Name: titration elisa as a method to determine the dissociation constant of receptor ligand interaction
Uploaded: 2018-02-15T12:00:00
Description: Watch this Scientific Journal Video about Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction at JoVE.com

The protocol and algorithm were developed within a project financed by the Deutsche Forschungsgemeinschaft (DFG grant SFB1009 A09 and EB177/13-1). The author thanks Barbara Schedding and Felix Schmalbein for technical support and Dr. Niland for critically reading the manuscript.

1. Stock Solutions
<ol>
	<li>To prepare 100 mL of 10x&#160;TBS pH 7.4 solution, dissolve 6.06 g of TRIS and 8.77 g of NaCl in 90 mL of deionized water, adjust the pH to 7.4 with 37% HCl solution, fill the volume to 100 mL with deionized water, and filter the solution.</li>
	<li>To prepare 100 mL of 1 M HEPES/NaOH, pH 7.4 solution, dissolve 23.83 g of HEPES in 90 mL of deionized water, adjust the pH to 7.4 with 1.5 M NaOH, fill the volume to 100 mL with deionized water, and filter the solution.</li>
	<li>To prepare 100 ...

<ol>
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M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ligand-receptor+complexes:+origin+and+development+of+the+concept.">Ligand-receptor complexes: origin and development of the concept.</a> J Biol Chem. 279 (1), 1-12 (2004).</li><li>Bisswanger, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ch.+1:+Multiple+Equilibria,+Principles+and+Derivations.">Ch. 1: Multiple Equilibria, Principles and Derivations.</a> Enzyme Kinetics: Principles and Methods. , 1-26 (2017).</li><li>Shimura, K., Kasai, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Affinity+gel+titration:+quantitative+analysis+of+the+binding+equilibrium+between+immobilized+protein+and+free+ligand+by+a+continuous+titration+procedure.">Affinity gel titration: quantitative analysis of the binding equilibrium between immobilized protein and free ligand by a continuous titration procedure.</a> Anal Biochem. 149 (2), 369-378 (1985).</li><li>Gong, M., Nikcevic, I., Wehmeyer, K. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Langmuir+isotherm:+a+commonly+applied+but+misleading+approach+for+the+analysis+of+protein+adsorption+behavior.">The Langmuir isotherm: a commonly applied but misleading approach for the analysis of protein adsorption behavior.</a> J Biomed Mater Res A. 103 (3), 949-958 (2015).</li><li>Stockell, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+binding+of+diphosphopyridine+nucleotide+by+yeast+glyceraldehyde-3-phosphate+dehydrogenase.">The binding of diphosphopyridine nucleotide by yeast glyceraldehyde-3-phosphate dehydrogenase.</a> J Biol Chem. 234 (5), 1286-1292 (1959).</li><li>Heyn, M. P., Weischet, W. 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S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+&#945;2&#946;1+integrin+inhibitor+rhodocetin+binds+to+the+A-domain+of+the+integrin+&#945;2+subunit+proximal+to+the+collagen-binding+site.">The &#945;2&#946;1 integrin inhibitor rhodocetin binds to the A-domain of the integrin &#945;2 subunit proximal to the collagen-binding site.</a> Biochem J. 376 (Pt 1), 77-85 (2003).</li><li>Eble, J. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+&#945;2&#946;1+integrin-specific+antagonist+rhodocetin+is+a+cruciform,+heterotetrameric+molecule.">The &#945;2&#946;1 integrin-specific antagonist rhodocetin is a cruciform, heterotetrameric molecule.</a> FASEB J. 23 (9), 2917-2927 (2009).</li><li>Eble, J. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dramatic+and+concerted+conformational+changes+enable+rhodocetin+to+block+&#945;2&#946;1+integrin+selectively.">Dramatic and concerted conformational changes enable rhodocetin to block &#945;2&#946;1 integrin selectively.</a> PLoS Biol. 15 (7), e2001492 (2017).</li><li>Bracht, T., Figueiredo de Rezende, F., Stetefeld, J., Sorokin, L. M., Eble, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monoclonal+antibodies+reveal+the+alteration+of+the+rhodocetin+structure+upon+&#945;2&#946;1+integrin+binding.">Monoclonal antibodies reveal the alteration of the rhodocetin structure upon &#945;2&#946;1 integrin binding.</a> Biochem J. 440 (1), 1-11 (2011).</li><li>Harlow, E., Lane, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+5:+Immunizations.">Chapter 5: Immunizations.</a> Antibodies, a laboratory manual. 5, 53-138 (1988).</li><li>Lu, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analyzing+interactions+between+SSB+and+proteins+by+the+use+of+fluorescence+anisotropy.">Analyzing interactions between SSB and proteins by the use of fluorescence anisotropy.</a> Methods Mol Biol. 922, 155-159 (2012).</li><li>Fielding, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NMR+methods+for+the+determination+of+protein-ligand+dissociation+constants.">NMR methods for the determination of protein-ligand dissociation constants.</a> Curr Top Med Chem. 3 (1), 39-53 (2003).</li><li>Leavitt, S., Freire, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+measurement+of+protein+binding+energetics+by+isothermal+titration+calorimetry.">Direct measurement of protein binding energetics by isothermal titration calorimetry.</a> Curr Opin Struct Biol. 11 (5), 560-566 (2001).</li><li>McDonnell, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+plasmon+resonance:+towards+an+understanding+of+the+mechanisms+of+biological+molecular+recognition.">Surface plasmon resonance: towards an understanding of the mechanisms of biological molecular recognition.</a> Curr Opin Chem Biol. 5 (5), 572-577 (2001).</li><li>Rich, R. L., Myszka, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+surface+plasmon+resonance+biosensor+analysis.">Advances in surface plasmon resonance biosensor analysis.</a> Curr Opin Biotechnol. 11 (1), 54-61 (2000).</li><li>Pesquero, N. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real-time+monitoring+and+kinetic+parameter+estimation+of+the+affinity+interaction+of+jArtinM+and+rArtinM+with+peroxidase+glycoprotein+by+the+electrogravimetric+technique.">Real-time monitoring and kinetic parameter estimation of the affinity interaction of jArtinM and rArtinM with peroxidase glycoprotein by the electrogravimetric technique.</a> Biosens Bioelectron. 26 (1), 36-42 (2010).</li><li>Scheuermann, T. H., Padrick, S. B., Gardner, K. H., Brautigam, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+acquisition+and+analysis+of+microscale+thermophoresis+data.">On the acquisition and analysis of microscale thermophoresis data.</a> Anal Biochem. 496, 79-93 (2016).</li></ol>

