power with respect to time over the period of titration. In the lower panels, change in molar heat is expressed as a function of molar ratio of corresponding peptide to WW1 domain. The red solid lines in the lower panels show the fit of data to a one-site binding model using the integrated ORIGIN software as described earlier [22, 20].

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Binding Assay, Titration, Software

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Thermodynamic parameters for the binding of WW1 and WW2 domains of YAP2 to PPXY peptides derived from the ICD of ErbB4

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Binding Assay, Derivative Assay, Sequencing

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Thermodynamic parameters for the binding of WW1 domain of YAP2 to wildtype (PY3_WT) and single alanine mutants of ErbB4_PY3 peptide

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Binding Assay, Sequencing

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Thermodynamic parameters for the binding of WW2 domain of YAP2 to wildtype (PY3_WT) and single alanine mutants of ErbB4_PY3 peptide

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Binding Assay, Sequencing

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Far-UV CD spectra of ErbB4_PY1 (red), ErbB4_PY2 (green) and ErbB4_PY3 (blue) peptides. Note that the mean ellipticity, [θ], was calculated using Eq [3].

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Circular Dichroism

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Structural models of WW1 (a) and WW2 (b) domains of YAP2 in complex with ErbB4_PY3 peptide containing the PPXY motif. The β-strands in the WW domains are shown in blue with loops depicted in gray and the peptide is colored yellow. Note that two orientations related by a 90°-rotation about the horizontal axis are depicted for the inquisitive eye. The sidechain moieties of all residues, including the PPXY motif (which corresponds to P0, P+1 and Y+3), within the bound peptide are shown in green. For the WW domains, the sidechain moieties colored in red denote all residues pointing toward the peptide on the concave side.

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques:

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Conformational dynamics as probed through MD simulations conducted on WW1 and WW2 domains of YAP2 in complex with ErbB4_PY3 peptide containing the PPXY motif. (a) RMSD of backbone atoms (N, Cα and C) within each simulated structure relative to the initial modeled structure of WW1 (top panel) and WW2 (bottom panel) domains in complex with ErbB4_PY3 peptide as a function of simulation time. Note that the overall RMSD for each WW-peptide complex (black) is deconvoluted into the WW domain alone (red) and the peptide alone (green). (b) RMSF of backbone atoms (N, Cα and C) averaged over the entire course of corresponding MD trajectory of WW1 (top panel) and WW2 (bottom panel) domains in complex with ErbB4_PY3 peptide as a function of residue number within each WW domain. The shaded vertical rectangular boxes denote residues located within the β1-β2 and β2-β3 loops. (c) RMSF of backbone atoms (N, Cα and C) averaged over the entire course of corresponding MD trajectory of WW1 (top panel) and WW2 (bottom panel) domains in complex with ErbB4_PY3 peptide as a function of residue number within the peptide (see Figure 1a for nomenclature). The PPXY motif and the flanking residues are overlayed for reference.

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Residue

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Intermolecular distances, as probed through MD simulations, between consensus residues within the PPXY motif of ErbB4_PY3 peptide and residues lining the binding groove within WW1 and WW2 domains of YAP2. (a) Distance between Cγ pyrrolidine carbon of P0 within the PPXY motif and Nε1 indole nitrogens of W199 and W258 located respectively within WW1 (top panel) and WW2 (bottom panel) domains. (b) Distance between Cγ pyrrolidine carbon of P+1 within the PPXY motif and Cζ phenolic carbons of Y188 and Y247 located respectively within WW1 (top panel) and WW2 (bottom panel) domains. (c) Distance between Oη phenolic oxygen of Y+3 within the PPXY motif and Nδ1 imidazole nitrogens of H192 and H251 located respectively within WW1 (top panel) and WW2 (bottom panel) domains.

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Binding Assay

Journal: Biochimie

Article Title: Molecular Basis of the Binding of YAP Transcriptional Regulator to the ErbB4 Receptor Tyrosine Kinase

doi: 10.1016/j.biochi.2014.01.011

Figure Lengend Snippet: Intermolecular distances, as probed through MD simulations, between residues flanking the PPXY motif of ErbB4_PY3 peptide and residues lining the binding groove within WW1 and WW2 domains of YAP2. (a) Distance between Cγ1/Cγ2 methyl carbons of V-3 within the PPXY motif and Cδ1/Cδ2 indole carbons of W199 and W258 located respectively within WW1 (top panel) and WW2 (bottom panel) domains. (b) Distance between Cδ1/Cδ2 methyl carbons of L-2 within the PPXY motif and Cδ carbons of Q186 and E245 located respectively within WW1 (top panel) and WW2 (bottom panel) domains. (c) Distance between Nη1/Nη2 guanidine nitrogens of R+6 within the PPXY motif and Oε1/Oε2 carbonyl oxygens of E178 and E237 located respectively within WW1 (top panel) and WW2 (bottom panel) domains.

