Structured Review

Biacore biaevaluation software
Kinetic analyses of the binding of IL18 with YLDV-IL18BP. SPR analysis was performed as described in Figure 7 with YLDV-IL18BP at 5 different concentrations. The binding curves were globally fitted with <t>BiaEvaluation</t> software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.
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1) Product Images from "A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein"

Article Title: A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1002876

Kinetic analyses of the binding of IL18 with YLDV-IL18BP. SPR analysis was performed as described in Figure 7 with YLDV-IL18BP at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.
Figure Legend Snippet: Kinetic analyses of the binding of IL18 with YLDV-IL18BP. SPR analysis was performed as described in Figure 7 with YLDV-IL18BP at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.

Techniques Used: Binding Assay, SPR Assay, Software

Kinetic analyses of the binding of IL18 with YLDV-IL18BP or ECTV-IL18BP. SPR analysis was performed as described in Figure 9 with IL18 at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.
Figure Legend Snippet: Kinetic analyses of the binding of IL18 with YLDV-IL18BP or ECTV-IL18BP. SPR analysis was performed as described in Figure 9 with IL18 at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.

Techniques Used: Binding Assay, SPR Assay, Software

2) Product Images from ""

Article Title:

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.114959

Effect of deglycosylation of ActRIIB. A , SDS-PAGE (reduced) analysis of ActRIIB.Fc treated with deglycosylation enzymes. ActRIIB.Fc was treated by PNGase F ( lane N-Gly ); O -glycanase ( lane O-Gly ), sialidase A ( lane SiaA ), or the combination of all three enzymes ( lane N-Gly/O-Gly/SiaA ) at 37 °C. Control ActRIIB.Fc ( lane ActRIIB.Fc ) and ActRIIB.Fc incubated at 37 °C without the addition of the enzymes ( lane Mock ) are shown for comparison. B , effect of deglycosylation on the activity of ActRIIB.Fc. Purified ActRIIB.Fc was treated with deglycosylation enzymes as described under “Experimental Procedures.” Deglycosylated proteins along with the control ActRIIB.Fc were captured on a Biacore sensor chip by immobilized anti-human Fc antibody; different concentrations of activin A and GDF-11 were injected over captured receptors in duplicates. Analysis was performed on a Biacore 3000 instrument at room temperature. Data were globally fit to a 1:1 binding model with mass transfer term using BIAevaluation software.
Figure Legend Snippet: Effect of deglycosylation of ActRIIB. A , SDS-PAGE (reduced) analysis of ActRIIB.Fc treated with deglycosylation enzymes. ActRIIB.Fc was treated by PNGase F ( lane N-Gly ); O -glycanase ( lane O-Gly ), sialidase A ( lane SiaA ), or the combination of all three enzymes ( lane N-Gly/O-Gly/SiaA ) at 37 °C. Control ActRIIB.Fc ( lane ActRIIB.Fc ) and ActRIIB.Fc incubated at 37 °C without the addition of the enzymes ( lane Mock ) are shown for comparison. B , effect of deglycosylation on the activity of ActRIIB.Fc. Purified ActRIIB.Fc was treated with deglycosylation enzymes as described under “Experimental Procedures.” Deglycosylated proteins along with the control ActRIIB.Fc were captured on a Biacore sensor chip by immobilized anti-human Fc antibody; different concentrations of activin A and GDF-11 were injected over captured receptors in duplicates. Analysis was performed on a Biacore 3000 instrument at room temperature. Data were globally fit to a 1:1 binding model with mass transfer term using BIAevaluation software.

Techniques Used: SDS Page, Incubation, Activity Assay, Purification, Chromatin Immunoprecipitation, Injection, Binding Assay, Software

3) Product Images from "Surface Plasmon Resonance Biosensor Method for Palytoxin Detection Based on Na+,K+-ATPase Affinity"

Article Title: Surface Plasmon Resonance Biosensor Method for Palytoxin Detection Based on Na+,K+-ATPase Affinity

Journal: Toxins

doi: 10.3390/toxins6010096

Analysis of ligand binding. Kinetic plot of apparent association rate constant K obs (s −1 ) obtained from plot in Figure 2 (calculated by the BiaEvaluation software) versus ouabain concentration. Representative of 4 experiments.
Figure Legend Snippet: Analysis of ligand binding. Kinetic plot of apparent association rate constant K obs (s −1 ) obtained from plot in Figure 2 (calculated by the BiaEvaluation software) versus ouabain concentration. Representative of 4 experiments.

Techniques Used: Ligand Binding Assay, Software, Concentration Assay

Analysis of ligand binding. Kinetic plot of apparent association rate constant K obs (s −1 ) obtained from plot in Figure 4 (calculated by the BiaEvaluation software) versus ouabain concentration. Representative of 4 experiments.
Figure Legend Snippet: Analysis of ligand binding. Kinetic plot of apparent association rate constant K obs (s −1 ) obtained from plot in Figure 4 (calculated by the BiaEvaluation software) versus ouabain concentration. Representative of 4 experiments.