The titration ELISA is a versatile test system to determine the dissociation of a receptor-ligand interaction. As the titration ELISA circumvents the necessity to separate free and bound ligands effectively and to analyze their concentrations quantitatively, substantially more studies and publications have employed titration ELISAs instead of recording binding curves. Moreover, titration ELISAs are easy to perform and require reasonably low amounts of receptor and ligand. For accurate analysis of dissociation constants, ...

The dissociation constant K is a key parameter to describe the affinity of a receptor (R) for its ligand (L). Based on the law of mass action, K is defined for the equilibrium, in which the receptor-ligand complex RL dissociates into the receptor R and the ligand L:
<img alt="Equation 1 " src="/files/ftp_upload/57334/57334eq1.jpg" />&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;Equation 1
with the indices f indicating the free/unbound state of receptor and ligand. The concentration of the receptor-ligand complex, RL, is identical to the concentration of the receptor-bound ligand Lb. As the total concentration of receptor Rt is the sum of the free receptor Rf and ligand-bound receptor Rb = Lb, the dissociation constant can also be written as:
<img alt="Equation 2 " src="/files/ftp_upload/57334/57334eq2.jpg" />&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;Equation 2
Therefore, the saturation yield Y, defined as the fraction of bound ligand Lb in relation of the total concentration of receptor Rt,
<img alt="Equation 3 " src="/files/ftp_upload/57334/57334eq3.jpg" />&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;Equation 3
depends on the concentration of free ligand Lf:
<img alt="Equation 4 " src="/files/ftp_upload/57334/57334eq4.jpg" />&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;Equation 4
This hyperbolic relation describes the binding curve of a receptor-ligand interaction and its plot shows the concentration of bound ligand Lb as a function of the concentration of free ligand Lf. From the binding curve, the dissociation constant K can be derived as the concentration of free ligand at half-maximal saturation yield. Moreover, different algorithms to linearize binding curves have been established, such as the double-reciprocal plot by Klotz1,2, or transformations according to Scatchard or Hanes (reviewed by Bisswanger3). However, all algorithms suffer from the problem that the maximum value of the saturation yield, which is asymptotically approached at high concentrations of free ligand in the binding curve, has to be estimated in a graphical pre-evaluation and therefore is error-prone.
In addition, the determination of a binding curve requires the quantification of free and bound ligand during the binding equilibrium. To this end, the free ligand has to be separated from the receptor-bound ligand and quantified. Therefore, the ligand and receptor have to differ in their properties, such as a non-protein ligand as opposed to a protein receptor. If both binding partners are proteins, they have to be distinguishable in their sizes, charges, or other molecular features. Nevertheless, the quantification of ligand concentrations in small-scale binding approaches is a difficult task. Radioactive labeling of the ligand has often been necessary to detect the low concentration of bound ligand, especially if substantial amounts of receptors were not available or affordable. Moreover, the receptor-bound ligand may dissociate during and after isolation in a non-negligible manner. Hence, complex methods, such as equilibrium gel filtration4, capillary electrophoresis5, and pulse proteolysis6, are required to quantify receptor-bound ligand and separate it from free ligand.
In contrast to these binding assays, titration experiments do not require the quantitative separation of bound and free ligand. To this end, a receptor at a constant concentration is titrated with different concentrations of added ligand. By binding to the receptor, the bound ligand has a biophysical property which distinguishes it from the free ligand and is measurable by, e.g., photometry, fluorometry, or antibody detection. Thus, a signal S, which is proportional to the saturation yield Y and consequently also to the concentration of receptor-bound ligand (Lb), is detected as a function of the total concentration of added ligand (Lt). Both parameters, the signal S and the total concentration of added ligand are quantified in a direct and easier manner than the concentrations of bound and free ligand. Especially, the detection of receptor-bound ligand by enzyme-linked immunosorbent assay (ELISA) allowed the reduction of sample volumes to below 100 &#181;L as well as parallel measurements of several ligand concentrations in multi-well microtiter plates. In a titration ELISA, a receptor is physically adsorbed to a microtiter plate at the same concentration and titrated with soluble ligand. The receptor is immobilized to the plastic surface essentially by hydrophobic adsorption. The surface concentration of immobilized receptor correlates with the coating concentration of the receptor in a nonlinear relation, likely according to Langmuir&#180;s adsorption isotherm7. In addition to the overall number of adsorbed receptor molecules, their activity state is another important parameter for titration assays. Only immobilized receptors which have retained ligand binding activity, are relevant for the titration assay and eventually contribute to the total concentration of active receptors Rt of the titration assay, which cannot be determined directly.
