Thermal Analysis of Protein Stability and Ligand Binding in Complex Media

ABSTRACTScreening of ligands that can bind to biologic products of in vitro expression systems typically requires some purification of the expressed biologic target. Such purification is often laborious and time consuming and a limiting challenge. What is required, that could represent an enormous advantage, is the ability to screen expressed proteins in the crude lysate stage without purification. For that purpose, we explore here the utility of differential scanning calorimetry (DSC) measurements for detecting the presence of specific proteins and their interactions with ligands in the complex media where they were prepared, i.e. crude lysates. Model systems were designed to mimic analogous conditions comparable to those that might be encountered in actual in vitro expression systems. Results are reported for several examples where DSC measurements distinctly showed differences in the thermal denaturation behaviors of the crude lysate alone, proteins and proteins plus binding ligands added to the crude lysate. Results were obtained for Streptavidin/Biotin binding in E. coli lysate, and binding of Angiotensin Converting Enzyme 2 (ACE2) by captopril or lisinopril in the lysate supernatant derived from cultured Human Kidney cells (HEK293). ACE2 binding by the reactive binding domain (RBC) of SARS-CoV-2 was also examined. Binding of ACE2 by RBC and lisinopril were similar and consistent with the reported ACE2 inhibitory activity of lisinopril.

Capture the Tag: Mitigation of Biotin Interference in ELISA and Automated Immunoassays by Pre-Conjugating Biotinylated Antibodies to the Streptavidin Surface

Introduction Streptavidin to biotin binding is one of the strongest non-covalent interactions in nature, and is therefore, successfully incorporated into many immunoassays to facilitate antibody capture. Biotin-streptavidin coupling assays are susceptible to interference from free biotin in patient specimens, which may falsely decrease or increase the result depending on assay format. Currently, biotin-stripping methods capture free biotin in patient specimens by pre-incubation with streptavidin-coated microparticles. However, this approach increases turnaround time, test cost, and testing steps, which increases the chance of error. Our objective was to determine if pre-conjugating biotinylated antibodies to the assay’s streptavidin solid surface before adding patient specimen could mitigate biotin interference in ELISA and automated sandwich immunoassays. Methods We performed this study on 3 different ELISAs (CYFRA-21, NSE, S100B) and one automated assay (thyroglobulin); all are a sandwich immunoassay format. Serum pools were spiked with biotin (25 - 1000 µg/L) or PBS control. Manufacturer protocols were followed in both the ELISAs and automated assay to evaluate baseline concentration-dependent biotin interference. Mitigation of biotin interference by pre-incubation was then evaluated in the ELISAs by adding biotinylated antibody to the streptavidin-coated wells 0, 10, 15, or 60 min before adding biotin- or PBS-spiked serum specimens. For the automated assay, streptavidin-coated beads and biotinylated antibody were removed from the reagent cartridge, mixed, and incubated 4.5 hours. The mixture containing biotin-tagged antibody bound to streptavidin beads was added back to the cartridge and placed on the analyzer to evaluate spiked specimens. Lastly, we compared the pre-incubation method to a standard biotin-stripping protocol in the ELISAs to compare the effectiveness of mitigating biotin interference. Results We observed biotin interference across the three ELISAs, where 400 µg/L biotin spiked in serum pools reduced analyte detection to between 10 – 15% of the total activity using the standard assay format. Our time-course studies showed 84 – 95% recovery of the total activity when the biotinylated antibody was pre-incubated in the streptavidin-coated wells for 1 hour prior to addition of serum specimens, compared to 69 – 99% by a standard biotin stripping protocol. We extended this concept to the automated immunoassay where at 1000 µg/L biotin in the specimen, only 9 ±0.01% of the total analyte was measured by the conventional method. However, pre-mixing biotinylated antibody and streptavidin beads resulted in 97 ±0.01% of the total analyte recovery in the presence of 1000 µg/L biotin. Conclusion We have demonstrated that pre-conjugating the biotin antibody to streptavidin is as effective as biotin-stripping methods to avoid biotin interference in sandwich immunoassays that utilize the biotin-streptavidin system, with the additional benefit of optimizing turnaround times, cost, and labor. A simple change in manufacturer assay design could make immunoassays more robust against biotin interference in patient samples.

Structural origins of altered spectroscopic properties upon ligand binding in proteins containing a fluorescent non-canonical amino acid

ABSTRACTFluorescent non-canonical amino acids (fNCAAs) could serve as starting points for the rational design of protein-based fluorescent sensors of biological activity. However, efforts toward this goal are likely hampered by a lack of atomic-level characterization of fNCAAs within proteins. Here, we describe the spectroscopic and structural characterization of five streptavidin mutants that contain the fNCAA L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) at sites proximal to the binding site of its substrate, biotin. Many of the mutants exhibited altered fluorescence spectra in response to biotin binding, which included both increases and decreases in fluorescence intensity as well as red or blue shifted emission maxima. Structural data were also obtained for three of the five mutants. The crystal structures shed light on interactions between 7-HCAA and functional groups—contributed either by the protein or substrate—that may be responsible for the observed changes in the 7-HCAA spectra. These data could be used in future studies aimed at the rational design of fluorescent, protein-based sensors of small molecule binding or dissociation.