Techniques Used: Ligand Binding Assay, Software, Concentration Assay

4) Product Images from "Towards a Structural Comprehension of Bacterial Type VI Secretion Systems: Characterization of the TssJ-TssM Complex of an Escherichia coli Pathovar"

Article Title: Towards a Structural Comprehension of Bacterial Type VI Secretion Systems: Characterization of the TssJ-TssM Complex of an Escherichia coli Pathovar

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1002386

Measure of the interaction between TssM-ekto and TssJ by Surface Plasmon Resonance. ( A ) Sensorgram and saturation curve of the titration of Trx-TssJ by Trx-TssM-ekto. The CM5 chip (BIAcore) was coated with TssJ N-terminal thioredoxine fusion with 600 response units (RU) and the Trx-TssM-ekto was injected in the microfluidic channel. ( B ) Sensorgram and saturation curve of the titration of Trx-TssM-ekto by TssJ. The CM5 chip was coated with TssM-ekto N-terminal thioredoxine fusion with 3000 response units, and TssJ was injected in the microfluidic channel. The K D values were obtained using the fitting tool of the BIAevaluation software (BIAcore).
Figure Legend Snippet: Measure of the interaction between TssM-ekto and TssJ by Surface Plasmon Resonance. ( A ) Sensorgram and saturation curve of the titration of Trx-TssJ by Trx-TssM-ekto. The CM5 chip (BIAcore) was coated with TssJ N-terminal thioredoxine fusion with 600 response units (RU) and the Trx-TssM-ekto was injected in the microfluidic channel. ( B ) Sensorgram and saturation curve of the titration of Trx-TssM-ekto by TssJ. The CM5 chip was coated with TssM-ekto N-terminal thioredoxine fusion with 3000 response units, and TssJ was injected in the microfluidic channel. The K D values were obtained using the fitting tool of the BIAevaluation software (BIAcore).

Techniques Used: SPR Assay, Titration, Chromatin Immunoprecipitation, Injection, Software

5) Product Images from "Multisite phosphorylation of S6K1 directs a kinase phospho-code that determines substrate selection"

Article Title: Multisite phosphorylation of S6K1 directs a kinase phospho-code that determines substrate selection

Journal: Molecular cell

doi: 10.1016/j.molcel.2018.11.017

S6K1* exhibits altered conformation compared to S6K1, facilitating high-affinity binding to EPRS for site-selective Ser 999 phosphorylation (A) Triple phospho-mimetic S6K1* binds and phosphorylates EPRS linker in absence of insulin. 3’UTR-specific S6K1 siRNA, C-terminus Myc-tagged S6K1 ORFs, and Flag-tagged EPRS linker were co-transfected into 3T3-L1 adipocytes. Lysates were subjected to co-immunoprecipitation with anti-Myc antibody to probe Flag-EPRS linker/Myc-S6K1 interaction. EPRS linker Ser 999 phosphorylation was determined by immunoblot. (B) SPR analysis of binding of S6K1 forms to EPRS linker. Wild-type (WT) and mutant S6K1 proteins (1.25 nmol) were flowed over EPRS linker immobilized on a Biacore CM5 sensor chip. Binding was measured as relative response units. Smoothed association and dissociation curves determined by BIAevaluation software was used to calculate binding affinities expressed as dissociation constants, Kd. (C) Susceptibility of S6K1 forms to limited proteolysis. To establish appropriate limited proteolysis condition, purified Myc-S6K1* (75 ng) bearing T389E, S424D, and S429D mutations was treated with prolyl endopeptidase for 20 min, and probed with anti-Myc antibody (right). Myc-S6K1 bearing phospho-defective and phospho-mimetic mutations were cleaved with prolyl endopeptidase (40 ng, 20 min), and probed with anti-Myc antibody. Myc-S6K1 mutants generated by in vitro translation in wheat germ extract, and purified by Ni-affinity, were detected by silver staining. (D) Conformational alteration of S6K1* determined by antibody affinity. WT and S6K1 mutants (1.25 nmol) were flowed over anti-S6K1 antibody raised against human S6K1 C-terminus (amino acids 490-502) immobilized on a CM5 Biacore sensor chip. Binding was determined as in (B).
Figure Legend Snippet: S6K1* exhibits altered conformation compared to S6K1, facilitating high-affinity binding to EPRS for site-selective Ser 999 phosphorylation (A) Triple phospho-mimetic S6K1* binds and phosphorylates EPRS linker in absence of insulin. 3’UTR-specific S6K1 siRNA, C-terminus Myc-tagged S6K1 ORFs, and Flag-tagged EPRS linker were co-transfected into 3T3-L1 adipocytes. Lysates were subjected to co-immunoprecipitation with anti-Myc antibody to probe Flag-EPRS linker/Myc-S6K1 interaction. EPRS linker Ser 999 phosphorylation was determined by immunoblot. (B) SPR analysis of binding of S6K1 forms to EPRS linker. Wild-type (WT) and mutant S6K1 proteins (1.25 nmol) were flowed over EPRS linker immobilized on a Biacore CM5 sensor chip. Binding was measured as relative response units. Smoothed association and dissociation curves determined by BIAevaluation software was used to calculate binding affinities expressed as dissociation constants, Kd. (C) Susceptibility of S6K1 forms to limited proteolysis. To establish appropriate limited proteolysis condition, purified Myc-S6K1* (75 ng) bearing T389E, S424D, and S429D mutations was treated with prolyl endopeptidase for 20 min, and probed with anti-Myc antibody (right). Myc-S6K1 bearing phospho-defective and phospho-mimetic mutations were cleaved with prolyl endopeptidase (40 ng, 20 min), and probed with anti-Myc antibody. Myc-S6K1 mutants generated by in vitro translation in wheat germ extract, and purified by Ni-affinity, were detected by silver staining. (D) Conformational alteration of S6K1* determined by antibody affinity. WT and S6K1 mutants (1.25 nmol) were flowed over anti-S6K1 antibody raised against human S6K1 C-terminus (amino acids 490-502) immobilized on a CM5 Biacore sensor chip. Binding was determined as in (B).