Sites on the plastic surface, which are not covered by the immobilized receptor are prone to adsorb other proteins, such as the ligand. Physical adsorption of the ligand to such plastic surface sites would result in a similar signal as the receptor-bound ligand, yet in a nonspecific manner. To reduce this nonspecific signal, the plastic surface sites of the microtiter plates which have not been coated with protein yet will be blocked with bovine serum albumin (BSA). However, for some receptor-ligand titration assays, nonspecific background signals may be observed. Then, other blocking agents, such as a solution of 0.2% gelatin or of 0.04% Tween 20, are recommended.
After binding to the receptor, the free ligand is removed by two washing steps. Bound ligand remains with the receptor, which is immobilized to the plastic surface of the microtiter well, and optionally reinforced by chemical fixation. For the subsequent covalent cross-linkage of bound ligand and immobilized receptor with glutaraldehyde, the buffer substance TRIS is replaced for HEPES, without any change in ligand binding. HEPES, in contrast to TRIS, does not inactivate glutaraldehyde. The covalent cross-linkage with glutaraldehyde fixes the bound ligand with its receptor and prevents its dissociation during subsequent washing and incubation steps. Thus, the receptor-ligand interaction is chemically frozen and warrants a titration curve which is unaffected by subsequent steps of washing and incubation. However, glutaraldehyde fixation may chemically modify the ligand and receptor in such a way that their interaction is reduced or abolished. Moreover, modification of epitopes within the ligand may change the binding affinity of the detecting antibody, especially if a monoclonal antibody is used to quantify bound ligand. Although neither of these adverse effects of glutaraldehyde fixation occurs in this titration ELISA, the sensitivity of the test towards glutaraldehyde must be tested for every receptor-ligand interaction prior to the titration experiment. After fixation, excess glutaraldehyde is removed in three washing steps with TRIS-containing buffer. TRIS inactivates remaining aldehyde groups, which might nonspecifically react with detecting antibodies in the subsequent step.
The amount of bound ligand is quantified with enzyme-linked antibodies, which provide a photometric ELISA signal S. This is plotted versus the total ligand concentration Lt added to each well. Despite its easier acquisition, the titration curve is not a hyperbolic function in contrast to the binding curve. Furthermore, it has been unclear how to calculate the dissociation constant K from a titration curve. Although algorithms to linearize spectroscopically acquired titration curves have been independently reported by Stockell8 and Heyn and Weischet9, they fell short due to their uncertainty of estimating the maximum signal value that the saturation yield approaches at high concentrations of added ligand.
Here, a titration ELISA and a non-linear regression algorithm are described to derive the dissociation constant K for a receptor ligand interaction from a titration curve. This protocol is exemplified for the interaction of the collagen-binding A-domain of the integrin &#945;2&#946;1 with a snake venom-derived inhibitor. Integrins are cell adhesion molecules, which mediate the anchorage of cells to the surrounding extracellular matrix or the underlying basement membrane10,11. Moreover, integrins convey important signals between cells and the extracellular matrix by recruiting additional signaling molecules and forming new cell organelles, adhesomes, upon cell-matrix interaction12,13,14. Collagen, the ligand of &#945;2&#946;1 integrin, is the most abundant protein of the human body and is a crucial scaffolding component of the connective tissue15. The interaction between &#945;2&#946;1 integrin and collagen is mediated by the A-domain of the integrin &#945;2 subunit. The integrin &#945;2A-domain contains a divalent cation, which is required for collagen binding and stabilizes its structure. The wild-type form as well as mutants of the &#945;2A domain, such as the one in which the surface-exposed residue Y216 had been replaced for a glycine, can easily be produced recombinantly in a bacterial expression system and isolated via their oligo-His-tags with a NiNTA superflow column with a subsequent dialysis against TRIS-buffered saline (TBS; 50 mM TRIS/HCl, pH 7.4, 150 mM NaCl) containing 2 mM MgCl216. Their concentrations were determined with the bicinchoninic acid assay (BCA) and their purities are tested by conventional SDS-PAGE and stained with Coomassie-Brilliant Blue R250.
The interaction between &#945;2&#946;1 integrin and collagen is blocked by binding of the snake venom component, rhodocetin, from the Malayan pit viper (Calloselasma rhodostoma)16,17. Used as a soluble ligand in this titration ELISA, rhodocetin was purified from the crude venom as described previously16. It is dissolved in HEPES-buffered saline (HBS; 10 mM HEPES/NaOH, pH 7.4, 150 mM NaCl) and is stored frozen at -20 &#176;C. Its concentration was determined by BCA and its purity was proven by SDS-PAGE. As an antagonist, rhodocetin not only blocks collagen binding to the integrin &#945;2&#946;1 A-domain, but also stabilizes the inactive conformation of the integrin thereby preventing any signaling from collagen into cells or platelets18. It is of great biomedical importance to determine the dissociation constant of rhodocetin with its receptor target and thus unravel its molecular mechanism and pharmaceutical potential e.g., as an antithrombotic agent. To this end, a titration ELISA is described including its evaluation, which is applicable to almost any receptor-ligand interaction with a 1:1 interaction stoichiometry.

