Name: protein purification-free method of binding affinity determination by microscale thermophoresis
Uploaded: 2013-08-15T13:00:00
Description: Watch this Scientific Journal Video about Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis at JoVE.com

This work was partially supported by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research; Collaborative Research Agreement between NCI and Calidris Therapeutics; American Cancer Society grant IRG 97-152-17 to O.T; and federal funds from the National Cancer Institute, NIH, under contract HHSN26120080001E.

1. Preparation of Cell Lysate
This protocol is intended for adherent cells expressing any GFP-fused protein. Needed cell number can vary from as low as 106 to as many as 20 x 106 cells, depending on the level of protein expression. For example, lysate of HEK cells overexpressing GFP-STAT3 was prepared by treating cells grown in 10 T75 flasks to near 70% confluency with 1 ml lysis buffer. However, this lysate had to be diluted 150-fold to provide optimal level of fluorescenc...

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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+JAK-STAT+pathway+at+twenty.">The JAK-STAT pathway at twenty.</a> Immunity. 36, 503-514 (2012).</li><li>Ehret, G. B., Reichenbach, P., 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=DNA+binding+specificity+of+different+STAT+proteins.+Comparison+of+in+vitro+specificity+with+natural+target+sites.">DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites.</a> J. Biol. Chem. 276, 6675-6688 (2001).</li><li>Yang, J., Stark, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Roles+of+unphosphorylated+STATs+in+signaling.">Roles of unphosphorylated STATs in signaling.</a> Cell Res. 18, 443-451 (2008).</li><li>Timofeeva, O. A., Chasovskikh, S., 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=Mechanisms+of+unphosphorylated+STAT3+transcription+factor+binding+to+DNA.">Mechanisms of unphosphorylated STAT3 transcription factor binding to DNA.</a> J. Biol. Chem. 287, 14192-14200 (2012).</li><li>Timofeeva, O. A., Tarasova, N. 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Protein expression and purification is a laborious and expensive step, which is, however, necessary for determination of interactions' KD by most currently used method. Application of MST allows avoiding protein purification thus significantly simplifying and accelerating quantitative characterization of interactions. It presents particularly significant advantages in the case of difficult-to-express and purify proteins, such as membrane proteins and transcription factors.
The major...

Quantitative characterization of affinity of intermolecular interactions is important in many areas of biomedical research. Binding dissociation constant (KD) is essential not only in drug discovery but is also an important parameter in characterization of any binary interaction in any biological system. Biochemical methods used for detection of protein-protein interactions, such as immunoprecipitation and yeast two-hybrid screens, do not inform us on how tight are those interactions, while affinity defines whether this particular complex exists under given conditions in vivo. In drug discovery process, binding assay development is one of the necessary and frequently the most time-consuming steps. Most commonly used methods of KD determination include fluorescence polarization,1 surface plasmon resonance (SPR) technology,2 radioligand binding,3 isothermal titration calorimetry,4 equilibrium dialysis (ED),5 ultrafiltration (UF),5 and ultracentrifugation (UC).6 All of them require significant quantities of purified target protein. Microscale thermophoresis (MST) is a rapidly developing method that detects directed movement of molecules in a microscopic temperature gradient. Any changes of the hydration shell of biomolecules result in a relative change of movement along the temperature gradient.7 MST is used to determine binding affinities and has been applied for studying ligand binding to fluorescently labeled proteins or fluorescent ligands to a target protein.8, 9 MST allows measurement of interactions directly in solution without the need of immobilization to a surface (immobilization-free technology). Practically, any binding is accompanied by a change in MST signal, although the size of the change differs from system to system significantly. For the detection of molecule motion by MST, they have to be fluorescent. This major limitation of the method can be turned into an advantage. If a protein is expressed as a GFP fusion in any system, it will be the only fluorescent molecule and thus can be studied without isolation from the cell lysate or cell-free expression system. Generation of cell lysates that allow for binding conditions with minimal artifacts is the major challenge. Here we describe a protocol of cell lysate preparation and MST experiment that can be used for many soluble and membrane proteins.
STAT proteins are latent cytoplasmic transcription factors activated by tyrosine phosphorylation in response to extracellular signals and are involved in many biological processes including immunity, hematopoiesis, inflammation, and development.10 In mammals, the STAT family consists of STAT 1, 2, 3, 4, 5A, 5B, and 6. All activated STATs are known to bind to the same DNA sequence, so called GAS motif, IFN-gamma activated sequence. However, the transcriptional effects of different STATs are very different.11 In spite of involvement in many pathological processes and extensive studies yielding over 17,000 publications, the KD of STAT interactions with different DNA sequences have not been determined. Only relative affinity of different STATs to variants of GAS motif has been characterized.11 Difficulties in protein expression and purification are the major impediments in characterization of STATs' DNA binding selectivity. Although the majority of the studies have focused on the role of "activated" STATs, which became synonymous to Tyr-phosphorylated transcription factor, the role of non-phosphorylated STATs (U-STATs) in regulation of transcription is emerging rapidly.12 However, these mechanisms are poorly understood, and it was unclear whether U-STATs actually bind to DNA or act through interactions with other transcription factors. We have recently shown that U-STAT3 can bind to DNA sequences different from GAS motifs with even higher affinity.13 The finding has significant implications for our understanding of the biological functions of this important protein. We have applied microscale thermophoresis to determine relative affinities of STAT3 to GAS and AT-rich oligonucleotide S+100 (Figure 4). Almost identical protocol has been used for KD determination for binding of a different STAT3 ligand, a lipopeptide inhibitor.14 No binding to a related transcription factor, GFP-STAT1 that was used as a negative control could be detected thus confirming selectivity of interaction.14