Article Snippet: Peptide synthesis 12-mer wildtype and mutant peptides spanning various PPXY motifs within the ICD of human ErbB4 were commercially obtained from GenScript Corporation.

Techniques: Binding Assay

Journal: Malaria Journal

Article Title: Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the Plasmodium falciparum circumsporozoite protein (CSP)

doi: 10.1186/1475-2875-12-185

Figure Lengend Snippet: CSP peptides used in ELISPOT and ICS assays

Article Snippet: Sixty-five 15mer peptides overlapping by 11 amino acids and spanning the full length of CSP (3D7 strain) were synthesized commercially (Mimotopes, VIC, Australia, >80% purity) and grouped into nine peptide pools containing three to 12 peptides in each (Figure ).

Techniques: Enzyme-linked Immunospot, Sequencing

Journal: Malaria Journal

Article Title: Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the Plasmodium falciparum circumsporozoite protein (CSP)

doi: 10.1186/1475-2875-12-185

Figure Lengend Snippet: ELISpot IFN-γ activity of CSP peptide pools and individual 15-mer peptides within these pools

Article Snippet: Sixty-five 15mer peptides overlapping by 11 amino acids and spanning the full length of CSP (3D7 strain) were synthesized commercially (Mimotopes, VIC, Australia, >80% purity) and grouped into nine peptide pools containing three to 12 peptides in each (Figure ).

Techniques: Enzyme-linked Immunospot, Activity Assay, Sequencing

Journal: Malaria Journal

Article Title: Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the Plasmodium falciparum circumsporozoite protein (CSP)

doi: 10.1186/1475-2875-12-185

Figure Lengend Snippet: Predicted CD8 + T cell - restricted epitopes specific for each volunteer within CSP 15mer peptides

Article Snippet: Sixty-five 15mer peptides overlapping by 11 amino acids and spanning the full length of CSP (3D7 strain) were synthesized commercially (Mimotopes, VIC, Australia, >80% purity) and grouped into nine peptide pools containing three to 12 peptides in each (Figure ).

Techniques:

Journal: Malaria Journal

Article Title: Identification of minimal human MHC-restricted CD8+ T-cell epitopes within the Plasmodium falciparum circumsporozoite protein (CSP)

doi: 10.1186/1475-2875-12-185

Figure Lengend Snippet: Summary of predicted and confirmed minimal CSP identified in this study epitopes

Article Snippet: Sixty-five 15mer peptides overlapping by 11 amino acids and spanning the full length of CSP (3D7 strain) were synthesized commercially (Mimotopes, VIC, Australia, >80% purity) and grouped into nine peptide pools containing three to 12 peptides in each (Figure ).

Techniques: Sequencing, Enzyme-linked Immunospot, Activity Assay

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Boosting of HIV-1 Neutralizing Antibody Responses by a Distally Related Retroviral Envelope Protein

doi: 10.4049/jimmunol.1301898

Figure Lengend Snippet: A) Gelfiltration chromatography analysis of the soluble gp140 trimers from SIVmac239 and HIV-1YU2. Both complexes elute as a single symmetric peak at the expected elution volume for the trimeric species demonstrating that the gp140 trimers produced were pure and homogenous. The chromatography trace for HIVYU2 is representative for the different HIV-1 gp140 used in this study. B) Non-reducing (N/R) and reducing (Red) SDS PAGE analysis of SIVmac239 and HIV-1YU2 gp140. The SIVmac239 gp140 protein runs as a high molecular weight band under non-reducing conditions, indicating that the three polypeptides of the trimer are covalently linked by disulfide bonds between the three gp140 chains. HIV-1YU2 gp140 runs as a smear under non-reducing conditions suggesting that the three polypeptides of the trimer are not covalently linked. C) Surface plasmon resonance analysis of SIVmac239 gp140 and HIV-1 UG37 gp140 binding to human CD4 and anti-HIV-1 NAbs. SIVmac239 (right panel) or HIV-1UG37 (left panel) were immobilized and their binding to tetrameric soluble human CD4 (CD4-IgG2) as well as mAb F105, HGP68 and HR10 was measured.

Article Snippet: Overlapping linear 15-mer and circularized 15-mer peptides based on gp140 of HIV-1 CN54 were tested for reactivity against heat-inactivated rabbit sera by Pepscan Therapeutics (Netherlands).