Nucleic Acid-Based Lateral Flow Biosensor for Salmonella Typhi and Salmonella Paratyphi: A Detection in Stool Samples of Suspected Carriers

A multiplex rapid detection system, based on a PCR-lateral flow biosensor (mPCR-LFB) was developed to identify Salmonella Typhi and Salmonella Paratyphi A from suspected carriers. The lower detection limit for S. Typhi and S. Paratyphi A was 0.16 and 0.08 ng DNA equivalent to 10 and 102 CFU/mL, respectively. Lateral flow biosensor was used for visual detection of mPCR amplicons (stgA, SPAint, ompC, internal amplification control) by labeling forward primers with fluorescein-isothiocyanate (FITC), Texas Red, dinitrophenol (DNP) and digoxigenin (DIG) and reverse primers with biotin. Binding of streptavidin-colloidal gold conjugate with the amplicons resulted in formation of a red color dots on the strip after 15–20 min of sample exposure. The nucleic acid lateral flow analysis of the mPCR-LFB was better in sensitivity and more rapid than the conventional agarose gel electrophoresis. Moreover, the mPCR-LFB showed 100% sensitivity and specificity when evaluated with stools spiked with 100 isolates of Salmonella genus and other bacteria. A prospective cohort study on stool samples of 1176 food handlers in outbreak areas (suspected carriers) resulted in 23 (2%) positive for S. Typhi. The developed assay has potential to be used for rapid detection of typhoid carriers in surveillance program.

Bacterial avidins are a widely distributed protein family in Actinobacteria, Proteobacteria and Bacteroidetes

Background Avidins are biotin-binding proteins commonly found in the vertebrate eggs. In addition to streptavidin from Streptomyces avidinii, a growing number of avidins have been characterized from divergent bacterial species. However, a systematic research concerning their taxonomy and ecological role has never been done. We performed a search for avidin encoding genes among bacteria using available databases and classified potential avidins according to taxonomy and the ecological niches utilized by host bacteria. Results Numerous avidin-encoding genes were found in the phyla Actinobacteria and Proteobacteria. The diversity of protein sequences was high and several new variants of genes encoding biotin-binding avidins were found. The living strategies of bacteria hosting avidin encoding genes fall mainly into two categories. Human and animal pathogens were overrepresented among the found bacteria carrying avidin genes. The other widespread category were bacteria that either fix nitrogen or live in root nodules/rhizospheres of plants hosting nitrogen-fixing bacteria. Conclusions Bacterial avidins are a taxonomically and ecologically diverse group mainly found in Actinobacteria, Proteobacteria and Bacteroidetes, associated often with plant invasiveness. Avidin encoding genes in plasmids hint that avidins may be horizontally transferred. The current survey may be used as a basis in attempts to understand the ecological significance of biotin-binding capacity.

Understanding the avidin-biotin binding based on polarized protein-specific charge

In this study, charge updating schemes based on the local polarized protein-specific charge (LPPC) were introduced to vary the atomic charges of the biotin molecule and the residues in close...

A novel cell permeability assay for macromolecules

Background Many cell permeabilisation methods to mediate internalisation of various molecules to mammalian or bacterial cells have been developed. However, no size-specific permeability assay suitable for both cell types exists. Results We report the use of intrinsically biotinylated cell components as the target for reporter molecules for assessing permeabilisation. Due to its well-described biotin binding activity, we developed an assay using Streptavidin (SAv) as a molecular weight marker for assessing eukaryotic and prokaryotic cell internalisation, using flow cytometry as a readout. This concept was tested here as part of the development of host DNA depletion strategies for microbiome analysis of formalin-fixed (FF) samples. Host depletion (HD) strategies require differential cell permeabilisation, where mammalian cells but not bacterial cells are permeabilised, and are subsequently treated with a nuclease. Here, the internalisation of a SAv-conjugate was used as a reference for nucleases of similar dimensions. With this assay, it was possible to demonstrate that formalin fixation does not generate pores which allow the introduction of 60 KDa molecules in mammalian or bacterial membranes/envelopes. Among surfactants tested, Saponin derived from Quillaja bark showed the best selectivity for mammalian cell permeabilisation, which, when coupled with Benzonase nuclease, provided the best results for host DNA depletion, representing a new HD strategy for formalin fixed samples. Conclusion The assay presented provides researchers with a sensitive and accessible tool for discerning membrane/cell envelop permeability for different size macromolecules.