This work was supported by Wellcome Trust grant 088419 to MDB.

1. Reinigung von GST-tagged GTPase <ol><li> Kultur ein E. coli-Stamm, wie beispielsweise BL21 mit pGEX-Rac1 O / N transformierten bei 37 ° C, bei 220 Upm Schütteln in 500 ml Autoinduktion Medium (25 mM Na 2 HPO 4, 25 mM KH 2 PO 4, 50 mM NH 4 Cl, 5 mM Na 2 SO 4, 2 mM MgSO 4, 2 mM CaCl 2, 0,5% Glycerin, 0,05% Glucose, 0,2% Lactose, 5 g Trypton, 2,5 g Hefeextrakt, 100 ug / ml Ampicillin). </li><li> Ernte Bakterien durch Zentrifugation für 10 min bei 10.000 × g, 4 ° C. </li><li> Resuspendieren Bakterienpellet in 20 ml Protein Extraktionsreagens, 1x Proteaseinhibitor und Inkubation für 20 min bei RT mit Inversion. </li><li> Klärung des Lysats durch Zentrifugation bei 40.000 xg für 30 min. </li><li> 2 ml Glutathion-magnetische Kügelchen, mit Phosphat-gepufferter Salzlösung (PBS: 10 mM Na 2 HPO 4, 1,8 mM KH 2 PO 4, 137 mM NaCl, 2,7 mM KCl). </li><li> Inkubation für 2 h, das Mischen durch Inversion bei 4 ° C. </li><li> Viermal Waschen Kügelchen proteinbeladene mit 10 ml PBS unter Verwendung eines magnetischen Teilchens Sortierer, um die Perlen in jedem Schritt auszufällen. </li><li> Resuspendieren Protein beladenen Kügelchen in 2 ml PBS und bei -80 ° C in 100 ul Aliquots bis sie benötigt. </li></ol> 2. Expression von GTPase-bindenden Proteinen <ol><li> Am Tag vor dem Experiment Transfektion Plasmide grün fluoreszierende Protein (GFP) kodiert -markierte Versionen jedes GTPase-bindenden Proteins in einem separaten 75-cm 2 -Kolben von HEK293T wie folgt. Zur Validierung von Nukleotid-Laden, transfizieren GFP-markierten TrioD1 in ein drittes 75-cm 2-Kolben von HEK293T. <ol><li> Verdünnter polyethylamine bis 1 mg / ml in 100 &amp; mgr; l sterilem 150 mM NaCl. </li><li> In 27 ul verdünnt polyethylamine bis 223 &amp; mgr; l reduziert Serum Medien. </li><li> In 12 &amp; mgr; g Plasmid-DNA zu 250 &amp; mgr; l reduziert Serum Medien. </li><li> Inkubieren jedes Röhrchen für 2 min bei RT. </li&gt; <li> Kombinieren Sie die polyethylamine und DNA vermischt sich in einem einzigen Rohr und Vortex für 2 min. </li><li> Inkubieren Sie für 15-20 min bei RT. </li><li> Ersetzen Sie das Wachstumsmedium (Dulbeccos modifiziertem Eagle Medium, das 10% fötales Rinderserum, 2 mM L-Glutamin, keine Antibiotika), die auf 90% konfluent HEK293T mit 5 ml frisches Wachstumsmedium. </li><li> In der kombinierten polyethylamine / DNA-Gemisch in den Kolben und Inkubation O / N bei 37 ° C, 5% CO 2. </li></ol></li></ol> 3. Reinigung der GTPase-bindenden Proteinen <ol><li> Spülen Sie die Flasche aus transfizierten Zellen in PBS und Drain-Kolben für 5 min, Absaugen freie Flüssigkeit. </li><li> Abzukratzen Zellen in 500 ul Lysepuffer (50 mM Tris-HCl (pH 7,8), 1% Nonidet P-40, 1x Proteaseinhibitor) in Mikrozentrifugenröhrchen. </li><li> Zellen lysieren durch Mischen durch Inversion bei 4 ° C für 30 min. </li><li> Während der Lyse, waschen zwei Lose von 40 ul GFP-Trap-Kügelchen dreimal mit frischem Lysepuffer, sedimentierenden Perlen bei 2700 × g für 2 Minuten zwischen den Waschvorgängen. </li><li> Klärung Lysate durch Zentrifugation bei 21.000 × g für 10 min. </li><li> Übertragungs geklärte Lysat eines jeden der Wettbewerber Proteine ​​gewaschen GFP-trap Perlen abzutrennen und zu ermöglichen GFP-Fusionsproteine, für 2 h binden, Mischen durch Umdrehen bei 4 ° C. Halten Lysat aus GFP-TrioD1 Zellen auf Eis. </li><li> Zweimal waschen geladen GFP-Trap-Perlen in 50 mM Tris-HCl (pH 7,8), 50 mM NaCl, 0,7% (w / v) Nonidet P-40 und zweimal in 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2 , sedimentierenden Perlen bei 2700 × g für 2 Minuten zwischen den Waschgängen. </li><li> Eluieren GFP-Fusionsproteinen durch Zugabe von 40 ul 0,2 M Glycin (pH 2,5) und Auf- und Abpipettieren für 30 sec. Sofort Sediment Kügelchen bei 21.000 × g für 60 s und Transferflüssigkeit auf ein neues Mikrozentrifugenröhrchen, enthaltend 4 &amp; mgr; l 1 M Tris-HCl (pH 10,4). Tun dies schnell zur Beschädigung des gereinigten Proteins zu begrenzen. </li><li> Analyse 1 ul jedes gereinigten Proteins durch Western-Blot und die Sonde mit einem anti-GFP-Antikörper, um die relative Ausbeute herzustellen unter Verwendung eines quantitativen Blotting System gemäß dem Protokoll des Herstellers. Alternativ bestimmen Proteinkonzentrationen von Bicinchoninsäure (BCA) Assay aber dies führt Fehler, wenn die Proteine ​​nicht mit dem Assay in einer identischen Weise reagiert oder es kontaminierende Proteine. </li><li> Leichen molaren Proteinkonzentration durch die Zugabe von 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2. </li></ol> 4. Nucleotide Belastung der GTPase <ol><li> Tauwetter ein Aliquot von GST-Rac1 magnetische Kügelchen, die in Schritt 1 hergestellt. </li><li> Nehmen 90 ul von GST-Rac1 Perlen und dreimal mit 20 mM Tris-HCl (pH 7,6), 25 mM NaCl, 0,1 mM DTT, 4 mM EDTA, unter Verwendung eines magnetischen Partikelsortierer, um die Perlen in jedem Schritt auszufällen. </li><li> Saugen Sie Puffer aus Perlen und fügen Sie 100 ul 20 mM Tris-HCl (pH 7,6), 25 mM NaCl, 0,1 mM DTT, 4 mM EDTA. </li><li> Je nachdem, ob das BIP, GTP oder keine Nukleotid-Belastung für den Wettbewerb Experiment erforderlich, fügen Sie 12 ul 100 mM BIP, 12 &amp; mgr; l 10 mM guanosine 5 &#39;- [γ-thio] Triphosphat (GTP &amp; ggr;) oder keine Nukleotid bis 60 &amp; mgr; l GST-Rac1 Perlen. </li><li> Für die Nukleotid-Ladesteuerungen, teilen Sie die restlichen Perlen in drei 10-ul-Aliquots und fügen Sie 2 ul 100 mM GDP, 2 &amp; mgr; l 10 mM GTPyS oder keine Nukleotid in jedes Röhrchen. </li><li> Inkubieren Wulst Mischungen für 30 Minuten bei 30 ° C unter Rühren. </li><li> Stabilisierung Nucleotid gebundene Rac1 durch Zugabe von 1 M MgCl 2: 3 &amp; mgr; l auf die Versuchsmischung (Schritt 4.4), 0,5 &amp; mgr; l zu jeder der Kontrollmischungen (Schritt 4.5). </li></ol> 5. Wettbewerb bindend. <ol><li> Einrichten 6 Mikrozentrifugenröhrchen, die jeweils: 200 ul 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2 10 &amp; mgr; experimentelle Nukleotid-beladenen Rac1-Perlen (ab Schritt 4.7) 5 ul Rac1-bindenden Protein A (Konstante Bindungsprotein) </li><li> Zu jedem Röhrchen hinzu 0, 1, 2,5, 5, 10 oder 20 ul Rac1-bindendes Protein B (variable Bindungsprotein). Diese Bände davon ausgehen, approximately gleich stock Konzentrationen der konstanten und variablen Bindungsproteine ​​und muss unter Umständen angepasst werden. <ol><li> Einstellen Volumina bindende Proteine ​​A und B, wenn es große Unterschiede in den Bindungsaffinitäten der beiden Proteine ​​und dies sollte empirisch durch die Versuchswiederholungen bestimmt werden. Bilden das Gesamtvolumen des Bindungsgemisch auf 235 &amp; mgr; l durch Zugabe von 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2. </li></ol></li><li> Einrichtung eines Mikrozentrifugenröhrchen enthält: 200 ul 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2 10 &amp; mgr; experimentelle Nukleotid-beladenen Rac1-Perlen (ab Schritt 4.7) 10 ul Rac1-bindenden Protein A (Konstante Bindungsprotein) </li><li> Einrichten des BIP, GTPyS und keine Nukleotid-Kontrollröhrchen: 200 ul 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2 10 ul Steuer Rac1 Perlen in Schritt 4.5 mit dem BIP, GTPyS oder kein Nukleotid geladen und in Schritt 4.7 stabilisiert. 180 ul HEK293T GFP-TrioD1 Lysat, wie in Schritt 3.6 hergestellten 4 &amp; mgr; l 1 M MgCl 2 </li><li> Inkubieren der Mischung für 2 h, das Mischen durch Inversion bei 4 ° C. </li><li> Dreimal mit 50 mM Tris-HCl (pH 7,6), 20 mM MgCl 2 Waschen der Kügelchen. </li><li> Eluieren die gebundenen Proteine ​​werden in 20 ul reduzierendem Probenpuffer (50 mM Tris-HCl (pH 7), 5% SDS, 20% Glycerin, 0,02 mg / ml Bromphenolblau, 5% β-Mercaptoethanol). </li></ol> 6. Analyse der Wettbewerbs <ol><li> Beheben 10 ul des gebundenen Proteins (Schritt 5.6), bestimmt durch Natriumdodecylsulfat-Polyacrylamidgelelektrophorese (SDS-PAGE) und Western-Blot. </li><li> Inkubieren der Membran bei 4 ° CO / N im anti-GFP-Antikörper, verdünnt 1/1000 in Blockierungspuffer verdünnt, in PBS 1X, 0,1% Tween-20 auf die beiden markierten GTPase-bindende Proteine ​​erkennen. </li><li> Dreimal 10 min mit PBS, 0,1% Tween-20 waschen der Membran. </li><li> Inkubieren der Membran für 30 min bei RT in 800 DyLight konjugiertem Anti-Kaninchen-secondary Antikörper, verdünnt 1 / 10.000 in Blockierungspuffer verdünnt, in PBS, 0,1% Tween-20 1 x auf. </li><li> Dreimal 10 min mit PBS, 0,1% Tween-20 waschen der Membran. </li><li> Scannen der Membran unter Verwendung eines Infrarot-Abbildungssystem mit der Software, um die Bandintensität nach dem Protokoll des Herstellers gemessen. </li><li> Zur Erstellung der Bandintensität jedes Proteins vor der Verstellpumpe Konkurrent (Protein B). </li><li> Teilen das Volumen der variable Konkurrent an dem Punkt, an dem die Linien sich durch das Volumen konstant Konkurrent (Protein A, 5 &amp; mgr; l), um den Konkurrenzverhältnis, bei dem ein Gleichgewicht erreicht bestimmen. </li><li> Zur Validierung der Nukleotid-Ladezustand, Sondenmembranen für p21-activated kinase 1 (PAK1) (ein Effektor) und GFP-TrioD1 (a GEF), wie in den Schritten 6.1-6.6 beschrieben. </li></ol>

