Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay

The overall goal of this bio-layer interferometry or BLI assay, is to measure the potential interaction between purified hEAG1 ion channel protein and small molecule lipids. This method can help answer key questions in the ion channel pharmacology field, such as whether the small molecule of interest can directly interact with this ion channel and what are the kinetics of the interaction? The main advantage of this technique is that it is a labor free and high throughput method.

Only a small amount of immobilized protein is needed. Generally, individuals who are new to this method will struggle because a successful assay involves multiple steps, including protein expression, purification, labeling, accurately tuned sensor, and data analysis. After culturing HEK293 T cells stabling expressing hEAG1 for two to three days, harvest the cells by removing the growth medium, and use four milliliters of PBS to wash the cells twice.

Discard the PBS. Scape the cells into two milliliters of PBS per dish, and use a one milliliter pipette to transfer to cells into a 15 milliliter tube. Centrifuge the cell suspension at 420 times gravity and four degrees Celsius for five minutes.

Then, decant the supernatant and use four milliliters of lysis buffer to resuspend the pellet. Incubate the suspension on ice for 30 minutes, thoroughly vortexing the lysate every 10 minutes. Next, centrifuge the cell lysate at 12, 000 times gravity and four degrees Celsius for 10 minutes.

Then, transfer the supernatant to a five milliliter tube and keep it on ice for immediate use. To prepare the anti-FLAG M2 affinity resin thoroughly suspend the resin by gentle inversion to make sure the bottle of anti-FLAG M2 ffinity gel is a uniform suspension of gel beads. Immediately transfer 400 microliters of suspension to a chilled 1.5 milliliter tube.

Then, centrifuge the suspension at 8, 000 times gravity and four degrees Celsius for 30 seconds, And carefully discard the supernatant to wash out the storage buffer. To resuspend the resin pellet, add 500 microliters of protein extract supernatant to the resin, and transfer the suspension to a new, chilled, five milliliter tube. Pipette an additional 500 microliters of protein extract into the original tube to collect any remaining beads, and transfer the extract to the five milliliter tube.

Incubate the mixture on a shaker at eight rpm and four degrees Celsius overnight to bind the FLAG fusion protein to the resin. Then, centrifuge the mixture at 1, 000 times gravity at four degrees Celsius for 10 minutes. Discard the supernatant and wash the pellet three times with 500 microliters of one x PBS.

Keep it on ice for immediate use. Add 10 microliters of three x FLAG elution solution to 390 microliters of PBS for a final concentration of 200 nanograms per microliter. Then, add 400 microliters of three x FLAG elution solution to the previously prepared gel beads.

Incubate the sample on a shaking incubator at eight rpm and four degrees Celsius for two hours. Then, centrifuge the resin at 8000 times gravity for 30 seconds. Transfer the supernatant to a fresh 1.5 milliliter tube, and store it at four degrees Celsius for immediate use.

Use the BCA protein assay according to the manufacturer's instructions to determine the concentration of the purified protein. Then, use a 30 microliter sample for Western Blot analysis with an anti-Flag antibody to confirm that the protein of interest has been purified. To label the purified protein with biotin, prepare five milligrams per milliliter of biotin stock solution in PBS.

For each test of two biosensors add a three fold molar excess of biotin to 20 micrograms of purified protein to achieve a preferable N-terminal biotinylation of the purified protein in PBS. Incubate the sample in the dark on ice for at least 30 minutes. To remove the unbound biotin and buffer, exchange the protein into SD buffer.

Transfer the protein to an ultrafiltration device with a molecular cut off of 30 kilodaltons. Then, add SD buffer and centrifuge the sample at 12, 000 times gravity and four degrees Celsius for 10 minutes. Remove the ultrafiltrate from the centrifuge tube.

Add 200 microliters of SD buffer into the filter device and centrifuge the sample again. Repeat the process at least three times. Collect the buffer exchanged sample by flipping the filtration device and place it into a 1.5 milliliter tube.

Centrifuge the sample at 2, 000 times gravity and four degrees Celsius for five minutes. Keep the sample on ice for immediate use. To carry out the BLI assay, 30 minutes before the study, prewarm the equipment by turning on the instrument.

Check the instrument status window to confirm the machine is at ready state before beginning. Make sure the door of the instrument is closed before opening the data acquisition software and in the experiment wizard, choose the New Kinetics Experiment. Define the wells to be used on the 96 well plate by right clicking to choose the buffer, the load, and the sample.

For sample wells, the unit of concentration of PIP2 should be input as molars. To define the assay steps, choose a step, and double click on the respective column. A duplicate of the assay definition is set for the control sensors.

Set the rpm to 1, 000. Choose one minute for the baseline step, and five to 10 minutes for loading, association, and dissociation respectively. Perform the test at room temperature.

Click the columns which contain the sensors and click fill to indicate the location of sensors in the sensor tray. Review all planned steps to check for mistakes and go back to correct them. In the entire operation of BLI assay the step of reviewing all planned steps could be neglected by the researcher.

However, it's very important to check that all the planned steps are correct. Set the location of data files and click go to start the assay. Run the assay and analyze the data according to the text protocol.

As seen in this patch clamp experiment in an HEK293 T cell, stably expressing hEAG1, the voltage dependent outward potassium currents suggests that functional hEAG1 channels are highly expressed in the cells. Using the anti-FLAG antibody this Western Blot of hEAG1 from purified protein samples indicates the quality and specificity of the purified protein. The purified channel protein was biotinylated to perform an interaction assay with the lipid PIP2 by using the real time BLI assay.

A typical binding curve between hEAG1 and PIP2 is shown here. hEAG1 is bound to PIP2 in a concentration dependent manner. The accumulated concentrations of PIP2 correspond to the biosensor's data traces.

This representative assay shows the changes in optical interference in different concentrations of PIP2. Finally, a curve fit with the Hill equation was obtained from the peak value of the optical interference signal measured at different PIP2 concentrations and determined the equilibrium dissociation constants between hEAG1 and PIP2. Once mastered, this technique can be done in about one hour if it is performed properly.

When attempting this procedure, it's very important to remember to review all planned steps, to make sure this procedure is correct. Following this procedure, other methods like patch clamp can be performed in order to answer additional questions like identifying the function of this ion channel after binding the small molecule. After its development, this technique paved the way for researchers in the field of ligand screening of ion channels to explore the novel ligands in ion channel drug discovery.

After watching this video, you should have a good understanding of how to prepare the ion channel protein and how to test its interaction with small molecules, with the BLI method.