Techniques Used: Binding Assay, Transfection, Immunoprecipitation, SPR Assay, Mutagenesis, Chromatin Immunoprecipitation, Software, Purification, Generated, In Vitro, Silver Staining

6) Product Images from "Role of HIV membrane in neutralization by two broadly neutralizing antibodies"

Article Title: Role of HIV membrane in neutralization by two broadly neutralizing antibodies

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.0908713106

Interaction of 4E10 scFv and its mutants with the HIV-1 gp41 prehairpin intermediate. 92UG-gp41-inter-Fd was immobilized on a CM5 chip. Each of the following analytes was passed over a freshly prepared, gp41-inter surface, as the chip could not be completely regenerated (see Materials and Methods ): ( A ) 4E10 scFv (10 and 100 nM); ( B ) 4E10-mut1 scFv (10 and 100 nM); ( C ) 4E10-mut2 scFv (10 and 100 nM); and ( D ) 4E10-mut3 scFv (10 and 100 nM). ( E ) 4E10-mut4 scFv at various concentrations (10, 25, 50, 75, and 100 nM) was passed over a single chip regenerated between runs by a solution containing 50 mM NaOH and 2 M NaCl. Binding kinetics were evaluated using BIAevaluation software (Biacore) and a 1:1 Langmuir binding model. The recorded sensorgrams are shown in black and the fits in green. The derived constants are summarized in ( F ). All experiments were repeated at least three times using different preparations of the proteins and gave essentially the same results.
Figure Legend Snippet: Interaction of 4E10 scFv and its mutants with the HIV-1 gp41 prehairpin intermediate. 92UG-gp41-inter-Fd was immobilized on a CM5 chip. Each of the following analytes was passed over a freshly prepared, gp41-inter surface, as the chip could not be completely regenerated (see Materials and Methods ): ( A ) 4E10 scFv (10 and 100 nM); ( B ) 4E10-mut1 scFv (10 and 100 nM); ( C ) 4E10-mut2 scFv (10 and 100 nM); and ( D ) 4E10-mut3 scFv (10 and 100 nM). ( E ) 4E10-mut4 scFv at various concentrations (10, 25, 50, 75, and 100 nM) was passed over a single chip regenerated between runs by a solution containing 50 mM NaOH and 2 M NaCl. Binding kinetics were evaluated using BIAevaluation software (Biacore) and a 1:1 Langmuir binding model. The recorded sensorgrams are shown in black and the fits in green. The derived constants are summarized in ( F ). All experiments were repeated at least three times using different preparations of the proteins and gave essentially the same results.

Techniques Used: Chromatin Immunoprecipitation, Binding Assay, Software, Derivative Assay

7) Product Images from "Gd-nanoparticles functionalization with specific peptides for ß-amyloid plaques targeting"

Article Title: Gd-nanoparticles functionalization with specific peptides for ß-amyloid plaques targeting

Journal: Journal of Nanobiotechnology

doi: 10.1186/s12951-016-0212-y

Interaction of functionalized nanoparticles for Aβ(1–42) fibrils or V30M-TTR fibrils assessed by SPR experiments. a Remaining signal of AGuIX@PEG, AGuIX@PEG@Cy5.5, AGuIX@PEG@LPFFD@Cy5.5 and AGuIX@PEG@KLVFF@Cy5.5 at 2.5 mM in Gd 3+ on Aβ(1–42) fibrils. The R.U. were measured 141 s after the end of the analyte injection. b, c The sensorgrams ( colored curves ) obtained for AGuIX@PEG@LPFFD@Cy5.5 ( b ) and for AGuIX@PEG@KLVFF@Cy5.5 ( c ) on Aβ(1–42) fibrils were fitted thanks to the Biaevaluation ® software with the Langmuir 1:1 model ( black curves ). c Remaining signal of AGuIX@PEG@LPFFD@Cy5.5 ( plain curves ) and AGuIX@PEG@KLVFF@Cy5.5 ( dashed curves ) on Aβ(1–42) fibrils ( blue ) and V30M-TTR fibrils ( red ). The R.U. values plotted on the graph correspond to the measures at the time-point 141 s after the end of nanoparticles injection
Figure Legend Snippet: Interaction of functionalized nanoparticles for Aβ(1–42) fibrils or V30M-TTR fibrils assessed by SPR experiments. a Remaining signal of AGuIX@PEG, AGuIX@PEG@Cy5.5, AGuIX@PEG@LPFFD@Cy5.5 and AGuIX@PEG@KLVFF@Cy5.5 at 2.5 mM in Gd 3+ on Aβ(1–42) fibrils. The R.U. were measured 141 s after the end of the analyte injection. b, c The sensorgrams ( colored curves ) obtained for AGuIX@PEG@LPFFD@Cy5.5 ( b ) and for AGuIX@PEG@KLVFF@Cy5.5 ( c ) on Aβ(1–42) fibrils were fitted thanks to the Biaevaluation ® software with the Langmuir 1:1 model ( black curves ). c Remaining signal of AGuIX@PEG@LPFFD@Cy5.5 ( plain curves ) and AGuIX@PEG@KLVFF@Cy5.5 ( dashed curves ) on Aβ(1–42) fibrils ( blue ) and V30M-TTR fibrils ( red ). The R.U. values plotted on the graph correspond to the measures at the time-point 141 s after the end of nanoparticles injection