<ol>
	<li>Burridge, K., Rho Wennerberg, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=and+Rac+take+center+stage.">and Rac take center stage.</a> Cell. 116 (2), 167-179 (2004).</li><li>Raftopoulou, M., Hall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+migration:+Rho+GTPases+lead+the+way.">Cell migration: Rho GTPases lead the way.</a> Dev Biol. 265 (1), 23-32 (2004).</li><li>Rossman, K. L., Der, C. J., Sondek, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GEF+means+go:+turning+on+RHO+GTPases+with+guanine+nucleotide-exchange+factors.">GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors.</a> Nat Rev Mol Cell Biol. 6 (2), 167-180 (2005).</li><li>Worthylake, D. K., Rossman, K. L., Crystal Sondek, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=structure+of+Rac1+in+complex+with+the+guanine+nucleotide+exchange+region+of+Tiam1.">structure of Rac1 in complex with the guanine nucleotide exchange region of Tiam1.</a> Nature. 408 (6813), 682-688 (2000).</li><li>Scheffzek, K., Ahmadian, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GTPase+activating+proteins:+structural+and+functional+insights+18+years+after+discovery.">GTPase activating proteins: structural and functional insights 18 years after discovery.</a> Cell Mol Life Sci. 62 (24), 3014-3038 (2005).</li><li>Del Pozo, ., A, M., 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=Integrins+regulate+GTP-Rac+localized+effector+interactions+through+dissociation+of+Rho-GDI.">Integrins regulate GTP-Rac localized effector interactions through dissociation of Rho-GDI.</a> Nat Cell Biol. 4 (3), 232-239 (2002).</li><li>Williamson, R. 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=Coronin-1C+and+RCC2+guide+mesenchymal+migration+by+trafficking+Rac1+and+controlling+GEF+exposure.">Coronin-1C and RCC2 guide mesenchymal migration by trafficking Rac1 and controlling GEF exposure.</a> J Cell Sci. 127 (Pt 19), 4292-4307 (2014).</li><li>Del Pozo, M. A., Price, L. S., Alderson, N. B., Ren, X. D., Schwartz, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adhesion+to+the+extracellular+matrix+regulates+the+coupling+of+the+small+GTPase+Rac+to+its+effector+PAK.">Adhesion to the extracellular matrix regulates the coupling of the small GTPase Rac to its effector PAK.</a> Embo J. 19 (9), 2008-2014 (2000).</li><li>Van Rijssel, J., Hoogenboezem, M., Wester, L., Hordijk, P. L., Van Buul, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+N-terminal+DH-PH+domain+of+Trio+induces+cell+spreading+and+migration+by+regulating+lamellipodia+dynamics+in+a+Rac1-dependent+fashion.">The N-terminal DH-PH domain of Trio induces cell spreading and migration by regulating lamellipodia dynamics in a Rac1-dependent fashion.</a> PLoS. 7 (1), e29912 (2012).</li><li>Self, A. J., Hall, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+intrinsic+nucleotide+exchange+and+GTP+hydrolysis+rates.">Measurement of intrinsic nucleotide exchange and GTP hydrolysis rates.</a> Methods Enzymol. 256, 67-76 (1995).</li></ol>