Techniques: Chromatography, Produced, SDS Page, High Molecular Weight, SPR Assay, Binding Assay

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Boosting of HIV-1 Neutralizing Antibody Responses by a Distally Related Retroviral Envelope Protein

doi: 10.4049/jimmunol.1301898

Figure Lengend Snippet: A) Schematic immunization schedules of two independent studies (n= 48) and a comparative group 5 (n=4) with arrows depicting immunizations. Sera were collected before immunization (wk 0). Animals (New Zealand white rabbits) received a mix of three clade B env-DNA plasmids at weeks 0 (twice first week), 4, 8 and 12 (200 μg DNA by i.d. electroporation). Sera were collected 4 weeks after last DNA immunization (wk 16). Animals then received a heterologous protein SIVmac239 gp140 by i.d. injection and sera were collected 4 weeks after first protein boost (50 μg)(wk 20). Animals received a second protein boost with SIVmac239 gp140 4 weeks after the first protein immunization and sera were collected 2 weeks after second protein boost (50 μg) (wk 22). Three months later sera were analyzed for memory responses (wk 34). In the first study, twelve animals were included in Gr. 1 and the second study entailed six animals in this group. In the first study, Gr. 2 (n=12) received AAC adjuvant during the DNA priming phase and in the second study Gr. 2 (n=6) received a TLR5 agonist pFliC. Gr. 3 (n=6) received control DNA and albumin protein and Gr. 4 received three immunizations with SIVmac239 gp140 protein by i.d. injection (n=6). Gr.5 received the mix of three clade B env DNA immunizations followed by one i.d. injection with HIV-1ITM-1_4 gp140 (n=4). (B) Endpoint titres (log10) of IgG binding to SIVmac239 gp140 (white bars) or heterologous HIV-1UG37 gp140 (black bars) as measured by ELISA analyzing sera obtained before immunizations (wk 0) and after immunizations at wk 22 from the first study. Data are depicted as median and range. (C) Endpoint IgG titres from the second study are shown for binding to heterologous HIV-1UG37 gp140 and SIVmac239 gp140, as marked, in sera obtained at wk 0 (black bars), after the DNA priming (grey bars), and after the first gp140 boost (white bars) from the second study. Statistically significant lower endpoint IgG titres against SIVmac239 were found in Gr. 3 and against HIV-1UG37 in Groups 3 and 4 when compared with Groups 1 and 2 (One-way ANOVA using Bonferroni’s Multiple Comparison Test p<0.05).

Article Snippet: Overlapping linear 15-mer and circularized 15-mer peptides based on gp140 of HIV-1 CN54 were tested for reactivity against heat-inactivated rabbit sera by Pepscan Therapeutics (Netherlands).

Techniques: Electroporation, Injection, Adjuvant, Control, Binding Assay, Enzyme-linked Immunosorbent Assay, Comparison

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Boosting of HIV-1 Neutralizing Antibody Responses by a Distally Related Retroviral Envelope Protein

doi: 10.4049/jimmunol.1301898

Figure Lengend Snippet: Data are shown for individual animals from groups 1 and 2 combined (n=24) (A–H). Lines represent median. Sera were collected before immunization (wk 0), 4 weeks after last DNA immunization (DNA), 4 weeks after first SIVmac239gp140 boost (DNA/gp140) and 2 weeks after the second SIVmac239gp140 boost (DNA/gp140/gp140). Three months later sera were analyzed for the longevity of responses (3 mo after last boost). High ID50 neutralizing titres were detected in a TZM-bl assay against tier 1 isolates from clade B SF162.LS (A) and MN.3 (B). Purified IgGs were tested in a TZM-bl assay against HIV-1 clade B SF162 and BX08 (C and D). Percent neutralization is shown using 130 μg/ml IgG final concentration approximately corresponding to a 1/80 serum dilution and dotted line indicates ID50. Neutralizing titres in sera were detected in a TZM-bl assay against tier 1 isolates from clade C (MW965.26, E) and CRF01 AE (TH023.6, F). An arbitrary color code indicate the animals with the highest titres against SF162.LS in red (n=8), lowest in blue (n=8) and those in between in yellow (n=8). These colors are kept throughout the figure to be able to track the animals and their respective response to other viruses. ID50 titres in sera from groups 1 and 2 were tested in the A3R5.7 assay against clade B viruses RHPA.LucR (G) and SC22.3C2.LucR (H). Neutralization titres obtained in the TZM-bl assay for the control groups that received control DNA and albumin (Gr.3, displayed in green) or only SIVmac239 protein without a DNA prime (Gr.4, displayed in blue) are shown for neutralization of HIV-1 MN.3 (I) and the lab-adapted sensitive TCLA-SIVmac251 isolate (J). Significant values are indicated by *** p<0.001, **p<0.01 and *p<0.05 using One-Way ANOVA with Multiple Comparison Test.