Techniques Used: SPR Assay, Injection, Software

Interaction of KLVFF ( a ) and LPFFD ( b ) peptides at several concentrations with Aβ(1–42) fibrils measured by SPR. The sensorgrams obtained ( colored curves ) were fitted thanks to the Biaevaluation ® software with the Langmuir 1:1 model ( black curves )
Figure Legend Snippet: Interaction of KLVFF ( a ) and LPFFD ( b ) peptides at several concentrations with Aβ(1–42) fibrils measured by SPR. The sensorgrams obtained ( colored curves ) were fitted thanks to the Biaevaluation ® software with the Langmuir 1:1 model ( black curves )

Techniques Used: SPR Assay, Software

8) Product Images from "A Novel Therapeutic Approach to Treating Obesity through Modulation of TGF? Signaling"

Article Title: A Novel Therapeutic Approach to Treating Obesity through Modulation of TGF? Signaling

Journal: Endocrinology

doi: 10.1210/en.2012-1016

A, Analysis of ActRIIB-Fc binding to different ligands by SPR. Purified ActRIIB-Fc was captured on a Biacore sensor chip by immobilized antihuman Fc antibody; different concentrations of ligands were injected over captured receptor in duplicates. Kinetic analysis was performed with Biacore T100 at 25C except for BMP-2, which was performed at 20C. Data were globally fit to a 1:1 binding model with mass transfer term using BIAevaluation software (Biacore). B–D, Expression of thermogenic genes in cultured, differentiated, primary adipocytes from WAT in response to treatments with select TGFβ members. UCP1 (B), cidea (C), and PGC-1α (D) mRNA expression levels as a function of treatment with GDF-3, GDF-8, GDF-9, GDF-11, activin A, and activin B ligands. E, Expression of UCP1 in cultured, differentiated, primary adipocytes from WAT in response to treatment with select TGFβ members with or without the addition of ActRIIB-Fc. Quantitative real-time PCR was used to assess relative expression of the genes of interest using TATA box binding protein mRNA expression as an internal control. Data shown are means (n = 3 per group). κa, Association rate constant; κd, dissociation rate constant; K D , equilibrium dissociation constant; NT, no treatment. *, P
Figure Legend Snippet: A, Analysis of ActRIIB-Fc binding to different ligands by SPR. Purified ActRIIB-Fc was captured on a Biacore sensor chip by immobilized antihuman Fc antibody; different concentrations of ligands were injected over captured receptor in duplicates. Kinetic analysis was performed with Biacore T100 at 25C except for BMP-2, which was performed at 20C. Data were globally fit to a 1:1 binding model with mass transfer term using BIAevaluation software (Biacore). B–D, Expression of thermogenic genes in cultured, differentiated, primary adipocytes from WAT in response to treatments with select TGFβ members. UCP1 (B), cidea (C), and PGC-1α (D) mRNA expression levels as a function of treatment with GDF-3, GDF-8, GDF-9, GDF-11, activin A, and activin B ligands. E, Expression of UCP1 in cultured, differentiated, primary adipocytes from WAT in response to treatment with select TGFβ members with or without the addition of ActRIIB-Fc. Quantitative real-time PCR was used to assess relative expression of the genes of interest using TATA box binding protein mRNA expression as an internal control. Data shown are means (n = 3 per group). κa, Association rate constant; κd, dissociation rate constant; K D , equilibrium dissociation constant; NT, no treatment. *, P

Techniques Used: Binding Assay, SPR Assay, Purification, Chromatin Immunoprecipitation, Injection, Software, Expressing, Cell Culture, Pyrolysis Gas Chromatography, Real-time Polymerase Chain Reaction

9) Product Images from "A maresin 1/RORα/12-lipoxygenase autoregulatory circuit prevents inflammation and progression of nonalcoholic steatohepatitis"

Article Title: A maresin 1/RORα/12-lipoxygenase autoregulatory circuit prevents inflammation and progression of nonalcoholic steatohepatitis