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This protocol describes a method for comparing the relative affinities of pairs of small GTPase-binding proteins. The key steps are the preparation of purified GTPase-binding proteins and the nucleotide loading of the GTPase. The use of GTPase-binding proteins with the same GFP tag, allows the concentrations at which similar amounts of each competitor binds to be accurately determined. The use of recombinant nucleotide-loaded GTPase allows interrogation of the binding properties of the GTPase under specific activity conditions. This step is also the most sensitive as nucleotides will both hydrolyze and detach from the GTPase if the magnesium conditions are not maintained precisely.
In the cell, the large number of GTPase-binding proteins combined with the rapid nucleotide turnover makes such pathways difficult to interpret. The simplicity of this method in comparing only pairs of binding proteins and using carefully controlled nucleotide-loading conditions allows signaling pathways to be elucidated. However, the greatest strength of the protocol is also the greatest weakness as it is a simplification of the in vivo situation. Competition assays can be used to build a robust hypothesis, but this should then be tested in cells by knockdown experiments.
There are three features that must be considered when selecting the GFP-tagged GTPase-binding proteins to be used in the experiment. First, the fusion proteins must express well in mammalian cells, such as HEK293T, as competition assays require a reasonable amount of protein. Second, it must be possible to purify the recombinant protein without significant degradation, and where this is not possible, cloning of a GTPase-binding fragment should be considered. Third, the two GTPase-binding proteins must resolve from one another on SDS-PAGE to allow analysis in section 6.
There are a number of potential caveats to the experiment that need to be considered, and possibly addressed:
Possible denaturation of purified GTPase-binding proteins during the acid elution step or steric hindrance by the GFP tag. In our hands, these have not been a problem, but must be tested. The purified proteins can be tested in functional assays 10. Commercial kits now exist for testing the activity of GEFs or GAPs without the need for isotope-labeled nucleotides. Sequestering proteins, by their nature protect GTPases from GEF or GAP activity, so can be used as competitive inhibitors in the commercial GEF or GAP assays, as we did in our recent publication 7. The relevant feature of proteins that traffic GTPase are the capacity to bind the GTPase, and this can be tested easily in a pull down assay. An alternative approach to testing protein integrity that is applicable to all binding proteins is to titrate protein eluted from GFP-trap beads with glycine with the same protein removed from GFP-trap beads by enzymatic cleavage. The experiment would be analyzed by probing both the GFP-tagged and cleaved protein with an antibody against the protein itself. If the protein is undamaged by elution, equilibrium should be achieved at a 1:1 ratio. This approach would also indicate whether the presence of the GFP tag itself compromises the binding properties of the candidate protein, though this does require the production of a construct with an enzymatic cleavage site between the tag and the binding protein. Whether the protein is compromised by the tag or the elution step, the problem could be addressed by modifying the protocol to use an alternative purification method. Rather than GFP, binding proteins could be His-tagged, purified using Ni-NTA and analyzed using an antibody against the His-tag. The important feature is that both binding proteins must share a common tag although, if necessary, two tags could be added to a protein, one for purification and the other for detection.
The protocol is designed to investigate competition between interactions with the switch I/II domains. Although the majority of GTPase interactions are mediated by this motif, there are some exceptions, most notably the interactions of GDIs that bind to the prenyl tail, as well as obscuring the switch domains. In principle, the protocol could be adapted to use GTPase purified from mammalian cells, so that the GTPase is prenylated, however, the presence of multiple binding sites or allosteric effects complicate the interpretation of competition-binding data. Further problems associated with such a modification are that GDIs co-purify with GTPase from mammalian cells, compromising the purity of the isolated proteins and the hydrophobic nature of the prenyl groups means that prenylated GTPases are associated with either GDI or lipid membrane and such factors would need to be considered in the experiment.
The amount of GST-Rac1 being used in the assay. The constant GTPase binding protein must be at a greater concentration than the Rac1, or when the competitor is added, it will simply bind to free Rac1. It will be immediately obvious if this has happened as binding of the competitor, without a loss of the constant protein, will be detected in much the same way as when the two competing proteins bind to one another as shown in Figure 3B. As an additional control (Step 5.3), a binding reaction containing double the amount of constant binding protein and no variable binding protein should be included (Step 5.3). If the Rac1 in the titration experiment is saturated, doubling the amount of constant binding protein will have no effect on the output. The volumes suggested in the protocol should be appropriate, but the amount of Rac1 can be easily reduced. If binding of the competitor without loss of the constant binding partner is observed, reducing the amount of Rac1 should be attempted before trying to map binding sites to avoid ternary complex formation.
Non-specific interaction of GTPase-binding proteins with the GST or bead, as well as specifically with Rac1. This problem would be manifested by residual binding of the constant GTPase-binding protein, even when the variable GTPase-binding protein has reached a plateau at high concentration. Identification of this issue will be aided by conducting reciprocal experiments where the constant and variable GTPase-binding proteins are swapped. Reciprocal experiments will also greatly improve the accuracy of the estimate of equilibrium point, so should always be included. In cases of non-specific binding, the relative concentrations at which equilibrium is achieved can still be calculated by comparing band intensity between the maxima and minima for each protein, or by measuring the extent of non-specific binding by using GST beads as bait, rather than GST-Rac1.
Pull down assays using different nucleotide-loading conditions should be used to complement the competition assay described in this protocol. Determining the nucleotide preference of partners is important for both understanding the competition events and understanding the signaling pathway that the GTPase-binding protein is involved in. In Figure 2B we analyze binding of proteins with established preference for GTP-loaded or nucleotide-free GTPase as a means to validate nucleotide loading. However, it is sensible to investigate the effect of nucleotide loading on each of the competitors as well. If the hypothetical competitors show different preferences, competition will make less of a contribution to the signaling pathway, and indeed nucleotide turnover is likely to be the mechanism that directs exchange of the binding proteins.