Article Snippet: Overlapping linear 15-mer and circularized 15-mer peptides based on gp140 of HIV-1 CN54 were tested for reactivity against heat-inactivated rabbit sera by Pepscan Therapeutics (Netherlands).

Techniques: Purification, Neutralization, Concentration Assay, Control, Comparison

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Boosting of HIV-1 Neutralizing Antibody Responses by a Distally Related Retroviral Envelope Protein

doi: 10.4049/jimmunol.1301898

Figure Lengend Snippet: (A, B). A comparative arm that received DNA clade B priming followed by the HIV-1 clade A ITM-1_4 gp140 boost (Gr.5), was tested against SF162.LS, MN.3, MW965 and TH023.6 with ID50 titres displayed in brown. (C) Magnitude-Breadth curves show pooled data from both TZM-bl and A3R5.7 assays for the viruses that were tested on all animals (HIV-1 clade B isolates MN.3, SF162.LS, 9020.A13.LucR., RHPA.LucR., SC22.3C2.LucR.). Data obtained after DNA prime and after one protein boost are shown for sera from groups 1 and 2 (left panel) as well as the HIV-1 comparative arm (group5) (right panel). A Mantel-Cox log-rank test was used for statistical comparison. **** p<0.0001; ns= not significant. (D–G) Sera were collected in another comparative study before immunization (wk 0), 4 weeks after last DNA immunization (DNA), 4 weeks after first SIVmac239gp140 boost (DNA/SIV) and 2 weeks after the second gp140 protein boost ((DNA/SIV/HIV-1) or (DNA/SIV/HIV-2)). An arbitrary color code indicate the animals with the highest titres against SF162.LS in red (n=2), lowest in blue (n=2) and those in between in yellow (n=2). These colors are kept throughout the figure to be able to track the animals and their respective response to other viruses. Significant values are indicated by *** p<0.001, **p<0.01 and *p<0.05 as well as non-significant (ns) using One-Way ANOVA, Friedman’s test with Dunns’s Multiple Comparison Test.

Article Snippet: Overlapping linear 15-mer and circularized 15-mer peptides based on gp140 of HIV-1 CN54 were tested for reactivity against heat-inactivated rabbit sera by Pepscan Therapeutics (Netherlands).

Techniques: Comparison

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Boosting of HIV-1 Neutralizing Antibody Responses by a Distally Related Retroviral Envelope Protein

doi: 10.4049/jimmunol.1301898

Figure Lengend Snippet: (A) Selected sera (n=2 per group from the first study) from time points after HIV-1 DNA-prime (wk 16, DNA) and after the first SIVmac239 protein boost (wk 20, DNA/gp140) were subjected to epitope mapping by pepscan peptide arrays using heterologous HIV-1CN54 peptides. (B) The change in response intensity after SIVmac239 protein boosting is shown for peptides that were undetectable after DNA immunizations (white) or showed positive responses after DNA priming (grey) (C) Percentage of positive peptides detected before (wk 16, DNA) and after the boost (wk20, DNA/gp140) in the peptide array. (D) ELISA binding titres to indicated peptides from HIV-1 or SIVmac239 were determined after the second protein boost (wk 22) in animals immunized without (Gr. 1; n=6) or with a cellular adjuvant AAC during the priming phase (Gr. 2; n=6) (mean+SEM). Significant values are indicated by *p<0.05, **p<0.01 and ****p<0.0001 as well as ns=not significant using a Mann-Whitney test (B), a paired t test (C), or a one-way ANOVA of log-transformed data with a Bonferroni’s Multiple Comparison Test (D).

Article Snippet: Overlapping linear 15-mer and circularized 15-mer peptides based on gp140 of HIV-1 CN54 were tested for reactivity against heat-inactivated rabbit sera by Pepscan Therapeutics (Netherlands).

Techniques: Peptide Microarray, Enzyme-linked Immunosorbent Assay, Binding Assay, Adjuvant, MANN-WHITNEY, Transformation Assay, Comparison

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Boosting of HIV-1 Neutralizing Antibody Responses by a Distally Related Retroviral Envelope Protein

doi: 10.4049/jimmunol.1301898

Figure Lengend Snippet: IgG from animals from the first study were assessed for their capacity to neutralize HIV-1SF162 in the TZM-bl assay in the presence of blocking peptides and representative individual results are displayed. IgG were purified from sera two weeks after the second SIVmac239 gp140 boost. Percent neutralization is depicted on the y-axis and concentration of purified IgG on the x-axis.

Article Snippet: Overlapping linear 15-mer and circularized 15-mer peptides based on gp140 of HIV-1 CN54 were tested for reactivity against heat-inactivated rabbit sera by Pepscan Therapeutics (Netherlands).

Techniques: Blocking Assay, Purification, Neutralization, Concentration Assay