<table>
	<tbody>
		<tr>
			<td>TRIS</td>
			<td>neoFrox</td>
			<td>1125KG001</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>H4034</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Applichem</td>
			<td>1,316,591,214</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Merck</td>
			<td>172571</td>
			<td></td>
		</tr>
		<tr>
			<td>integrin a2A, wild-type and mutant, recombinant</td>
			<td></td>
			<td>isolated in author&#39;s lab</td>
			<td></td>
		</tr>
		<tr>
			<td>NiNTA superflow column&#160;</td>
			<td>Qiagen, Germany</td>
			<td>30821</td>
			<td></td>
		</tr>
		<tr>
			<td>Coomassie-Brilliant Blue R250</td>
			<td>Serva</td>
			<td>35050</td>
			<td></td>
		</tr>
		<tr>
			<td>bicinchoninic acid assay (BCA), protein concentration determination kit</td>
			<td>Fisher Scientific</td>
			<td>23225</td>
			<td></td>
		</tr>
		<tr>
			<td>bovine serum albumine (BSA), fraction V</td>
			<td>Applichem</td>
			<td>A1391</td>
			<td></td>
		</tr>
		<tr>
			<td>25 % solution of glutaraldehyde</td>
			<td>Merck</td>
			<td>354400</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-rabbit immunglobulin-antibodies from goat, conjugated with alkaline phosphatase</td>
			<td>Sigma-Aldrich</td>
			<td>A9919</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Applichem</td>
			<td>A1377</td>
			<td></td>
		</tr>
		<tr>
			<td>Zn(II)-acetate</td>
			<td>Applichem</td>
			<td>A4324</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>Applichem</td>
			<td>A1551</td>
			<td></td>
		</tr>
		<tr>
			<td>Alkaline phosphatase substrate tablet (5 mg)</td>
			<td>Sigma-Aldrich</td>
			<td>S0942</td>
			<td></td>
		</tr>
		<tr>
			<td>Costar half-area microtiter plate</td>
			<td>Thermo Scientific</td>
			<td>Corning 3690</td>
			<td></td>
		</tr>
		<tr>
			<td>micro reaction tubes</td>
			<td>Eppendorf</td>
			<td>30120086</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate ELISA reader</td>
			<td>BioTek</td>
			<td>Synergy HT</td>
			<td></td>
		</tr>
	</tbody>
</table>

titration elisa as a method to determine the dissociation constant of receptor ligand interaction

The dissociation constant describes the interaction between two partners in the binding equilibrium and is a measure of their affinity. It is a crucial parameter to compare different ligands, e.g., competitive inhibitors, protein isoforms and mutants, for their binding strength to a binding partner. Dissociation constants are determined by plotting concentrations of bound versus free ligand as binding curves. In contrast, titration curves, in which a signal that is proportional to the concentration of bound ligand is plotted against the total concentration of added ligand, are much easier to record. The signal can be detected spectroscopically and by enzyme-linked immunosorbent assay (ELISA). This is exemplified in a protocol for a titration ELISA that measures the binding of the snake venom-derived rhodocetin to its immobilized target domain of &#945;2&#946;1 integrin. Titration ELISAs are versatile and widely used. Any pair of interacting proteins can be used as immobilized receptor and soluble ligand, provided that both proteins are pure, and their concentrations are known. The difficulty so far has been to determine the dissociation constant from a titration curve. In this study, a mathematical function underlying titration curves is introduced. Without any error-prone graphical estimation of a saturation yield, this algorithm allows processing of the raw data (signal intensities at different concentrations of added ligand) directly by mathematical evaluation via non-linear regression. Thus, several titration curves can be recorded simultaneously and transformed into a set of characteristic parameters, among them the dissociation constant and the concentration of binding-active receptor, and they can be evaluated statistically. When combined with this algorithm, titration ELISAs gain the advantage of directly presenting the dissociation constant. Therefore, they may be used more efficiently in the future.

After the ELISA has been developed, the yellow color of the converted alkaline phosphatase substrate, para-nitrophenolate, indicates that the amount of bound rhodocetin ligand decreases with decreasing concentrations of added rhodocetin from columns 1 to 11 (Figure 1). The colorless wells in the rhodocetin-free wells in column 12 show a low background signal.
Photometric quantification at 4...

Watch this Scientific Journal Video about Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction at JoVE.com

Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction

A detailed protocol to perform a titration ELISA is described. Moreover, a novel algorithm is presented to evaluate titration ELISAs and to obtain a dissociation constant of binding of a soluble ligand to a microtiter plate-immobilized receptor.

The dissociation constant describes the interaction between two partners in the binding equilibrium and is a measure of their affinity. It is a crucial ...