The actin cytoskeleton that determines the shape, polarity and migratory properties of mammalian cells is regulated by the Rho-family of small GTPases. The Rho-family GTPases include RhoA that stimulates cytoskeletal contraction, Rac1 that stimulates actin branching and membrane protrusion, and Cdc42 that has similar effects on actin polymerization to Rac1 and causes the formation of filopodia 1,2. GTPase signaling activity is determined by binding of a nucleotide, which controls the contraction and relaxation of the switch I and switch II loops that mediate the protein-protein interactions with both regulators and effectors. Guanosine 5&#8217;-triphosphate (GTP)-bound GTPases activate downstream effectors, whereas the Guanosine 5&#8217;-diphosphate (GDP)-bound form is inactive. In the cell, cycles of GTP hydrolysis and nucleotide exchange allow rapid turnover of GTPase signals that are necessary for cytoskeletal dynamics. Nucleotide turnover is regulated by three mechanisms. Guanine nucleotide exchange factors (GEFs) stabilize the nucleotide-free GTPase, catalyzing exchange of GDP for GTP, and thereby stimulating GTPase signaling activity 3,4. GTPase-activating proteins (GAPs) catalyze hydrolysis of GTP to GDP, thereby inhibiting GTPase signaling activity 5. Sequestering molecules such as regulator of chromatin condensation 2 (RCC2) and guanine nucleotide dissociation inhibitors (GDIs) obscure the switch loops and in the case of GDIs remove the GTPase from the membrane by interaction with the prenyl tail 6,7. Each of the three classes of regulatory molecule interact with the switch loops, as do the downstream effectors and some trafficking regulators such as coronin-1C 7. The purpose of this protocol is to measure competition for the switch I/II binding site between putative regulators and downstream signaling molecules. It should be noted that competition assays test binding to a shared binding site, so that this protocol is not suitable for testing interactions with other sites, such as binding of GDIs to the prenyl tail.
The subtlety of the conformation differences between active and inactive forms, combined with the labile nature of the bound nucleotide, has made study of GTPase-binding events difficult. The role of the bound nucleotide means that conventional binding assays such as immunoprecipitation or surface plasmon resonance are not well suited to investigation, as the nucleotide cannot be controlled. This obstacle is compounded by the overlap in the binding sites of GEFs, GAPs, effectors, sequestering molecules and trafficking molecules, which make binding data for a single interaction difficult to interpret in the context of the competition that will occur in the cell. Immunoprecipitation, in particular, is compromised by competition between binding partners, as under certain cellular conditions, one binding partner might be identified at the expense of all others, while under other conditions, another partner might dominate. The dynamic nature of GTPase signaling is essential to GTPase function and must be considered when analyzing the relationships between the binding interactions of different regulators. Indeed, we recently described a pathway that relied heavily on competitive binding. We identified coronin-1C as a trafficking molecule that bound to the switch loops of GDP-Rac1 7. In areas of low GEF activity, trafficking would dominate, removing Rac1 from those regions. However, when Rac1 is delivered to regions of the cell where GEF activity is high, the GEF would outcompete coronin-1C, thereby both activating Rac1 and preventing coronin-1C-mediated removal of Rac1 from that area. The model goes further, because the action of the GEF exchanges bound GDP for GTP, shifting the equilibrium still further from coronin-1C. Consequently, Rac1 activity could be explained entirely in terms of competition and relative affinity.
In this protocol, we describe a method for comparing the relative affinities of different binding partners for small GTPases, using Rac1 as an example. By using a purified protein approach, it is possible to piece together a chain of signaling events by pair wise comparison, in an experiment where the bound nucleotide can be closely controlled.

<table><tbody><tr><td>Bugbuster</td><td>Novagen</td><td>70584-3</td><td></td></tr><tr><td>COMPLETE protease inhibitor</td><td>Roche</td><td>05 056 489 001</td><td></td></tr><tr><td>Glutathione magnetic beads</td><td>Pierce</td><td>88821</td><td></td></tr><tr><td>Polyethylenimine, branched, average M&lt;sub&gt;w&lt;/sub&gt; ~25,000</td><td>Sigma Aldrich</td><td>408727-100ML</td><td></td></tr><tr><td>OPIMEM</td><td>Life Technologies</td><td>31985-047</td><td></td></tr><tr><td>Dulbecco&#039;s Modified Eagle Media</td><td>Sigma Aldrich</td><td>D5796</td><td></td></tr><tr><td>Fetal Bovine Serum</td><td>Life Technologies</td><td>10270-1-6</td><td></td></tr><tr><td>L-Glutamine</td><td>Life Technologies</td><td>25030-024</td><td></td></tr><tr><td>GFP-Trap_A</td><td>Chromotec</td><td>gta-20</td><td></td></tr><tr><td>GDP</td><td>Sigma Aldrich</td><td>G7127</td><td>Highly unstable. Aliquot and store at -80 immediately upon reconstritution</td></tr><tr><td>GTP&amp;gamma;S</td><td>Sigma Aldrich</td><td>G8634</td><td>Highly unstable. Aliquot and store at -80 immediately upon reconstritution</td></tr><tr><td>Blocking Buffer</td><td>Sigma Aldrich</td><td>B6429</td><td></td></tr><tr><td>Tween-20</td><td>Sigma Aldrich</td><td>P9416</td><td></td></tr><tr><td>Anti-GFP antibody</td><td>Living Colors</td><td>632592</td><td>Use at 1/1000 dilution</td></tr><tr><td>DyLight 800 conjugated goat anti-rabbit secondary antibody</td><td>Fisher Scientific</td><td>10733944</td><td></td></tr><tr><td>Anti-PAK1 antibody</td><td>Cell Signaling</td><td>2602S</td><td>Use at 1/1000 dilution</td></tr><tr><td>Odyssey SA Infrared Imaging System</td><td>Li-cor</td><td>9260-11PC</td><td></td></tr></tbody></table>

comparing the affinity of gtpase-binding proteins using competition assays

In this protocol we demonstrate a method for comparing the competition between GTPase-binding proteins. Such an approach is important for determining the binding capabilities of GTPases for two reasons: The fact that all interactions involve the same face of the GTPases means that binding events must be considered in the context of competitors, and the fact that the bound nucleotide must also be controlled means that conventional approaches such as immunoprecipitation are unsuitable for GTPase biochemistry. The assay relies on the use of purified proteins. Purified Rac1 immobilized on beads is used as the bait protein, and can be loaded with GDP, a non-hydrolyzable version of GTP or left nucleotide free, so that the signaling stage to be investigated can be controlled. The binding proteins to be investigated are purified from mammalian cells, to allow correct folding, by means of a GFP tag. Use of the same tag on both proteins is important because not only does it allow rapid purification and elution, but also allows detection of both competitors with the same antibody during elution. This means that the relative amounts of the two bound proteins can be determined accurately.