Journal: The Journal of Clinical Investigation

doi: 10.1172/JCI124219

MaR1 is a novel ligand of RORα. ( A ) BIAcore analysis for binding of MaR1, RvD1, or cholesterol sulfate (CS) to RORα. The increasing concentrations of ligands were injected over immobilized GST-RORα-His proteins on the sensor chip and K D value was calculated by the BIAevaluation 3.1 software. ( B ) TR-FRET assay was performed using Lanthascreen RORα coactivator assay kit. The y axis represents the ratio of fluorescence intensity at 520 nm (signal) and at 495 nm (background). The x axis represents log scale of RvD1 (black line), MaR1 (red line), or CS (blue line) concentration. ( C ) Molecular surface model of RORα-MaR1 (magenta) complex (transparent view) obtained by docking that allows visualization of ligand bound to the internal ligand binding pocket. The figure was generated using Tripos Benchware 3D Explorer. ( D ) Docked model showing binding mode of MaR1 (magenta) and cholesterol sulfate (cyan) in the ligand binding pocket of RORα. The COOH group of MaR1 makes H-bond contacts with NH1-Arg370 and NH-Tyr290, and C7-OH of MaR1 with CO-Val364. ( E ) Raw 264.7 cells were transfected with the RORE-Luc reporter with the indicated point mutated Myc-RORα construct (left), or the Gal4-tk-Luc reporter with the indicated point mutated pM-RORα construct (right). The transfected cells were treated with 200 nM MaR1 for 24 hours and then luciferase activity was measured and normalized by β-galactosidase activity. * P
Figure Legend Snippet: MaR1 is a novel ligand of RORα. ( A ) BIAcore analysis for binding of MaR1, RvD1, or cholesterol sulfate (CS) to RORα. The increasing concentrations of ligands were injected over immobilized GST-RORα-His proteins on the sensor chip and K D value was calculated by the BIAevaluation 3.1 software. ( B ) TR-FRET assay was performed using Lanthascreen RORα coactivator assay kit. The y axis represents the ratio of fluorescence intensity at 520 nm (signal) and at 495 nm (background). The x axis represents log scale of RvD1 (black line), MaR1 (red line), or CS (blue line) concentration. ( C ) Molecular surface model of RORα-MaR1 (magenta) complex (transparent view) obtained by docking that allows visualization of ligand bound to the internal ligand binding pocket. The figure was generated using Tripos Benchware 3D Explorer. ( D ) Docked model showing binding mode of MaR1 (magenta) and cholesterol sulfate (cyan) in the ligand binding pocket of RORα. The COOH group of MaR1 makes H-bond contacts with NH1-Arg370 and NH-Tyr290, and C7-OH of MaR1 with CO-Val364. ( E ) Raw 264.7 cells were transfected with the RORE-Luc reporter with the indicated point mutated Myc-RORα construct (left), or the Gal4-tk-Luc reporter with the indicated point mutated pM-RORα construct (right). The transfected cells were treated with 200 nM MaR1 for 24 hours and then luciferase activity was measured and normalized by β-galactosidase activity. * P

Techniques Used: Binding Assay, Injection, Chromatin Immunoprecipitation, Software, Fluorescence, Concentration Assay, Ligand Binding Assay, Generated, Transfection, Construct, Luciferase, Activity Assay

Related Articles

SPR Assay:

Article Title: Aggregatibacter actinomycetemcomitans Leukotoxin Utilizes a Cholesterol Recognition/Amino Acid Consensus Site for Membrane Association *
Article Snippet: .. All SPR measurements were performed on a Biacore® 3000, and the data were evaluated using the BIAevaluation® software. .. The data were fit using a 1:1 Langmuir binding model to obtain the equilibrium dissociation constant ( KD ), as well as the association ( ka ) and dissociation ( kd ) rates, where KD is given by the following equation.

Article Title: H-2Dd engagement of Ly49A leads directly to Ly49A phosphorylation and recruitment of SHP1
Article Snippet: Gels were stained with Sypro-orange (BioRad, Hercules, CA) and visualized on a 312-nm UV lightbox. .. Surface plasmon resonance was performed on a BIACORE®2000 machine (Biosensor AB, Uppsala, Sweden), using a Sensorchip-NTA, according to the manufacturer’s instructions. .. Data was evaluated using the BIAevaluation software provided by the manufacturer, and affinity constants were calculated using values from at least four different concentrations for each GST fusion protein.

Article Title: Analysis of Interactions with Mitochondrial mRNA Using Mutant Forms of Yeast NAD+-Specific Isocitrate Dehydrogenase
Article Snippet: .. SPR data were analyzed using BIAevaluation® software (Biacore). .. To analyze effects of expression in vivo , mutant forms of IDH were expressed in the idh1 Δ idh2 Δ strain using single copy pRS316 plasmids containing both IDH1 and IDH2 genes with a codon replacement in one of the subunit genes as previously described ( , , , ).

Article Title: Eosinophil peroxidase activates cells by HER2 receptor engagement and β1-integrin clustering with downstream MAPK cell signaling
Article Snippet: Fractions were further profiled by SDS-PAGE with Coomassie staining to confirm the homogeneity of each preparation. .. 2.3 Surface Plasmon resonance (SPR) Surface Plasmon resonance (SPR) analysis was performed using a Biacore® 3000 and data analysis was carried out using BIAevaluation 4.1 software™. ..

Software:

Article Title: Aggregatibacter actinomycetemcomitans Leukotoxin Utilizes a Cholesterol Recognition/Amino Acid Consensus Site for Membrane Association *
Article Snippet: .. All SPR measurements were performed on a Biacore® 3000, and the data were evaluated using the BIAevaluation® software. .. The data were fit using a 1:1 Langmuir binding model to obtain the equilibrium dissociation constant ( KD ), as well as the association ( ka ) and dissociation ( kd ) rates, where KD is given by the following equation.

Article Title: Analysis of Interactions with Mitochondrial mRNA Using Mutant Forms of Yeast NAD+-Specific Isocitrate Dehydrogenase
Article Snippet: .. SPR data were analyzed using BIAevaluation® software (Biacore). .. To analyze effects of expression in vivo , mutant forms of IDH were expressed in the idh1 Δ idh2 Δ strain using single copy pRS316 plasmids containing both IDH1 and IDH2 genes with a codon replacement in one of the subunit genes as previously described ( , , , ).

Article Title: PASylation of IL-1 receptor antagonist (IL-1Ra) retains IL-1 blockade and extends its duration in mouse urate crystal-induced peritonitis
Article Snippet: Real-time SPR receptor-binding analysis of PAS–IL-1Ra fusion proteins ) and the drug anakinra (Swedish Orphan Biovitrum, Stockholm, Sweden) were diluted in 4 m m KH2 PO4 , 16 m m Na2 HPO4 , 115 m m NaCl, 0.05% (v/v) Tween® 20, pH 7.4 (PBS/T), and injected in appropriate concentration series using PBS/T as running buffer. .. Complex formation was observed at a continuous flow rate of 25 μl/min, and the kinetic parameters were determined by fitting the data to the a 1:1 Langmuir binding model for bimolecular complex formation using BIAevaluation software version 4.1.1 (BIAcore). ..