The overall goal of this titration ELISA is to determine the affinity constant of two binding partners in a reproducible and efficient manner using a novel algorithm. This method can help answer key questions not only in the field of protein ligand interaction and receptor research but also in applied life sciences such as pharmaceutical research and pharmacology. The main advantage of this technique is that the affinity constant of a receptor ligand interaction can be determined easily by titrating a receptor with a ligand on an ELISA plate and by using a novel evaluation algorithm.Begin this procedure by diluting the stock solution of Integrin Alpha 2 A Domain to a final concentration of five micrograms per milliliter in TBS magnesium chloride buffer. Both a wild type and a mutant Integrin Alpha 2 A Domain will be used in this demonstration. Fill each well of a row on a half area microtiter plate with 50 microliters of the Integrin Alpha 2 A Domain coating solution.Perform every titration row at least in duplicates. In this example, every titration row is performed in quadruplets. Seal the plate with foil and leave the plate at four degrees Celsius overnight.On the following day, remove the coating solution and fill each well with 15 microliters of TBS magnesium chloride buffer. Remove the wash solution and fill the wells with new wash solution. The washes will remove soluble receptor molecules which have not been immobilized to the plastic surface by physical absorption.The next step is to block non-specific binding sites by adding 50 microliters of one percent BSA solution in TBS magnesium chloride buffer to each well. Reseal the plate and incubate at room temperature for one hour. While the wells of the microtiter plate are being blocked with BSA, prepare a serial dilution of the ligand Rhodocetin.A start concentration of 243 enamel-eroded Rhodocetin and a dilution factor of 2.3 are used in this case. For the eight titration curves in this experiment, prepare 920 microliters of Rhodocetin solution at the highest concentration in one per cent BSA in TBS magnesium chloride in test tube number one. Pipette 520 microliters of one per cent BSA solution in TBS magnesium chloride into each of the other ten test tubes labeled two through eleven.Transfer 400 microliters of the Rhodocetin solution from test tube to test tube two. Mix both solutions by chut-ter-a-tion and then transfer 400 microliters from this mixture to test tube three. Continue this serial dilution until test tube eleven.For the success of this procedure, it is important to always fill every well quickly with solution to make sure the wells do not dry out. At the completion of the one hour incubation, remove the blocking solution from the microtiter plate wells. Immediately add 50 microliters of the Rhodocetin solution from test tube one into the wells of column one, the solution from test tube two to the wells of column two, and continue through column eleven.Add 50 microliters of one per cent BSA and TBS magnesium chloride as a ligand-free control to the wells of column twelve. Reseal the plate and incubate at room temperature for one and a half hours. To remove non-bound ligand molecules, remove the binding solution and fill each well with 50 microliters of HBS magnesium chloride buffer.Then remove the HBS buffer and add new HBS buffer. To chemically fix the receptor and bound ligand, fill each well of the microtiter plate with 50 microliters of a 2.5 per cent glutaraldehyde solution in HBS magnesium chloride buffer. Incubate the microtiter plate at room temperature for ten minutes.Remove and in inactivate excess glutaraldehyde by removing the fixation solution and filling each well with 50 microliters of TBS magnesium chloride buffer. Remove the wash buffer and add new wash buffer to each well. To begin this assay, remove the wash buffer from all wells of the microtiter plate and add to each well 50 microliters of the primary antibody solution, diluted one to two thousand in one per cent BSA TBS magnesium chloride.Reseal the plate and incubate it at room temperature. Remove the primary antibody solution from all wells and add to each well 50 microliters of TBS magnesium chloride buffer. Wash three times with TBS magnesium chloride buffer.Next, add to each well 50 microliters of the secondary antibody solution, diluted one to two thousand in one per cent BSA in TBS magnesium chloride. Reseal the plate, and leave it standing at room temperature. Remove the secondary antibody solution from the wells, and add to each well 50 microliters of TBS magnesium chloride buffer.Wash three times. After the third wash, tap the microtiter plate onto a tissue cloth to remove all traces of liquid. Using a multi-channel pipette, promptly add 50 microliters of the alkaline phosphatase detecting solution to each well of the microtiter plate to start the enzymatic conversion as simultaneously as possible.Incubate the plate at room temperature until the solution in the wells with the highest ligand concentration turns yellow. Depending on signal intensity, the incubation time may vary between five minutes and one hour. Stop the conversion of the phosphatase substrate by using a multi-channel pipette to add 50 microliters of a 1.5 molar sodium hydroxide solution to each well in the same order of the alkaline phosphatase detecting solution was added.Leave the plate for several minutes to ensure streak-free mixing of both solutions. Measure the optical density at 405 nanometers of each well using an ELISA reader. Start the data analysis by opening the table of raw data.Copy the columns from the Excel file, open Graph Pad Prism Five, open a new project file in the Main Menu and under new data and graph, choose the X Y format. Choose the option Enter and Plot a Single Point for each value for the Y axis and paste them into the data sheet of Graph Pad Prism as X and y values respectively. Transpose the optical density at 405 nanometer values into a column format.In the data sheet, the first column represents the concentrations as added ligand as X values, while the columns to the right contain the signal values of the eight titration curves as Y values. As a semi-logarithmic plot will be drawn, the last row, which counts the signals of the ligand-free controls, concentration zero, is deleted. Graph Pad Prism draws the plot which is seen in the graph section.For the X axis, a semi-logarithmic scaling is selected. The X axis shows the signal values measured as OD values at 405 nanometers. By double-clicking any of the symbols, they can be selected and marked by simple shape and color.The titration values for the wild-type form are highlighted with circles in different red shadings, whereas the titration signals for the mutant form are marked with blue squares. Open the analysis sub-program and under X Y Analysis, choose the option Non-linear Regression and press the New button to create a new equation. Type the titration curve equation into the newly opened template sheet and define the appropriate constraints.Analyze the values of the data sheet by choosing the newly created user-defined equation. Open the table with the calculated approximation values, which are shown under the results section on the left side of the software screen. In this representative microtiter plate for a Titration ELISA, the yellow color of the converted alkaline phosphatase substrate indicates that the amount of bound-ward ascetant ligand decreases with decreasing concentrations of added Rhodocetin.The lack of color in the Rhodocetin-free wells indicates a low background signal. A novel algorithm processes the raw data from photometric quantification at 405 nanometers to calculate the signal as a function of the total concentration of added Rhodocetin. The four titration curves for each receptor form while type and mutant are highly reproducible and almost superpose each other.In contrast, the two groups of titration curves are clearly separated from each other. The titration curves of the mutant alpha 2 A domain are shifted to higher Rhodocetin concentrations, indicating that Rhodocetin binds with lower affinity to the mutated receptor. The dissociation constants of the eight titration curves were plotted and grouped for the wild type and mutant form of the alpha 2 A domain.The affinity constant for the binding of Rhodocetin to the wild type alpha 2 A domain is 5.80 plus or minus 0.15 nanomolar, whereas Rhodocetin binds to the mutated receptor with a significantly lower affinity of 9.68 plus or minus 0.18 nanomolar. Once optimized for routine, this technique can be done within six to seven hours. While attempting this procedure, it is important to remember that the glutaraldehyde might affect ligand binding to the receptor and might harm the epitopes of the ligand, thereby compromising antibody detection.This must be tested beforehand. If the equipment for surface plasma resonance is available, the SPR method could be used as an alternative, however, SPR evaluates kinetics data to determine the affinity constant. This Titration ELISA in combination with the novel evaluation algorithm is versatile and can, for instance, be used to compare the affinities of different ligands to analyze structure activity relations and to unravel the molecule mechanism of protein-ligand interactions.After watching this video, you should have a good understand of how to perform the Titration ELISA and how to implement this novel evaluation algorithm so that the affinity constant for any protein-ligand interaction can be determined easily and routinely, even for multiple ligands simultaneously. Don't forget that working with glutaraldehyde can be hazardous. Therefore, safety measures such as wearing gloves and goggles should always be taken while performing the fixation step of this protocol.