Dieses Protokoll wurde entwickelt, um die relativen Affinitäten von Bindungspartnern für Rac1 zu berechnen, ohne die Notwendigkeit, die genaue Konzentration der Wettbewerber zu geben (Abbildung 1). Bestimmung der Proteinkonzentration führt Fehler und bei der Betrachtung der Wettbewerb zwischen Molekülen in einem Signalweg, ist nicht erforderlich. Jedoch ist es wichtig zu wissen, dass die beiden Wettbewerber haben die gleiche molare Konzentration in der Stammlösungen für einfache, Verhältnisse berechnet werden, wenn die Zugabe verschiedener Volumina auf den Test. 40 ul von GFP-Trap-Perlen eine Bindungskapazität von ~ 300 pmol so eine konfluente 75 cm 2-Kolben hoch exprimierenden Zellen werden die Perlen zu sättigen, mit dem Ergebnis, dass die Vorbereitungen der beiden unterschiedlichen Bindungsproteine ​​ähnlich vor Anpassung (Abbildung 2A). Wenn eines der Proteine ​​schlecht exprimiert, kann dieses Problem durch Reinigen dieses Proteins aus mehr als einem Kolben von Zellen überwunden werden können. <p class = &quot;jove_content&quot;&gt; Die Bindung der meisten GTPase Effektoren und Regler abhängig von der Nukleotid-Beladung des Köder GTPase, so ist es wichtig zu untersuchen, ob Laden erfolgreich gewesen ist. Belastung kann durch Ausfällen bekannten Bindungsproteinen aus Zellysaten überprüft werden. Effektor-Proteine, wie PAK1 binden an GTP-Rac1 und kann leicht aus Lysaten präzipitiert und durch Western Blotting 8 (2B) erfasst werden. GEFs Substanzen binden Nukleotid freien GTPase den Übergangszustand zu stabilisieren. Wie GEFs sind von geringer Menge, in der Regel nicht aktiv und häufig schlecht auslöschen, ist es besser, ein GEF oder GEF-Fragment zu Test Nukleotid-freien GTPase überexprimieren. Wir verwenden häufig die erste Dbl Homologie von Trio, ausgedrückt als GFP-Fusions (GFP-TrioD1 9) (2B) aber jede GEF funktionieren würde. Proteine, die an der BIP-geladen GTPase binden, sind seltener. Vor kurzem berichteten wir RCC2 als eine solche Protein 7 oder BIP-Belastung kann einfach als bindi validiert werdenng bis weder GEF noch Effektorzellen. Der Ausgang aus dem Experiment wird ein Western-Blot-Darstellung die beiden GFP-markierten Bindungspartner für die GTPase gebunden sein. Durch die Verwendung eines einzelnen Antikörpers, beide Proteine ​​zu erkennen, können die Konzentrationen, bei denen gleiche Mengen der beiden Wettbewerber binden bestimmt und daher die relativen Affinitäten abgeleitet. In diesem Beispiel ist der Wettbewerb zwischen dem Propeller-Domäne des Rac1-Trafficking-Protein Coronin-1C (Rac1-bindenden Protein A) und die Rac1 sequestrierenden Protein RCC2 (Rac1-bindendes Protein B) wird nachgewiesen (3A). Unter Verwendung eines konstanten Volumens Coronin 1C Propeller (5 ul), und das Hinzufügen von steigenden Mengen von RCC2, wir von der GFP sehen auslöschen, dass ein Gleichgewicht bei 1,25-2,5 ul RCC2 (Sternchen) erreicht ist, was zeigt, dass RCC2 hat eine stärkere Affinität für Rac1 als Coronin-1C. Durch Messen der Intensität der Banden mittels quantitativer Western Blot und Aufzeichnen der Mittelwerte für jede competitor kann der Gleichgewichtspunkt genau durch Ermittlung der Mengen an denen die Kurven schneiden (3B) berechnet werden. Eine der möglichen Hindernisse für eine erfolgreiche Konkurrenz-Assay ist, wenn die Bindungspartner miteinander sowie die Bindung an Rac1 binden. In 3A + B zeigen wir den Wettbewerb zwischen RCC2 und Propeller-Domäne von Coronin-1C, anstatt voller Länge Coronin-1C. Der Grund für die Verwendung des trunkierten Coronin dass Coronin 1C bindet ebenfalls RCC2 durch die Schwanzdomäne. Bei voller Länge Coronin-1C gegen RCC2 titriert, Bindung beider Proteine ​​erkannt wird, aufgrund von ternären Komplexbildung, anstatt den Wettbewerb (3C). Wenn Konkurrenz auftritt, wird Bindung eines Proteins, während das andere abnimmt erhöhen und gesamte gebundene GFP-Fusions konstant. In Fällen, in denen ein ternärer Komplex bildet es notwendig ist, eine der GTPase-bindendes Protein abzuschneiden, so dass der competitors nicht mehr interagieren. <img alt="Abbildung 1" src="/files/ftp_upload/53254/53254fig1.jpg" /> Abbildung 1. Arbeitsablauf. Schematische Darstellung der Arbeitsablauf zur Bestimmung der Affinität der GTPase-bindende Proteine ​​mit Konkurrenz-Assays. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig1large.jpg" target="_blank">Bitte klicken Sie hier, um eine größere Version dieser Figur zu sehen.</a> <img alt="Figur 2" src="/files/ftp_upload/53254/53254fig2.jpg" /> Abbildung 2. Validierung von gereinigten Proteinen. (A) gereinigtes GFP-markierten Rac1 bindenden Proteinen durch Western-Blot analysiert, Sondierung mit Anti-GFP, um die relative Ausbeute der beiden Proteine ​​zu bestimmen. Diese Art von Entzerrung während des Experiments kann die Konzentration der beiden Proteine ​​angepasst werden, so dass sie in dem Bindungsexperiment übereinstimmen. (B) GDP, GTPyS und keine Nukleotid-beladenen GST-Rac1 mit Lysat aus HEK293T, die GFP-TrioD1 Proteine ​​durch Auftragen einer endogenen PAK1 oder überexprimiert GFP-TrioD1 erkannt inkubiert und gebunden. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig2large.jpg" target="_blank">Bitte klicken Sie hier, um eine größere Version dieser Figur zu sehen.</a> <img alt="Figur 3" src="/files/ftp_upload/53254/53254fig3.jpg" /> Abbildung 3. Western-Blot-Analyse der relativen Proteinbindung. Beispiel Ausgaben von Konkurrenz-Bindungs-Assays. (A) BIP belasteten Rac1 wurde mit 5 ul GFP-Coronin-1C-Propellerdomäne gemischt und steigenden Mengen von GFP-RCC2 wurden titriert. Durch Westernblot gebundenen Proteine ​​GFP, sind Probleme mit der Differenzerfassung der beiden Proteine ​​vermieden und das GFP-Signal meldet das Molverhältnis zwischen den beiden Fusionsproteinen. Sternchen zeigen die Wettbewerbsverhältnisse auf either Seite des Gleichgewichtspunkt. (B) Bandenintensitäten von gebundenem GFP-Fusionsproteinen aus drei unabhängigen Experimenten wurden durch quantitative Western-Blotting gemessen, wobei Fluorophor-konjugierten sekundären Antikörpern und Mittelwerte aufgetragen, um die Menge an RCC2 Berechnung erforderlich, um das Gleichgewicht zu erreichen. (C ) Ausgabe aus einem Experiment, wo Rac1-bindende Proteine ​​binden aneinander und bilden einen ternären Komplex, anstatt konkurrierende. BIP belasteten Rac1 wurde mit 5 ul GFP-RCC2 gemischt und steigenden Mengen von GFP-Coronin-1C in voller Länge wurden ohne Verlust an gebundenem GFP-RCC2 titriert. Der Anstieg der gebundenen GFP-Coronin-1C zeigt ternären Komplexbildung. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig3large.jpg" target="_blank">Bitte Klicken Sie hier, um eine größere Version dieser Figur zu sehen.</a>

Watch this Scientific Journal Video about Comparing the Affinity of GTPase-binding Proteins using Competition Assays at JoVE.com

Comparing the Affinity of GTPase-binding Proteins using Competition Assays

This protocol compares the relative affinities of binding partners for Rho-family GTPases, including Rac1. In vivo, Rac1-binding proteins compete for a single binding interface, the conformation of which is dictated by a bound nucleotide. The nucleotide is both important and difficult to control experimentally, due to the high hydrolysis rate.

Vergleicht man die Affinität der GTPase-bindende Proteine ​​mit Competition-Assays

In this protocol we demonstrate a method for comparing the competition between GTPase-binding proteins. Such an approach is important for determining the ...

comparing-affinity-gtpase-binding-proteins-using-competition

Research

JoVE Journal

Biology

9.1K Aufrufe.  University of Bristol. This protocol compares the relative affinities of binding partners for Rho-family GTPases, including Rac1. In vivo, Rac1-binding proteins compete for a single binding interface, the conformation of which is dictated by a bound nucleotide. The nucleotide is both important and difficult to control experimentally, due to the high hydrolysis rate.