Article Title: Eosinophil peroxidase activates cells by HER2 receptor engagement and β1-integrin clustering with downstream MAPK cell signaling
Article Snippet: Fractions were further profiled by SDS-PAGE with Coomassie staining to confirm the homogeneity of each preparation. .. 2.3 Surface Plasmon resonance (SPR) Surface Plasmon resonance (SPR) analysis was performed using a Biacore® 3000 and data analysis was carried out using BIAevaluation 4.1 software™. ..

Article Title: Impact of Glycation on Antibody Clearance
Article Snippet: RNAse B is a high mannose containing protein ( ) that served as a positive control for MR binding, much like mannan or mannosylated IgG have been used in a previous study ( ). .. On-rate, off-rate, and equilibrium dissociation constants were calculated using the 1:1 binding model on BIAevaluation® software (Biacore, GE Healthcare). .. Incubation conditions were manipulated to generate a mouse antibody, mAbA, decorated with specific levels of mannosylation through chemical attachment.

Article Title: Plasmodium falciparum Inhibitor-3 Homolog Increases Protein Phosphatase Type 1 Activity and Is Essential for Parasitic Survival
Article Snippet: Binding curves were obtained over a range of analyte concentrations. .. The data were analyzed, and association/dissociation constants were calculated using BIAevaluation 4.1 software (Biacore®, GE Healthcare). .. The data were analyzed, and association/dissociation constants were calculated using BIAevaluation 4.1 software (Biacore®, GE Healthcare).

Binding Assay:

Article Title: PASylation of IL-1 receptor antagonist (IL-1Ra) retains IL-1 blockade and extends its duration in mouse urate crystal-induced peritonitis
Article Snippet: Real-time SPR receptor-binding analysis of PAS–IL-1Ra fusion proteins ) and the drug anakinra (Swedish Orphan Biovitrum, Stockholm, Sweden) were diluted in 4 m m KH2 PO4 , 16 m m Na2 HPO4 , 115 m m NaCl, 0.05% (v/v) Tween® 20, pH 7.4 (PBS/T), and injected in appropriate concentration series using PBS/T as running buffer. .. Complex formation was observed at a continuous flow rate of 25 μl/min, and the kinetic parameters were determined by fitting the data to the a 1:1 Langmuir binding model for bimolecular complex formation using BIAevaluation software version 4.1.1 (BIAcore). ..

Article Title: Impact of Glycation on Antibody Clearance
Article Snippet: RNAse B is a high mannose containing protein ( ) that served as a positive control for MR binding, much like mannan or mannosylated IgG have been used in a previous study ( ). .. On-rate, off-rate, and equilibrium dissociation constants were calculated using the 1:1 binding model on BIAevaluation® software (Biacore, GE Healthcare). .. Incubation conditions were manipulated to generate a mouse antibody, mAbA, decorated with specific levels of mannosylation through chemical attachment.

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    Biacore biaevaluation 3 0 software
    TPV-2L binds to human TNF with high affinity but not murine TNF or human IL-2, IL-5, or LT-α. TPV-2L was immobilized on one flow cell of a CM-5 BIAcore sensor chip whereas the other flow cell acted as a blank control surface. Over the TPV-2L sensor chip was passed 100 μl of human TNF, IL-2, IL-5, LT-α, or murine TNF ( a ) or duplicate injections of 0.3, 0.9, 2.8, or 8.3 nM human TNF at a flow rate of 50 μl/min ( b ). The amount of protein bound to the surface was recorded as response units as a function of time. After completion of the injection phase (arrow), the dissociation phase was monitored during the injection of buffer alone (HBS-EP). The sensorgrams shown were normalized by subtracting the control surface sensorgram and a blank injection sensorgram. The binding kinetics were determined by using BIAEVALUATION 3.0 and a 1:1 mass transport model to determine the rate of association ( K on ), the rate of dissociation ( K off ), and the rate constant ( K d ).
    Biaevaluation 3 0 Software, supplied by Biacore, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Biacore biaevaluation 3 1 software
    SPR measurements of the α − τ C 16 and DNA–τ C 24 interactions. ( A ) Solutions of decreasing concentrations of α (3.0, 2.0, 1.0, 0.6, 0.3 nM and blank; from top to bottom) were tested for interaction with immobilized bio-τ C 16. Curves, shown in colours, were fitted globally to a 1:1 Langmuir model with mass transfer using BIAevaluation 3.1 software. Sensorgrams were simulated (black curves) using the same model and the fitted parameters  k a  = (1.52 ± 0.01) × 10 6  M −1  s −1 ,  k d  = (4.02 ± 0.01) × 10 −4  s −1 ,  k t  (mass transfer coefficient) = 2.98 × 10 8  RU M −1  s −1 , yielding  K D (α–bio-τ C 16) = 265 ± 2 pM. Measurements were carried out in SPR buffer at 20°C. ( B ) Salt dependence of binding of τ C 24 (1 μM) to ss, ds and primer-template DNA, studied by SPR at 20°C, as described in the Materials and methods section. Binding was monitored in 10 mM Na.HEPES buffer, pH 7.4, 0.005% P20, containing 75 mM NaCl (green sensorgrams), 50 mM NaCl (red) or 25 mM NaCl (blue). Under all conditions studied, the dissociation phase was complete within seconds, indicating that the interaction is rapidly reversible (not shown). Similar responses were seen with τ C 22, while no binding was detected in any condition with τ C 16.
    Biaevaluation 3 1 Software, supplied by Biacore, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/biaevaluation 3 1 software/product/Biacore
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    biaevaluation 3 1 software - by Bioz Stars, 2021-07
    86/100 stars
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    86
    Biacore biaevaluation software
    Kinetic analyses of the binding of IL18 with YLDV-IL18BP. SPR analysis was performed as described in Figure 7 with YLDV-IL18BP at 5 different concentrations. The binding curves were globally fitted with <t>BiaEvaluation</t> software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.
    Biaevaluation Software, supplied by Biacore, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/biaevaluation software/product/Biacore
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    biaevaluation software - by Bioz Stars, 2021-07
    86/100 stars
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    TPV-2L binds to human TNF with high affinity but not murine TNF or human IL-2, IL-5, or LT-α. TPV-2L was immobilized on one flow cell of a CM-5 BIAcore sensor chip whereas the other flow cell acted as a blank control surface. Over the TPV-2L sensor chip was passed 100 μl of human TNF, IL-2, IL-5, LT-α, or murine TNF ( a ) or duplicate injections of 0.3, 0.9, 2.8, or 8.3 nM human TNF at a flow rate of 50 μl/min ( b ). The amount of protein bound to the surface was recorded as response units as a function of time. After completion of the injection phase (arrow), the dissociation phase was monitored during the injection of buffer alone (HBS-EP). The sensorgrams shown were normalized by subtracting the control surface sensorgram and a blank injection sensorgram. The binding kinetics were determined by using BIAEVALUATION 3.0 and a 1:1 mass transport model to determine the rate of association ( K on ), the rate of dissociation ( K off ), and the rate constant ( K d ).