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Research

JoVE Journal

Biochemistry

Method for Identifying Small Molecule Inhibitors of the Protein-protein Interaction Between HCN1 and TRIP8b

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed ubiquitously throughout the brain, where they function to regulate the excitability of neurons. The subcellular distribution of these channels in pyramidal neurons of hippocampal area CA1 is regulated by tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), an auxiliary subunit. Genetic knockout of HCN pore forming subunits or TRIP8b, both lead to an increase in antidepressant-like behavior, suggesting that limiting the function of HCN channels may be useful as a treatment for Major Depressive Disorder (MDD). Despite significant therapeutic interest, HCN channels are also expressed in the heart, where they regulate rhythmicity. To circumvent off-target issues associated with blocking cardiac HCN channels, our lab has recently proposed targeting the protein-protein interaction between HCN and TRIP8b in order to specifically disrupt HCN channel function in the brain. TRIP8b binds to HCN pore forming subunits at two distinct interaction sites, although here the focus is on the interaction between the tetratricopeptide repeat (TPR) domains of TRIP8b and the C terminal tail of HCN1. In this protocol, an expanded description of a method for purifying TRIP8b and executing a high throughput screen to identify small molecule inhibitors of the interaction between HCN and TRIP8b, is described. The method for high throughput screening utilizes a Fluorescence Polarization (FP) -based assay to monitor the binding of a large TRIP8b fragment to a fluorophore-tagged eleven amino acid peptide corresponding to the HCN1 C terminal tail. This method allows &#39;hit&#39; compounds to be identified based on the change in the polarization of emitted light. Validation assays are then performed to ensure that &#39;hit&#39; compounds are not artifactual.

The interaction between HCN channels and their auxiliary subunit has been identified as a therapeutic target in Major Depressive Disorder. Here, a fluorescence polarization-based method for identifying small molecule inhibitors of this protein-protein interaction, is presented.

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed ubiquitously throughout the brain, where they function to regulate the ...

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

Here we describe a simple protocol for rapidly producing hundreds of nematode growth media agar, 96-well culture plates with consistent numbers of Caenorhhabditis elegans per well. These cultures are useful for the phenotypic screening of whole organisms. We focus here on using these cultures to screen chemicals for pro-longevity effects.

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages ...

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be greatly facilitated by the production of milligram amounts of pure, folded ligand binding domains. Attempts to heterologously express periplasmic ligand binding domains of bacterial chemoreceptors in Escherichia coli (E. coli) often result in their targeting into inclusion bodies. Here, a method is presented for protein recovery from inclusion bodies, its refolding and purification, using the periplasmic dCACHE ligand binding domain of Campylobacter jejuni (C. jejuni) chemoreceptor Tlp3 as an example. The approach involves expression of the protein of interest with a cleavable His6-tag, isolation and urea-mediated solubilisation of inclusion bodies, protein refolding by urea depletion, and purification by means of affinity chromatography, followed by tag removal and size-exclusion chromatography. The circular dichroism spectroscopy is used to confirm the folded state of the pure protein. It has been demonstrated that this protocol is generally useful for production of milligram amounts of dCACHE periplasmic ligand binding domains of other bacterial chemoreceptors in a soluble and crystallisable form.

A procedure is presented for the refolding of the dCACHE periplasmic ligand binding domain of Campylobacter jejuni chemoreceptor Tlp3 from inclusion bodies and the purification to yield milligram quantities of protein.