Serie: Comparing the Affinity of GTPase-binding Proteins using Competition Assays

Measuring G-protein-coupled Receptor Signaling via Radio-labeled GTP Binding

G-Protein-Coupled Receptors (GPCRs) are a large family of transmembrane receptors that play critical roles in normal cellular physiology and constitute a major pharmacological target for multiple indications, including analgesia, blood pressure regulation, and the treatment of psychiatric disease. Upon ligand binding, GPCRs catalyze the activation of intracellular G-proteins by stimulating the incorporation of guanosine triphosphate (GTP). Activated G-proteins then stimulate signaling pathways that elicit cellular responses. GPCR signaling can be monitored by measuring the incorporation of a radiolabeled and non-hydrolyzable form of GTP, [35S]guanosine-5&#39;-O-(3-thio)triphosphate ([35S]GTP&#947;S), into G-proteins. Unlike other methods that assess more downstream signaling processes, [35S]GTP&#947;S binding measures a proximal event in GPCR signaling and, importantly, can distinguish agonists, antagonists, and inverse agonists. The present protocol outlines a sensitive and specific method for studying GPCR signaling using crude membrane preparations of an archetypal GPCR, the &#181;-opioid receptor (MOR1). Although alternative approaches to fractionate cells and tissues exist, many are cost-prohibitive, tedious, and/or require non-standard laboratory equipment. The present method provides a simple procedure that enriches functional crude membranes. After isolating MOR1, various pharmacological properties of its agonist, [D-Ala, N-MePhe, Gly-ol]-enkephalin (DAMGO), and antagonist, naloxone, were determined.

Guanosine triphosphate (GTP) binding is one of the earliest events in G-Protein-Coupled Receptor (GPCR) activation. This protocol describes how to pharmacologically characterize specific GPCR-ligand interactions by monitoring the binding of the radio-labeled GTP analog, [35S]guanosine-5&#39;-O-(3-thio)triphosphate ([35S]GTP&#947;S), in response to a ligand of interest.

Messung der G-Protein-gekoppelten Rezeptorsignalisierung über radioaktiv markierte GTP-Bindung

G-Protein-Coupled Receptors (GPCRs) are a large family of transmembrane receptors that play critical roles in normal cellular physiology and constitute a ...

Forschung

Biochemie

Measuring Protein Binding to F-actin by Co-sedimentation

Filamentous actin (F-actin) organization within cells is regulated by a large number of actin-binding proteins that control actin nucleation, growth, cross-linking and/or disassembly. This protocol describes a technique &#8211; the actin co-sedimentation, or pelleting, assay &#8211; to determine whether a protein or protein domain binds F-actin and to measure the affinity of the interaction (i.e., the dissociation equilibrium constant). In this technique, a protein of interest is first incubated with F-actin in solution. Then, differential centrifugation is used to sediment the actin filaments, and the pelleted material is analyzed by SDS-PAGE. If the protein of interest binds F-actin, it will co-sediment with the actin filaments. The products of the binding reaction (i.e., F-actin and the protein of interest) can be quantified to determine the affinity of the interaction. The actin pelleting assay is a straightforward technique for determining if a protein of interest binds F-actin and for assessing how changes to that protein, such as ligand binding, affect its interaction with F-actin.

This protocol describes a method to test the ability of a protein to co-sediment with filamentous actin (F-actin) and, if binding is observed, to measure the affinity of the interaction.

Messung der Proteinbindung an F-Aktin durch Co-Sedimentation

Filamentous actin (F-actin) organization within cells is regulated by a large number of actin-binding proteins that control actin nucleation, growth, ...

Detection of Small GTPase Prenylation and GTP Binding Using Membrane Fractionation and  GTPase-linked Immunosorbent Assay

The Rho GTPase family belongs to the Ras superfamily and includes approximately 20 members in humans. Rho GTPases are important in the regulation of diverse cellular functions, including cytoskeletal dynamics, cell motility, cell polarity, axonal guidance, vesicular trafficking, and cell cycle control. Changes in Rho GTPase signaling play an essential regulatory role in many pathological conditions, such as&#160;cancer, central nervous system diseases, and immune system-dependent diseases. The posttranslational modification of Rho GTPases (i.e., prenylation by mevalonate pathway intermediates) and GTP binding are key factors which affect the activation of this protein. In this paper, two essential and simple methods are provided to detect a broad range of Rho GTPase prenylation and GTP binding activities. Details of the technical procedures that have been used are explained step by step in this manuscript.

Here we describe a protocol to investigate the prenylation and guanosine-5'-triphosphate (GTP)-loading of Rho GTPase. This protocol consists of two detailed methods, namely membrane fractionation and a GTPase-linked immunosorbent assay. The protocol can be used for measuring the prenylation and GTP loading of different other small GTPases.

Erkennung von kleine GTPase Prenylation und GTP binden mit Membran Fraktionierung und GTPase verbundene Immunosorbentprobe Assay

The Rho GTPase family belongs to the Ras superfamily and includes approximately 20 members in humans. Rho GTPases are important in the regulation of ...

A Semi-High-Throughput Adaptation of the NADH-Coupled ATPase Assay for Screening Small Molecule Inhibitors

ATPase enzymes utilize the free energy stored in adenosine triphosphate to catalyze a wide variety of endergonic biochemical processes in vivo that would not occur spontaneously. These proteins are crucial for essentially all aspects of cellular life, including metabolism, cell division, responses to environmental changes and movement. The protocol presented here describes a nicotinamide adenine dinucleotide (NADH)-coupled ATPase assay that has been adapted to semi-high throughput screening of small molecule ATPase inhibitors. The assay has been applied to cardiac and skeletal muscle myosin II's, two actin-based molecular motor ATPases, as a proof of principle. The hydrolysis of ATP is coupled to the oxidation of NADH by enzymatic reactions in the assay. First, the ADP generated by the ATPase is regenerated to ATP by pyruvate kinase (PK). PK catalyzes the transition of phosphoenolpyruvate (PEP) to pyruvate in parallel. Subsequently, pyruvate is reduced to lactate by lactate dehydrogenase (LDH), which catalyzes the oxidation of NADH in parallel. Thus, the decrease in ATP concentration is directly correlated to the decrease in NADH concentration, which is followed by change to the intrinsic fluorescence of NADH. As long as PEP is available in the reaction system, the ADP concentration remains very low, avoiding inhibition of the ATPase enzyme by its own product. Moreover, the ATP concentration remains nearly constant, yielding linear time courses. The fluorescence is monitored continuously, which allows for easy estimation of the quality of data and helps to filter out potential artifacts (e.g., arising from compound precipitation or thermal changes).

A nicotinamide adenine dinucleotide (NADH)-coupled ATPase assay has been adapted to semihigh throughput screening of small molecule myosin inhibitors. This kinetic assay is run in a 384-well microplate format with total reaction volumes of only 20 &#181;L per well. The platform should be applicable to virtually any ADP producing enzyme.

Eine semi-High-Throughput-Anpassung des NADH-gekoppelten ATPase-Assays zum Screening kleiner Molekülinhibitoren

ATPase enzymes utilize the free energy stored in adenosine triphosphate to catalyze a wide variety of endergonic biochemical processes in vivo that would ...