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: A secreted high-affinity inhibitor of human TNF from Tanapox virus

    doi: 10.1073/pnas.0737244100

    Figure Lengend Snippet: TPV-2L binds to human TNF with high affinity but not murine TNF or human IL-2, IL-5, or LT-α. TPV-2L was immobilized on one flow cell of a CM-5 BIAcore sensor chip whereas the other flow cell acted as a blank control surface. Over the TPV-2L sensor chip was passed 100 μl of human TNF, IL-2, IL-5, LT-α, or murine TNF ( a ) or duplicate injections of 0.3, 0.9, 2.8, or 8.3 nM human TNF at a flow rate of 50 μl/min ( b ). The amount of protein bound to the surface was recorded as response units as a function of time. After completion of the injection phase (arrow), the dissociation phase was monitored during the injection of buffer alone (HBS-EP). The sensorgrams shown were normalized by subtracting the control surface sensorgram and a blank injection sensorgram. The binding kinetics were determined by using BIAEVALUATION 3.0 and a 1:1 mass transport model to determine the rate of association ( K on ), the rate of dissociation ( K off ), and the rate constant ( K d ).

    Article Snippet: The data were analyzed globally with the BIAEVALUATION 3.0 software (BIAcore) by using a 1:1 mass transport model.

    Techniques: Flow Cytometry, Chromatin Immunoprecipitation, Injection, Binding Assay

    SPR measurements of the α − τ C 16 and DNA–τ C 24 interactions. ( A ) Solutions of decreasing concentrations of α (3.0, 2.0, 1.0, 0.6, 0.3 nM and blank; from top to bottom) were tested for interaction with immobilized bio-τ C 16. Curves, shown in colours, were fitted globally to a 1:1 Langmuir model with mass transfer using BIAevaluation 3.1 software. Sensorgrams were simulated (black curves) using the same model and the fitted parameters  k a  = (1.52 ± 0.01) × 10 6  M −1  s −1 ,  k d  = (4.02 ± 0.01) × 10 −4  s −1 ,  k t  (mass transfer coefficient) = 2.98 × 10 8  RU M −1  s −1 , yielding  K D (α–bio-τ C 16) = 265 ± 2 pM. Measurements were carried out in SPR buffer at 20°C. ( B ) Salt dependence of binding of τ C 24 (1 μM) to ss, ds and primer-template DNA, studied by SPR at 20°C, as described in the Materials and methods section. Binding was monitored in 10 mM Na.HEPES buffer, pH 7.4, 0.005% P20, containing 75 mM NaCl (green sensorgrams), 50 mM NaCl (red) or 25 mM NaCl (blue). Under all conditions studied, the dissociation phase was complete within seconds, indicating that the interaction is rapidly reversible (not shown). Similar responses were seen with τ C 22, while no binding was detected in any condition with τ C 16.