<table border="1">
	<tbody>
 <tr>
 <td>Name of the Reagent/material</td>
 <td>Company</td>
 <td>Catalogue Number</td>
 <td>Comments </td>
 </tr>
 <tr>
 <td>RIPA buffer</td>
 <td>Millipore</td>
 <td>20-188</td>
 <td>Other manufacturer's buffers work as well</td>
 </tr>
 <tr>
 <td>Protease inhibitors cocktail</td>
 <td>Sigma-Aldrich</td>
 <td>P2714</td>
 <td></td>
 </tr>
 <tr>
 <td>Monolith NT.115</td>
 <td>NanoTemper Technologies GmbH</td>
 <td>G008</td>
 <td></td>
 </tr>
 <tr>
 <td>Monolith NT.115 Capillary Tray</td>
 <td>NanoTemper Technologies GmbH</td>
 <td>T001</td>
 <td></td>
 </tr>
 <tr>
 <td>Monolith NT.115 Standard Treated Capillaries</td>
 <td>NanoTemper Technologies GmbH</td>
 <td>K002</td>
 <td></td>
 </tr>
 <tr>
 <td>NT Control software</td>
 <td>NanoTemper Technologies GmbH</td>
 <td>2.0.2.29</td>
 <td></td>
 </tr>
 <tr>
 <td>NT Analysis software</td>
 <td>NanoTemper Technologies GmbH</td>
 <td>1.4.27</td>
 <td></td>
 </tr>
 <tr>
 <td>Table-top refrigerated centrifuge</td>
 <td>Eppendorf </td>
 <td>5417R</td>
 <td>Other microtube refrigerated centrifuges</td>
 </tr>
 <tr>
 <td>Protein LoBind Tube 0.5 ml</td>
 <td>Eppendorf </td>
 <td>22431064</td>
 <td></td>
 </tr>
	 </tbody>
 </table>

protein purification-free method of binding affinity determination by microscale thermophoresis

Quantitative characterization of protein interactions is essential in practically any field of life sciences, particularly drug discovery. Most of currently available methods of KD determination require access to purified protein of interest, generation of which can be time-consuming and expensive. We have developed a protocol that allows for determination of binding affinity by microscale thermophoresis (MST) without purification of the target protein from cell lysates. The method involves overexpression of the GFP-fused protein and cell lysis in non-denaturing conditions. Application of the method to STAT3-GFP transiently expressed in HEK293 cells allowed to determine for the first time the affinity of the well-studied transcription factor to oligonucleotides with different sequences. The protocol is straightforward and can have a variety of application for studying interactions of proteins with small molecules, peptides, DNA, RNA, and proteins.

Measuring the affinity of non-phosphorylated STAT3 protein binding to oligonucleotides.
HEK293 cells expressing STAT3-GFP were used as a source of fluorescently labeled STAT3 for DNA binding assay. Cell lysates were prepared using RIPA buffer (20x106cells/ml). For binding studies, the lysates were diluted 150x with MST DNA-binding buffer to provide the optimal level of the fluorescent protein in the binding reaction (about 20 nM). Non-transfected HEK293 cells have been...

Watch this Scientific Journal Video about Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis at JoVE.com

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Microscale thermophoresis (MST) can be widely used for determination of binding affinity without purification of the target protein from cell lysates. The protocol involves overexpression of the GFP-fused protein, cell lysis in non-denaturing conditions, and detection of MST signal in the presence of varying concentrations of the ligand.

Quantitative characterization of protein  interactions is essential in practically any field of life sciences,  particularly drug discovery. Most of ...

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