Identification of natural ligands of chemoreceptors and structural studies aimed at elucidation of the molecular basis of the ligand specificity can be ...

A Colorimetric Method for Measuring Iron Content in Plants

Iron, one of the most important micronutrients in living organisms, is involved in basic processes, such as respiration and photosynthesis. Iron content is rather low in all organisms, amounting in plants to about 0.009% of dry weight. To date, one of the most accurate methods for measuring iron concentration in plant tissues is flame absorption atomic spectroscopy. However, this approach is time-consuming and expensive and requires specific equipment not commonly found in plant laboratories. Therefore, a simpler, yet accurate method that can be routinely used is needed. The colorimetric Prussian Blue method is regularly used for qualitative iron staining in animal and plant histological sections. In this study, we adapted the Prussian Blue method for quantitative measurements of iron in tobacco leaves. We validated the accuracy of this method using both atomic spectroscopy and Prussian Blue staining to measure iron content in the same samples and found a linear regression (R2 = 0.988) between the two procedures. We conclude that the Prussian Blue method for quantitative iron measurement in plant tissues is precise, simple, and inexpensive. However, the linear regression presented here may not be appropriate for other plant species, due to potential interactions between the sample and the reagent. Establishment of a regression curve is thus needed for different plant species.

We present a simple and reliable protocol for measuring iron content in plant tissues using the colorimetric Prussian Blue method.

Iron, one of the most important micronutrients in living organisms, is involved in basic processes, such as respiration and photosynthesis. Iron content ...

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Secreted factors, membrane-tethered receptors, and their interacting partners are main regulators of cellular communication and initiation of signaling cascades during homeostasis and disease, and as such represent prime therapeutic targets. Despite their relevance, these interaction networks remain significantly underrepresented in current databases; therefore, most extracellular proteins have no documented binding partner. This discrepancy is primarily due to the challenges associated with the study of the extracellular proteins, including expression of functional proteins, and the weak, low affinity, protein interactions often established between cell surface receptors. The purpose of this method is to describe the printing of a library of extracellular proteins in a microarray format for screening of protein-protein interactions. To enable detection of weak interactions, a method based on multimerization of the query protein under study is described. Coupled to this microbead-based multimerization approach for increased multivalency, the protein microarray allows robust detection of transient protein-protein interactions in high throughput. This method offers a rapid and low sample consuming-approach for identification of new interactions applicable to any extracellular protein. Protein microarray printing and screening protocol are described. This technology will be useful for investigators seeking a robust method for discovery of protein interactions in the extracellular space.

Here, we present a protocol to screen extracellular protein microarrays for identification of novel receptor-ligand interactions in high throughput. We also describe a method to enhance detection of transient protein-protein interactions by using protein-microbead complexes.

Secreted factors, membrane-tethered receptors, and their interacting partners are main regulators of cellular communication and initiation of signaling ...

Visualizing Surface T-Cell Receptor Dynamics Four-Dimensionally Using Lattice Light-Sheet Microscopy

The signaling and function of a cell are dictated by the dynamic structures and interactions of its surface receptors. To truly understand the structure-function relationship of these receptors in situ, we need to visualize and track them on the live cell surface with enough spatiotemporal resolution. Here we show how to use recently developed Lattice Light-Sheet Microscopy (LLSM) to image T-cell receptors (TCRs) four-dimensionally (4D, space and time) at the live cell membrane. T cells are one of the main effector cells of the adaptive immune system, and here we used T cells as an example to show that the signaling and function of these cells are driven by the dynamics and interactions of the TCRs. LLSM allows for 4D imaging with unprecedented spatiotemporal resolution. This microscopy technique therefore can be generally applied to a wide array of surface or intracellular molecules of different cells in biology.

The goal of this protocol is to show how to use Lattice Light-Sheet Microscopy to four-dimensionally visualize surface receptor dynamics in live cells. Here T cell receptors on CD4+ primary T cells are shown.

The signaling and function of a cell are dictated by the dynamic structures and interactions of its surface receptors. To truly understand the ...

A Planarian Motility Assay to Gauge the Biomodulating Properties of Natural Products

A straightforward, controllable means of using the non-parasitic planarian, Dugesia tigrina, a free-living aquatic flatworm, to study the stimulant and withdrawal properties of natural products is described. Experimental assays benefitting from unique aspects of planarian physiology have been applied to studies on wound healing, regeneration, and tumorigenesis. In addition, because planarians exhibit sensitivity to a variety of environmental stimuli and are capable of learning and developing conditioned responses, they can be used in behavioral studies examining learning and memory. Planarians possess a basic bilateral symmetry and a central nervous system that uses neurotransmitter systems amenable to studies examining the effects of neuromuscular biomodulators. Consequently, experimental systems monitoring planarian movement and motility have been developed to examine substance addiction and withdrawal. Because planarian motility offers the potential for a sensitive, easily standardized motility assay system to monitor the effect of stimuli, the planarian locomotor velocity (pLmV) test was adapted to monitor both stimulation and withdrawal behaviors by planarians through the determination of the number of grid lines crossed by the animals with time. Here, the technique and its application are demonstrated and explained.

Planarian motility is used to gauge the stimulant and withdrawal properties of natural products when compared to the movement of the animals in spring water alone.

A straightforward, controllable means of using the non-parasitic planarian, Dugesia tigrina, a free-living aquatic flatworm, to study the stimulant and ...