Parallel Interrogation of &#946;-Arrestin2 Recruitment for Ligand Screening on a GPCR-Wide Scale using PRESTO-Tango Assay

As the largest and most versatile gene superfamily and mediators of a gamut of cellular signaling pathways, G-protein-coupled receptors (GPCRs) represent one of the most promising targets for the pharmaceutical industry. Ergo, the design, implementation, and optimization of GPCR ligand screening assays is crucial, as they represent remote-control tools for drug discovery and for manipulating GPCR pharmacology and outcomes. In the past, G-protein dependent assays typified this area of research, detecting ligand-induced events and quantifying the generation of secondary messengers. However, since the advent of functional selectivity, as well as an increased awareness of several other G protein-independent pathways and the limitations associated with G-protein dependent assays, there is a greater push towards the creation of alternative GPCR ligand screening assays. Towards this endeavor, we describe the application of one such resource, the PRESTO-Tango platform, a luciferase reporter-based system that enables the parallel and simultaneous interrogation of the human GPCR-ome, a feat which was previously considered technically and economically unfeasible. Based on a G-protein independent &#946;-arrestin2 recruitment assay, the universality of &#946;-arrestin2-mediated trafficking and signaling at GPCRs makes PRESTO-TANGO an apt tool for studying approximately 300 non-olfactory human GPCRs, including approximately 100 orphan receptors. PRESTO-Tango&#39;s sensitivity and robustness make it suitable for primary high-throughput screens using compound libraries, employed to uncover new GPCR targets for known drugs or to discover new ligands for orphan receptors.

Given that GPCRs are attractive druggable targets, GPCR ligand screening is thus indispensable for the identification of lead compounds and for deorphanization studies. Towards these efforts, we describe PRESTO-Tango, an open-source resource platform used for simultaneous profiling of transient &#946;-arrestin2 recruitment at approximately 300 GPCRs using a TEV-based reporter assay.

Parallele Vernehmung der Rekrutierung von '-Arrestin2 für Ligand Screening auf einer GPCR-weiten Skala mit PRESTO-Tango Assay

As the largest and most versatile gene superfamily and mediators of a gamut of cellular signaling pathways, G-protein-coupled receptors (GPCRs) represent ...

RhoC GTPase Activation Assay

RhoC GTPase has 91% homology to RhoA GTPase. Because of its prevalence in cells, many reagents and techniques for RhoA GTPase have been developed. However, RhoC GTPase is expressed in metastatic cancer cells at relatively low levels. Therefore, few RhoC-specific reagents have been developed. We have adapted a Rho activation assay to detect RhoC GTPase. This technique utilizes a GST-Rho binding domain fusion protein to pull out active RhoC GTPase. In addition, we can harvest total protein at the beginning of the assay to determine levels of total (GTP and GDP bound) RhoC GTPase. This allows for the determination of active versus total RhoC GTPase in the cell. Several commercial versions of this procedure have been developed however, the commercial kits are optimized for RhoA GTPase and typically do not work well for RhoC GTPase. Parts of the assay have been modified as well as development of a RhoC-specific antibody.

This protocol utilizes a pull down assay to determine the levels of active RhoC GTPase within cells.

RhoC GTPase-Aktivierungs-Assay

RhoC GTPase has 91% homology to RhoA GTPase.  Because of its prevalence in cells, many reagents and techniques for RhoA GTPase have been developed.  ...

Biologie

Affinity Precipitation of Active Rho-GEFs Using a GST-tagged Mutant Rho Protein (GST-RhoA(G17A)) from Epithelial Cell Lysates

Proteins of the Rho family of small GTPases are central regulators of the cytoskeleton, and control a large variety of cellular processes, including cell migration, gene expression, cell cycle progression and cell adhesion 1. Rho proteins are molecular switches that are active in GTP-bound and inactive in GDP-bound state. Their activation is mediated by a family of Guanine-nucleotide Exchange Factor (GEF) proteins. Rho-GEFs constitute a large family, with overlapping specificities 2. Although a lot of progress has been made in identifying the GEFs activated by specific signals, there are still many questions remaining regarding the pathway-specific regulation of these proteins. The number of Rho-GEFs exceeds 70, and each cell expresses more than one GEF protein. In addition, many of these proteins activate not only Rho, but other members of the family, contributing further to the complexity of the regulatory networks. Importantly, exploring how GEFs are regulated requires a method to follow the active pool of individual GEFs in cells activated by different stimuli. Here we provide a step-by-step protocol for a method used to assess and quantify the available active Rho-specific GEFs using an affinity precipitation assay. This assay was developed a few years ago in the Burridge lab 3,4 and we have used it in kidney tubular cell lines 5,6,7. The assay takes advantage of a "nucleotide free" mutant RhoA, with a high affinity for active GEFs. The mutation (G17A) renders the protein unable to bind GDP or GTP and this state mimics the intermediate state that is bound to the GEF. A GST-tagged version of this mutant protein is expressed and purified from E. coli, bound to glutathione sepharose beads and used to precipitate active GEFs from lysates of untreated and stimulated cells. As most GEFs are activated via posttranslational modifications or release from inhibitory bindings, their active state is preserved in cell lysates, and they can be detected by this assay8. Captured proteins can be probed for known GEFs by detection with specific antibodies using Western blotting, or analyzed by Mass Spectrometry to identify unknown GEFs activated by certain stimuli.

Affinity Precipitation of Active Rho-GEFs Using a GST-tagged Mutant Rho Protein GST-RhoAG17A from Epithelial Cell Lysates

The method presented here describes an assay to follow activation of RhoA specific GDP/GTP Exchange Factors (GEFs) in cultured cells by making use of a mutant RhoA GST fusion protein that has high affinity for activated GEFs. GEFs are precipitated from cell lysates, detected by Western blotting and quantified by densitometry.

Affinity Niederschlag von Active Rho-GEFs Mit Hilfe eines GST-markiertes Mutant Rho-Protein (GST-RhoA (G17A)) aus epithelialen Zelllysate

Proteins of the Rho family of small GTPases are central regulators of the cytoskeleton, and control a large variety of cellular processes, including cell ...

Characterization of G Protein-coupled Receptors by a Fluorescence-based Calcium Mobilization Assay

For more than 20 years, reverse pharmacology has been the preeminent strategy to discover the activating ligands of orphan G protein-coupled receptors (GPCRs). The onset of a reverse pharmacology assay is the cloning and subsequent transfection of a GPCR of interest in a cellular expression system. The heterologous expressed receptor is then challenged with a compound library of candidate ligands to identify the receptor-activating ligand(s). Receptor activation can be assessed by measuring changes in concentration of second messenger reporter molecules, like calcium or cAMP. The fluorescence-based calcium mobilization assay described here is a frequently used medium-throughput reverse pharmacology assay. The orphan GPCR is transiently expressed in human embryonic kidney 293T (HEK293T) cells and a promiscuous G&#945;16 construct is co-transfected. Following ligand binding, activation of the G&#945;16 subunit induces the release of calcium from the endoplasmic reticulum. Prior to ligand screening, the receptor-expressing cells are loaded with a fluorescent calcium indicator, Fluo-4 acetoxymethyl. The fluorescent signal of Fluo-4 is negligible in cells under resting conditions, but can be amplified more than a 100-fold upon the interaction with calcium ions that are released after receptor activation. The described technique does not require the time-consuming establishment of stably transfected cell lines in which the transfected genetic material is integrated into the host cell genome. Instead, a transient transfection, generating temporary expression of the target gene, is sufficient to perform the screening assay. The setup allows medium-throughput screening of hundreds of compounds. Co-transfection of the promiscuous G&#945;16, which couples to most GPCRs, allows the intracellular signaling pathway to be redirected towards the release of calcium, regardless of the native signaling pathway in endogenous settings. The HEK293T cells are easy to handle and have proven their efficacy throughout the years in receptor deorphanization assays. However, optimization of the assay for specific receptors may remain necessary.

