Determination Of Relative Binding Affinities Research Articles

Quantitative cross-species comparison of serum albumin binding of per- and polyfluoroalkyl substances from five structural classes.

Per- and polyfluoroalkyl substances (PFAS) are a class of over 8000 chemicals, many of which are persistent, bioaccumulative, and toxic to humans, livestock, and wildlife. Serum protein binding affinity is instrumental in understanding PFAS toxicity, yet experimental binding data is limited to only a few PFAS congeners. Previously, we demonstrated the usefulness of a high-throughput, in vitro differential scanning fluorimetry assay for determination of relative binding affinities of human serum albumin for 24 PFAS congeners from 6 chemical classes. In the current study, we used this assay to comparatively examine differences in human, bovine, porcine, and rat serum albumin binding of 8 structurally informative PFAS congeners from 5 chemical classes. With the exception of the fluorotelomer alcohol 1H, 1H, 2H, 2H-perfluorooctanol (6:2 FTOH), each PFAS congener bound by human serum albumin was also bound by bovine, porcine, and rat serum albumin. The critical role of the charged functional headgroup in albumin binding was supported by the inability of albumin of each species tested to bind 6:2 FTOH. Significant interspecies differences in serum albumin binding affinities were identified for each of the bound PFAS congeners. Relative to human albumin, perfluoroalkyl carboxylic and sulfonic acids were bound with greater affinity by porcine and rat serum albumin, and the perfluoroalkyl ether acid congener bound with lower affinity to porcine and bovine serum albumin. These comparative affinity data for PFAS binding by serum albumin from human, experimental model, and livestock species reduce critical interspecies uncertainty and improve accuracy of predictive bioaccumulation and toxicity assessments for PFAS.

A quantitative LC–MS/MS method for comparative analysis of capture-antibody affinity toward protein antigens

A mass spectrometry-based antibody selection procedure was developed to evaluate optimal ‘capture’ monoclonal antibodies that can be used in a variety of analytical measurement applications. The isotope-dilution liquid chromatography-tandem mass spectrometry (ID LC–MS/MS) methodology is based on the use of multiple-reaction monitoring of tryptic peptide fragments derived from protein antigens. A panel of monoclonal antibodies (mAb) was evaluated based on a quantitative determination of relative binding affinity to human cardiac troponin I following immunoprecipitation. Dissociation constants ( K d ) were determined for ‘bound mAb–antigen’ vs. ‘unbound antigen’ using non-linear regression analysis. Relative quantification of both antigen and antibody was based on the use of stable isotope-labeled synthetic peptides as internal standards. Optimal ‘capture’ mAbs were determined through evaluation of relative K d constants of all monitored peptide transitions. A panel of six pre-screened candidate capture mAbs was concluded to consist of two subsets of mAbs, each with statistically equivalent K d constants as determined using NIST Standard Reference Material (SRM) 2921 – Human Cardiac Troponin Complex. This ID LC–MS/MS method is shown to be capable of quantitatively differentiating mAbs based on relative binding affinities. Selection of optimal capture mAbs can be applied toward a number of analytical applications which require metrological traceability and unbiased quantification.

In vitro DNA-binding profile of transcription factors: methods and new insights

The DNA-binding specificity of transcription factors (TFs) has broad impacts on cell physiology, cell development and in evolution. However, the DNA-binding specificity of most known TFs still remains unknown. The specificity of a TF protein is determined by its relative affinity to all possible binding sites. In recent years, the development of several in vitro techniques permits high-throughput determination of relative binding affinity of a TF to all possible k bp-long DNA sequences, thus greatly promoting the characterization of DNA-binding specificity of many known TFs. All DNA sequences that can be bound by a TF with various binding affinities form their DNA-binding profile (DBP). The DBP is important to generate an accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This study reviewed these techniques, especially two master techniques: double-stranded DNA microarray and systematic evolution of ligands by exponential enrichment in combination with parallel DNA sequencing techniques (SELEX-seq).

Determination of relative binding affinities of labeling molecules with amino acids by using scanning tunneling microscopy

The binding behaviour of labeling molecule copper phthalocyanine tetrasulfonate sodium (PcCu(SO(3)Na)(4)) on the assemblies of representative polyamino acids has been studied by using scanning tunneling microscopy (STM). By directly visualizing the adsorption and distribution of the labeling species on the peptide assemblies in STM images, one could obtain relative binding affinities of the labeling molecule with different amino acid residues.