A High-Throughput Enzyme-Coupled Activity Assay to Probe Small Molecule Interaction with the dNTPase SAMHD1

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this enzyme can hydrolyze dNTPs into their corresponding nucleosides and inorganic triphosphates. Due to its critical role in nucleotide metabolism, its association to several pathologies, and its role in therapy resistance, intense research is currently being carried out for a better understanding of both the regulation and cellular function of this enzyme. For this reason, development of simple and inexpensive high-throughput amenable methods to probe small molecule interaction with SAMHD1, such as allosteric regulators, substrates, or inhibitors, is vital. To this purpose, the enzyme-coupled malachite green assay is a simple and robust colorimetric assay that can be deployed in a 384-microwell plate format allowing the indirect measurement of SAMHD1 activity. As SAMHD1 releases the triphosphate group from nucleotide substrates, we can couple a pyrophosphatase activity to this reaction, thereby producing inorganic phosphate, which can be quantified by the malachite green reagent through the formation of a phosphomolybdate malachite green complex. Here, we show the application of this methodology to characterize known inhibitors of SAMHD1 and to decipher the mechanisms involved in SAMHD1 catalysis of non-canonical substrates and regulation by allosteric activators, exemplified by nucleoside-based anticancer drugs. Thus, the enzyme-coupled malachite green assay is a powerful tool to study SAMHD1, and furthermore, could also be utilized in the study of several enzymes which release phosphate species.

SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase with critical roles in human health and disease. Here we present a versatile enzyme-coupled SAMHD1 activity assay, deployed in a 384-well microplate format, that allows for the evaluation of small molecules and nucleotide analogues as SAMHD1 substrates, activators, and inhibitors.

Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a pivotal regulator of intracellular deoxynucleoside triphosphate (dNTP) pools, as this ...

Cellular Membrane Affinity Chromatography Columns to Identify Specialized Plant Metabolites Interacting with Immobilized Tropomyosin Kinase Receptor B

Chemicals synthesized by plants, fungi, bacteria, and marine invertebrates have been a rich source of new drug hits and leads. Medicines such as statins, penicillin, paclitaxel, rapamycin, or artemisinin, commonly used in medical practice, have been first identified and isolated from natural products. However, the identification and isolation of biologically active specialized metabolites from natural sources is a challenging and time-consuming process. Traditionally, individual metabolites are isolated and purified from complex mixtures, following the extraction of biomass. Subsequently, the isolated molecules are tested in functional assays to verify their biological activity. Here we present the use of cellular membrane affinity chromatography (CMAC) columns to identify biologically active compounds directly from complex mixtures. CMAC columns allow for the identification of compounds interacting with immobilized functional transmembrane proteins (TMPs) embedded in their native phospholipid bilayer environment. This is a targeted approach, which requires knowing the TMP whose activity one intends to modulate with the newly identified small molecule drug candidate. In this protocol, we present an approach to prepare CMAC columns with immobilized tropomyosin kinase receptor B (TrkB), which has emerged as a viable target for drug discovery for numerous nervous system disorders. In this article, we provide a detailed protocol to assemble the CMAC column with immobilized TrkB receptors using neuroblastoma cell lines overexpressing TrkB receptors. We further present the approach to investigate the functionality of the column and its use in the identification of specialized plant metabolites interacting with TrkB receptors.

The protocol describes the preparation of cell membrane affinity chromatography (CMAC) columns with immobilized cell membrane fragments containing functional transmembrane tropomyosin kinase receptor B proteins. The use of CMAC columns in the identification of specialized plant metabolites interacting with these receptors and present in complex natural mixtures is also explained.

Chemicals synthesized by plants, fungi, bacteria, and marine invertebrates have been a rich source of new drug hits and leads. Medicines such as statins, ...

Purification of Endogenous Drosophila Transient Receptor Potential Channels

Drosophila phototransduction is one of the fastest known G protein-coupled signaling pathways. To ensure the specificity and efficiency of this cascade, the calcium (Ca2+)-permeable cation channel, transient receptor potential (TRP), binds tightly to the scaffold protein, inactivation-no-after-potential D (INAD), and forms a large signaling protein complex with eye-specific protein kinase C (ePKC) and phospholipase C&#946;/No receptor potential A (PLC&#946;/NORPA). However, the biochemical properties of the Drosophila TRP channel remain unclear. Based on the assembling mechanism of INAD protein complex, a modified affinity purification plus competition strategy was developed to purify the endogenous TRP channel. First, the purified histidine (His)-tagged NORPA 863-1095 fragment was bound to Ni-beads and used as bait to pull down the endogenous INAD protein complex from Drosophila head homogenates. Then, excessive purified glutathione S-transferase (GST)-tagged TRP 1261-1275 fragment was added to the Ni-beads to compete with the TRP channel. Finally, the TRP channel in the supernatant was separated from the excessive TRP 1261-1275 peptide by size-exclusion chromatography. This method makes it possible to study the gating mechanism of the Drosophila TRP channel from both biochemical and structural angles. The electrophysiology properties of purified Drosophila TRP channels can also be measured in the future.

Purification of Endogenous Drosophila Transient Receptor Potential Channels

Based on the assembling mechanism of the INAD protein complex, in this protocol, a modified affinity purification plus competition strategy was developed to purify the endogenous Drosophila TRP channel.

Drosophila phototransduction is one of the fastest known G protein-coupled signaling pathways. To ensure the specificity and efficiency of this cascade, ...