The here described fluorescence-based calcium mobilization assay is a medium-throughput reverse pharmacology screening system for the identification of functionally activating ligand(s) of orphan G protein-coupled receptors (GPCRs).

Charakterisierung von G-Protein gekoppelten Rezeptoren durch eine Fluoreszenz-basierte Calciummobilisierungsassay

For more than 20 years, reverse pharmacology has been the preeminent strategy to discover the activating ligands of orphan G protein-coupled receptors ...

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

A wide range of methods are currently available for determining the dissociation constant between a protein and interacting small molecules. However, most of these require access to specialist equipment, and often require a degree of expertise to effectively establish reliable experiments and analyze data. Differential scanning fluorimetry (DSF) is being increasingly used as a robust method for initial screening of proteins for interacting small molecules, either for identifying physiological partners or for hit discovery. This technique has the advantage that it requires only a PCR machine suitable for quantitative PCR, and so suitable instrumentation is available in most institutions; an excellent range of protocols are already available; and there are strong precedents in the literature for multiple uses of the method. Past work has proposed several means of calculating dissociation constants from DSF data, but these are mathematically demanding. Here, we demonstrate a method for estimating dissociation constants from a moderate amount of DSF experimental data. These data can typically be collected and analyzed within a single day. We demonstrate how different models can be used to fit data collected from simple binding events, and where cooperative binding or independent binding sites are present. Finally, we present an example of data analysis in a case where standard models do not apply. These methods are illustrated with data collected on commercially available control proteins, and two proteins from our research program. Overall, our method provides a straightforward way for researchers to rapidly gain further insight into protein-ligand interactions using DSF.

Differential scanning fluorimetry is a widely used method for screening libraries of small molecules for interactions with proteins. Here, we present a straightforward method to extend these analyses to provide an estimate of the dissociation constant between a small molecule and its protein partner.

Bestimmung der Protein-Ligand-Wechselwirkungen mit Differential Scanning Fluorimetrie

A wide range of methods are currently available for determining the dissociation constant between a protein and interacting small molecules. However, most ...

A Flow Cytometry-based Assay to Identify Compounds That Disrupt Binding of Fluorescently-labeled CXC Chemokine Ligand 12 to CXC Chemokine Receptor 4

Pharmacological targeting of G protein-coupled receptors (GPCRs) is of great importance to human health, as dysfunctional GPCR-mediated signaling contributes to the progression of many diseases. The ligand/receptor pair CXC chemokine ligand 12 (CXCL12)/CXC chemokine receptor 4 (CXCR4) has raised significant clinical interest, for instance as a potential target for the treatment of cancer and inflammatory diseases. Small molecules as well as therapeutic antibodies that specifically target CXCR4 and inhibit the receptor&#39;s function are therefore considered to be valuable pharmacological tools. Here, a flow cytometry-based cellular assay that allows identification of compounds (e.g., small molecules) that abrogate CXCL12 binding to CXCR4, is described. Essentially, the assay relies on the competition for receptor binding between a fixed amount of fluorescently labeled CXCL12, the natural chemokine agonist for CXCR4, and unlabeled compounds. Hence, the undesirable use of radioactively labeled probes is avoided in this assay. In addition, living cells are used as the source of receptor (CXCR4) instead of cell membrane preparations. This allows easy adaptation of the assay to a plate format, which increases the throughput. This assay has been shown to be a valuable generic drug discovery assay to identify CXCR4-targeting compounds. The protocol can likely be adapted to other GPCRs, at least if fluorescently labeled ligands are available or can be generated. Prior knowledge concerning the intracellular signaling pathways that are induced upon activation of these GPCRs, is not required.

A flow cytometry-based cellular binding assay is described that is primarily used as a screening tool to identify compounds that inhibit the binding of a fluorescently labeled CXC chemokine ligand 12 (CXCL12) to the CXC chemokine receptor 4 (CXCR4).

Ein Flow Cytometry-basierte Assay, Verbindungen zu identifizieren, die Bindung von Eindringmittel beschriftet CXC-Chemokin-Liganden 12 an CXC-Chemokin-Rezeptor 4 stören

Vergleicht man die Affinität der GTPase-bindende Proteine mit Competition-Assays

Zusammenfassung

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Messung der G-Protein-gekoppelten Rezeptorsignalisierung über radioaktiv markierte GTP-Bindung

Messung der Proteinbindung an F-Aktin durch Co-Sedimentation

Erkennung von kleine GTPase Prenylation und GTP binden mit Membran Fraktionierung und GTPase verbundene Immunosorbentprobe Assay

Eine semi-High-Throughput-Anpassung des NADH-gekoppelten ATPase-Assays zum Screening kleiner Molekülinhibitoren

Parallele Vernehmung der Rekrutierung von '-Arrestin2 für Ligand Screening auf einer GPCR-weiten Skala mit PRESTO-Tango Assay

RhoC GTPase-Aktivierungs-Assay

Affinity Niederschlag von Active Rho-GEFs Mit Hilfe eines GST-markiertes Mutant Rho-Protein (GST-RhoA (G17A)) aus epithelialen Zelllysate

Charakterisierung von G-Protein gekoppelten Rezeptoren durch eine Fluoreszenz-basierte Calciummobilisierungsassay

Bestimmung der Protein-Ligand-Wechselwirkungen mit Differential Scanning Fluorimetrie

Ein Flow Cytometry-basierte Assay, Verbindungen zu identifizieren, die Bindung von Eindringmittel beschriftet CXC-Chemokin-Liganden 12 an CXC-Chemokin-Rezeptor 4 stören

Vergleicht man die Affinität der GTPase-bindende Proteine ​​mit Competition-Assays

Zusammenfassung

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Messung der G-Protein-gekoppelten Rezeptorsignalisierung über radioaktiv markierte GTP-Bindung

Messung der Proteinbindung an F-Aktin durch Co-Sedimentation

Erkennung von kleine GTPase Prenylation und GTP binden mit Membran Fraktionierung und GTPase verbundene Immunosorbentprobe Assay

Eine semi-High-Throughput-Anpassung des NADH-gekoppelten ATPase-Assays zum Screening kleiner Molekülinhibitoren

Parallele Vernehmung der Rekrutierung von '-Arrestin2 für Ligand Screening auf einer GPCR-weiten Skala mit PRESTO-Tango Assay

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Affinity Niederschlag von Active Rho-GEFs Mit Hilfe eines GST-markiertes Mutant Rho-Protein (GST-RhoA (G17A)) aus epithelialen Zelllysate

Charakterisierung von G-Protein gekoppelten Rezeptoren durch eine Fluoreszenz-basierte Calciummobilisierungsassay

Bestimmung der Protein-Ligand-Wechselwirkungen mit Differential Scanning Fluorimetrie

Ein Flow Cytometry-basierte Assay, Verbindungen zu identifizieren, die Bindung von Eindringmittel beschriftet CXC-Chemokin-Liganden 12 an CXC-Chemokin-Rezeptor 4 stören

Vergleicht man die Affinität der GTPase-bindende Proteine mit Competition-Assays