Engineering Antiviral Agents via Surface Plasmon Resonance

The present protocol describes new tools for SPR binding assays to examine CV-N binding to HA, S glycoprotein, related hybrid-type glycans, and high-mannose oligosaccharides. SPR is used to determine the K_D for binding either dimeric or monomeric CV-N to these glycans.

Surface plasmon resonance spectroscopy has been established for the determination of protein ligand in a medium throughput way. Different affinities for binding site variants of the same molecule are presented, namely for the of iron-binding high manners oligosaccharides on viruses. SPR is a label-free technique to study real-time macromolecular binding of surface immobilized receptors.

Multisite interactions are recognized in the kinetic analysis by competitive binding independently of the size of the Specific areas in research that use SPR are drug development to search for inhibitors or antibody characterization. Kinetic constants and affinities are directly calculated from the sensor response. To begin, transfer 100 microliters of the solution on LB-agar plates and spread it gently using a sterile cell spreader.

Start a series of sample reactions using multiple concentrations of double-stranded DNA template ranging from five to 50 nanograms while keeping the primer concentration constant. Then add the DpnI restriction enzyme below the mineral oil overlay and incubate immediately at 37 degrees Celsius for one hour for digesting the parental supercoiled double-stranded DNA. To thaw the XL1-Blue Supercompetent Cells, aliquot the cells to a pre-chilled, small, round bottom tube.

Next, transfer one microliter of the DpnI treated single-stranded DNA from each control and sample reaction to separate aliquots of the Supercompetent Cells which synthesize the complementary strand. After swirling the transformation reactions carefully to mix, incubate the reactions on ice for 30 minutes. Apply heat pulse to the transformation reactions at 42 degrees Celsius for 45 seconds and then place the reactions on ice for two minutes.

Then add 0.5 milliliters of NZY+Broth and incubate the transformation reactions at 37 degrees Celsius with shaking at 225 to 250 RPM for one hour. Afterward, plate the correct volume of each transformation reaction on LB Ampicillin Agar plates as demonstrated previously. For a seed culture, inoculate a small amount of ampicillin containing LB media with a single colony from the transformed plate.

Using the overnight culture, inoculate the expression culture with additives including 10 millimolar of magnesium chloride, 10 millimolar of magnesium sulfate, and 20 millimolar of glucose, diluting the seed culture to one by 100. Next, grow cells with vigorous shaking at 37 degrees Celsius to an absorbent 600 nanometer between 0.4 to 0.6 before cooling the cells to 20 degrees Celsius and induce with one millimolar IPTG and grow overnight. Then harvest the cells by centrifuging at 4, 000 g for 15 minutes at four degrees Celsius and discard the supernatant.

After resuspending the cell pellet in phosphate buffered saline buffer, recent refuge at 4, 000 g for 15 minutes at four degrees Celsius. Then discard the supernatant with a pipette. Next, resuspend the remaining pellet in 10 milliliters of lysis buffer and incubate the suspension for one hour at 37 degrees Celsius.

Then separate soluble and insoluble fractions by centrifugation at 4, 000 g for 15 minutes at four degrees Celsius. Additionally, use HIS-Select Ni2+Affinity Gel in 14 milliliters tubes to bind and resuspend his tagged recombinantly expressed cyanovirin-N in buffer solutions with 20 millimolar imidazole and 250 millimolar imidazole, respectively. Incubate in batch for at least 30 minutes between these steps.

Adding the elution buffer containing 250 millimolar imidazole to elute protein. Transfer the protein solutions to centrifugation tubes with a 10 kilo Dalton cutoff filter and concentrate them by centrifuging for 10 minutes at 4, 500 g and four degrees Celsius. Add SPR running buffer to a dilution factor of one to 10 and centrifuge four times to the initial volume for 10 minutes at 4, 500 g and four degrees Celsius.

Afterward, determine the protein concentration at 280 nanometer using a NanoDrop UV-Visible Spectrophotometer based on the calculated extinction co-efficient for the main protein CVN2L0 showing a size of 23, 474 Dalton. For the dual channel SPR system, use HBSCP plus as running buffer, 10 millimolar glycine hydrochloric acid of pH 1.5 to 1.6 as the regeneration buffer and turn on the instrument degasser, autosampler and pump. Then wash the entire system with double distilled water for one hour.

Next, drop immersion oil onto the detector and mount a glass sensor chip coated with a thin gold film. And on the upper side, functionalized with carboxymethyl dextran hydrogel directly onto the detector below the three-port flow cell. Then fix the setting by pulling down the handling.

To immobilize the proteinaceous ligands to sensor chips, open a run table by clicking on Form in the menu bar and run table editor in the integrated SPP auto link software. Then choose and click on Basic Immobilization from the list of available run tables and follow the steps of the experimental procedure on the computer screen. Next, click on Sample Set Editor in the form section to fill out the reagents list for two racks placed in the autosampler for further analysis.

Click on Autosampler Direct Control as a tool in the menu bar to bring the racks forward or back home and choose four degrees Celsius as the operating temperature. Start the pump to infuse double distilled water by clicking on tools and pump direct control. And record data by clicking on SPR Instrument Direct Control.

And each time, start in the newly appearing window. After adding the coupling reagents in 300 microliter vials, put them into the autosampler racks and start the run table by clicking on Run. For the simple protein-protein interaction, after refilling the pump at 25, 000 microliters per minute, perform baseline adjustment for 30 seconds.

Allow for the subsequent baseline adjustment with double distilled water for 1.5 minutes before quenching the activated chip surface with one molar ethanolamine hydrochloride, pH 8.5. Then switch the tubes from the liquid sampler to the degasser from double distilled water into the bottle with HBS-EP+Click on Form, scroll down, and change to Post-Processing by clicking this operation mode. Then click on Add to select binding curves generated over time in the data platform for each flow cell and export the overlay as a scrubber file.

Next, click on File to open the file saving options and obtain response curves by aligning left and right curves and subtracting signals of the second reference channel from those of the ligand channel. Single injections of CVN2L0 and variance V2 and V5 were first tested for binding to the haemagglutinin coupled sensor chip to estimate binding capacities using the autosampler and running table editor. Repeated injections were automated at various concentrations in the nanomolar and micromolar range in the system over time demonstrating that no saturation on the chip surface nor equilibrium binding was achieved.

Concentration versus response was plotted for CVN wild-type binding to RBD, assuming specific targeting of possibly conserved carbohydrates on the RBD S1 subunit with weaker affinity having a dissociation rate constant of 260 micromoles. The same affinity plot for CVN2L0-V4 binding to DM becomes no longer analyzable due to the replacement of disulphide bonds that interfere with high-affinity binding to small glycosylated peptides and yields a higher response than response maximum value. CVN wild-type binding to RBD on SARS-CoV-2 shows binding to S protein and RBD with a dissociation rage constant of 18.6 micromoles and 260 micromoles, respectively.

Although SPR response for analyte concentrations results in high response units and typical SPR sensorgrams for CVN wild-type and E41A binding. However, the mutant is unstable when diluted. SPR biosensing is addressing high-affinity and low-affinity binding of purified proteins and its variants to ligands.

In our case, glycoproteins exploiting optic readout and the dual channel flow system on sensor chip surface. Enzyme being immunosorbent assay is an alternate immunological methods recognizing protein epitopes but also providing data on the concentration of peptides and small molecules out of complex matrices. Testing recombinantly expressed proteins by SPR binding assays incorporated biosensing of confirmational changes which is useful for the verification and prediction of protein stability by computational protein side.