Protein microarray assay for the screening of SH3 domain interactions

Analysis of cellular signal transduction processes increasingly focuses on the systematic characterization of complete protein interaction networks. Understanding the interplay of signaling components enables insight into the molecular basis of diverse diseases such as cancer. This paves the way for the rational design of specific therapeutics. Protein interactions are often mediated by conserved modular domains, e.g., SH3-domains, which recognize proline-rich sequences in their cognate ligands. In the course of this study, different microarray formats (reactive silane monolayers and nitrocellulose on glass slides) and assay work flows were evaluated to develop a microarray based screening assay that permits the reliable identification of interactions between certain target proteins with a set of SH3 domains. Nine representative SH3 domains which were produced and purified as GST-fusion proteins were spotted on the microarray substrates and probed with two well-characterized ligands, the Nef protein from HIV-1 and the human protein Sam68. The best results from these low-density model arrays were obtained with nitrocellulose slides. We show that a straightforward and highly robust detection of ligand binding is achieved by staining with a fluorescently labeled antibody directed against the N-terminal His-tag attached to these proteins. The optimized assay protocol reported here allows for the identification of SH3-interactions with high reproducibility and adequate signal-to-background and signal-to-noise ratios, as well as the quantitative determination of relative binding affinities.

Determination of relative binding affinity of influenza virus N9 sialidases with the Fab fragment of monoclonal antibody NC41 using biosensor technology.

The relative binding affinities of influenza virus N9 sialidase from term and whale with the Fab fragment of monoclonal antibody NC41 were determined using biosensor technology (Pharmacia BIAcoreTM). The apparent association and dissociation rate constants were measured in real time for the interaction of the Fab with both sialidases, the Fab being immobilised on the sensor surface. Although three-dimensional structural studies have shown that there are no apparent structural differences between the term and whale N9 sialidase epitopes to which the NC41 Fab binds, the apparent binding constant for the interaction with tern N9 sialidase was approximately 2.4-fold higher than that with whale N9 sialidase. The kinetic analysis showed that the association rate constant for the binding of whale N9 sialidase was higher than that for tern N9 sialidase (12.0 x 10(4) M-1 s-1 compared to 4.3 x 10(4) M-1 s-1) and the dissociation rate constants for the whale N9-sialidase-Fab complex were approximately 6-fold higher than for the tern N9-sialidase-Fab complex. Furthermore, kinetic analysis of the dissociation reaction showed that it was composed of two stages, an initial, faster rate followed by a late, slower rate. The values of the relative affinity constants calculated using the initial dissociation rate constant were similar to the values measured at equilibrium in the BIAcore and those determined in true solution equilibrium studies using sedimentation equilibrium. The late, slower, dissociation rate constant yielded affinity constants significantly higher than those obtained by true solution methods.

Kinetic analysis of the binding of nomegestrol acetate to the progesterone receptors in rat uterus by competition studies

The characteristics of binding (Kinetic and equilibrium binding analysis) of nomegestrol acetate (NOM, 17 alpha-acetoxy-6 alpha-methyl-19-nor-pregna-4.6-diene-3.20-dione) to the progesterone receptor (PgR) in rat uterine cytosolic fraction were determined in comparison to progesterone (P), to fully appreciate the amplitude and specificity of the induced biological response. Since an appropriate radio-labelled form of this steroid molecule was not available, competition studies were performed against the synthetic progestin: [3H]-Organon 2058 [( 3H]-ORG). This allowed a direct comparison between the unlabelled forms of NOM and P, the kinetic constants of which were respectively: Inhibition constant (Ki): 22.8 and 34.3 nM; Association rate constant (k1): 0.39 X 10(3) and 0.21 X 10(3) M-1.s-1; Dissociation rate constant (k-1): 1.81 X 10(-5) and 2.16 X 10(-5) s-1. These results are much more informative than the mere determination of relative binding affinities which only reflect the specificity of the PgR. It was concluded that NOM behaves like the natural hormone in the cytosol of rat uterus.

Differential interaction of antiestrogens with cytosol estrogen receptors

Interaction of tamoxifen, trioxifene and LY117018 with cytosol-estrogen receptors from immature rat uteri was compared. Determination of relative binding affinity (RBA) by competition with [ 3H] estradiol under various assay conditions revealed that the RBA of LY117018 increased with temperature while that of tamoxifen and trioxifene declined. Furthermore, the RBA values of tamoxifen and trioxifene observed after 24 h of incubation at 4°C were significantly lower than those obtained with 1-h incubations. However RBA values obtained with 1- or 24-h incubations of LY117018 at 4°C were similar. The complex formed by estradiol or LY117018 at 4°C was relatively stable for 24 h, while significant dissociation of tamoxifen and trioxifene was detected under these conditions. At 30°C estradiol displayed a biphasic pattern of dissociation, but tamoxifen and trioxifene dissociated rapidly and little evidence of a stable phase was apparent. By contrast, the complex formed by LY117018 exhibited greater stability than that of estradiol at 30°C. These results establish a relationship between shifts in competition curves (RBA) and rates of dissociation relative to estradiol; and clearly reveal that LY117018 has different binding characteristics than tamoxifen and trioxifene.