    Journal: Nucleic Acids Research

    Article Title: The unstructured C-terminus of the ? subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the ? subunit

    doi: 10.1093/nar/gkm079

    Figure Lengend Snippet: SPR measurements of the α − τ C 16 and DNA–τ C 24 interactions. ( A ) Solutions of decreasing concentrations of α (3.0, 2.0, 1.0, 0.6, 0.3 nM and blank; from top to bottom) were tested for interaction with immobilized bio-τ C 16. Curves, shown in colours, were fitted globally to a 1:1 Langmuir model with mass transfer using BIAevaluation 3.1 software. Sensorgrams were simulated (black curves) using the same model and the fitted parameters k a = (1.52 ± 0.01) × 10 6  M −1  s −1 , k d = (4.02 ± 0.01) × 10 −4  s −1 , k t (mass transfer coefficient) = 2.98 × 10 8  RU M −1  s −1 , yielding K D (α–bio-τ C 16) = 265 ± 2 pM. Measurements were carried out in SPR buffer at 20°C. ( B ) Salt dependence of binding of τ C 24 (1 μM) to ss, ds and primer-template DNA, studied by SPR at 20°C, as described in the Materials and methods section. Binding was monitored in 10 mM Na.HEPES buffer, pH 7.4, 0.005% P20, containing 75 mM NaCl (green sensorgrams), 50 mM NaCl (red) or 25 mM NaCl (blue). Under all conditions studied, the dissociation phase was complete within seconds, indicating that the interaction is rapidly reversible (not shown). Similar responses were seen with τ C 22, while no binding was detected in any condition with τ C 16.

    Article Snippet: Sensorgrams were fit globally to a 1:1 Langmuir binding with mass transfer model, using BIAevaluation 3.1 software (Biacore).

    Techniques: SPR Assay, Software, Binding Assay

    Kinetic analyses of the binding of IL18 with YLDV-IL18BP. SPR analysis was performed as described in Figure 7 with YLDV-IL18BP at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.

    Journal: PLoS Pathogens

    Article Title: A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein

    doi: 10.1371/journal.ppat.1002876

    Figure Lengend Snippet: Kinetic analyses of the binding of IL18 with YLDV-IL18BP. SPR analysis was performed as described in Figure 7 with YLDV-IL18BP at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.

    Article Snippet: The sensorgrams were analyzed with BIAEVALUATION software (BIACORE).

    Techniques: Binding Assay, SPR Assay, Software

    Kinetic analyses of the binding of IL18 with YLDV-IL18BP or ECTV-IL18BP. SPR analysis was performed as described in Figure 9 with IL18 at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.

    Journal: PLoS Pathogens

    Article Title: A Unique Bivalent Binding and Inhibition Mechanism by the Yatapoxvirus Interleukin 18 Binding Protein

    doi: 10.1371/journal.ppat.1002876

    Figure Lengend Snippet: Kinetic analyses of the binding of IL18 with YLDV-IL18BP or ECTV-IL18BP. SPR analysis was performed as described in Figure 9 with IL18 at 5 different concentrations. The binding curves were globally fitted with BiaEvaluation software to a 1∶1 binding model. The colored and black lines are the actual responses in RU and globally fitted curves, respectively.

    Article Snippet: The sensorgrams were analyzed with BIAEVALUATION software (BIACORE).

    Techniques: Binding Assay, SPR Assay, Software

    Effect of deglycosylation of ActRIIB. A , SDS-PAGE (reduced) analysis of ActRIIB.Fc treated with deglycosylation enzymes. ActRIIB.Fc was treated by PNGase F ( lane N-Gly ); O -glycanase ( lane O-Gly ), sialidase A ( lane SiaA ), or the combination of all three enzymes ( lane N-Gly/O-Gly/SiaA ) at 37 °C. Control ActRIIB.Fc ( lane ActRIIB.Fc ) and ActRIIB.Fc incubated at 37 °C without the addition of the enzymes ( lane Mock ) are shown for comparison. B , effect of deglycosylation on the activity of ActRIIB.Fc. Purified ActRIIB.Fc was treated with deglycosylation enzymes as described under “Experimental Procedures.” Deglycosylated proteins along with the control ActRIIB.Fc were captured on a Biacore sensor chip by immobilized anti-human Fc antibody; different concentrations of activin A and GDF-11 were injected over captured receptors in duplicates. Analysis was performed on a Biacore 3000 instrument at room temperature. Data were globally fit to a 1:1 binding model with mass transfer term using BIAevaluation software.

    Journal: The Journal of Biological Chemistry

    Article Title:

    doi: 10.1074/jbc.M110.114959

    Figure Lengend Snippet: Effect of deglycosylation of ActRIIB. A , SDS-PAGE (reduced) analysis of ActRIIB.Fc treated with deglycosylation enzymes. ActRIIB.Fc was treated by PNGase F ( lane N-Gly ); O -glycanase ( lane O-Gly ), sialidase A ( lane SiaA ), or the combination of all three enzymes ( lane N-Gly/O-Gly/SiaA ) at 37 °C. Control ActRIIB.Fc ( lane ActRIIB.Fc ) and ActRIIB.Fc incubated at 37 °C without the addition of the enzymes ( lane Mock ) are shown for comparison. B , effect of deglycosylation on the activity of ActRIIB.Fc. Purified ActRIIB.Fc was treated with deglycosylation enzymes as described under “Experimental Procedures.” Deglycosylated proteins along with the control ActRIIB.Fc were captured on a Biacore sensor chip by immobilized anti-human Fc antibody; different concentrations of activin A and GDF-11 were injected over captured receptors in duplicates. Analysis was performed on a Biacore 3000 instrument at room temperature. Data were globally fit to a 1:1 binding model with mass transfer term using BIAevaluation software.

    Article Snippet: To obtain kinetic rate constants, the corrected data were fitted to a 1:1 interaction model with mass transport term using BiaEvaluation software (Biacore).

    Techniques: SDS Page, Incubation, Activity Assay, Purification, Chromatin Immunoprecipitation, Injection, Binding Assay, Software