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

1. A purificação de GTPase marcado com GST <ol><li> Cultura um E. coli tal como BL21 transformada com pGEX-Rac1 O / N a 37 ° C, agitação a 220 rpm, em 500 ml de meio de auto-indução (25 mM de Na 2 HPO 4, 25 mM de KH 2 PO 4, 50 mM de NH 4 Cl, 5 mM de Na 2 SO 4, 2 mM MgSO4, 2 mM de CaCl2, 0,5% de glicerol, 0,05% de glucose, 0,2% de lactose, 5 g de triptona, 2,5 g de extracto de levedura, 100 ug / ml de ampicilina). </li><li> Colheita bactérias por centrifugação durante 10 min a 10.000 xg, a 4 ° C. </li><li> Ressuspender o granulado em 20 ml bacteriana reagente de extracção de proteína, 1x inibidor de protease e incuba-se durante 20 min à TA com inversão. </li><li> Clarificar o lisado por centrifugação a 40.000 xg durante 30 min. </li><li> Adicionar 2 mL de glutationa esferas magnéticas, lavadas com solução salina tamponada com fosfato (PBS: 10 mM de Na 2 HPO 4, 1,8 mM de KH 2 PO 4, 137 mM de NaCl, KCl 2,7 mM). </li><li> Incubar durante 2 h, misturando por inversão a 4 ° C. </li><li> Lavar os grânulos carregados de proteína-se quatro vezes com 10 ml de PBS, utilizando um classificador de partículas magnéticas para precipitar os grânulos em cada passo. </li><li> Grânulos em 2 ml de PBS e armazenar Ressuspender proteína-carregado a -80 ° C em alíquotas de 100 ul até ser necessário. </li></ol> 2. Expressão de proteínas de ligação a GTPase <ol><li> O dia antes da experiência, os plasmídeos que codificam para transfectar proteína fluorescente verde (GFP) tagged versões de cada proteína de GTPase de ligação para um separado 75-cm2 de frasco HEK293T como se segue. Para a validação do carregamento de nucleotídeos, transfecção GFP-tagged TrioD1 em um terceiro de 75 cm 2 frasco de HEK293T. <ol><li> Diluir polyethylamine a 1 mg / ml em 100 ul de NaCl 150 mM estéril. </li><li> Adicionar 27 ul diluída para 223 ul polyethylamine meio de soro reduzido. </li><li> Adicionar 12 ug de DNA de plasmídeo a 250 ul de meio de soro reduzido. </li><li> Incubar cada tubo durante 2 min à temperatura ambiente. </li&gt; <li> Combinar o polyethylamine e mistura de ADN em um único tubo e vortex durante 2 min. </li><li> Incubar durante 15-20 minutos à temperatura ambiente. </li><li> Substituir o meio de crescimento (Meios de Eagle Modificado por Dulbecco, 10% de soro fetal bovino, 2 mM de L-glutamina, sem antibióticos) em 90% confluentes HEK293T com 5 ml de meio de crescimento fresco. </li><li> Adicionar a mistura polyethylamine / ADN combinado para o frasco e incubar O / N a 37 ° C, 5% de CO 2. </li></ol></li></ol> 3. Purificação de proteínas de ligação a GTPase <ol><li> Lavar frascos de células transfectadas em PBS e escorrer balão durante 5 min, a aspiração de líquido livre. </li><li> Raspar as células em 500 ul de tampão de lise (50 mM de Tris-HCl (pH 7,8), 1% de Nonidet P-40, 1x inibidor de protease) para dentro do tubo de microcentrífuga. </li><li> Lisar as células por misturar por inversão a 4 ° C durante 30 min. </li><li> Durante a lise, lavar dois lotes de esferas de 40 ul de GFP-Trap três vezes com tampão de lise fresco, grânulos que sedimentam em 2.700 xg durante 2 min entre as lavagens. </li><li> Esclarecer os lisados ​​por centrifugação a 21.000 xg durante 10 min. </li><li> Transferir o lisado clarificado de cada uma das proteínas concorrentes para separar os grânulos de GFP-trap lavadas e permitem que as proteínas de fusão GFP-para ligar durante 2 h, misturando por inversão a 4 ° C. Manter o lisado a partir de células de GFP-TrioD1 em gelo. </li><li> Lavar grânulos GFP-Trap carregadas duas vezes em 50 mM Tris-HCl (pH 7,8), NaCl 50 mM, 0,7% (w / v) Nonidet P-40 e duas vezes em 50 mM Tris-HCl (pH 7,6), MgCl 20 mM 2 , sedimentando esferas a 2700 xg por 2 min entre lavagens. </li><li> Elui-se as proteínas de fusão GFP-40 ul pela adição de 0,2 M de glicina (pH 2,5) e pipetando para cima e para baixo durante 30 seg. Imediatamente grânulos sedimento no 21.000 xg durante 60 segundos e de transferência de líquido para um novo tubo de microcentrifugadora contendo 4 mL de 1 M de Tris-HCl (pH 10,4). Faça isso rapidamente para limitar os danos à proteína purificada. </li><li> Analisar 1 ul de cada proteína purificada por transferência de Western e detecção com um anticorpo anti-GFP para estabelecer o rendimento relativamente quantitativo utilizando um Blotting sistema de acordo com o protocolo do fabricante. Alternativamente, a determinação das concentrações de proteína pelo ácido (BCA) ensaio bicinconínico mas isso introduz erros, se as proteínas não reagem com o ensaio de uma forma idêntica ou existem proteínas contaminantes. </li><li> Equalizar a concentração molar da proteína pela adição de 50 mM de Tris-HCl (pH 7,6), 20 mM de MgCl 2. </li></ol> 4. Nucleotide carregamento de GTPase <ol><li> Descongelar uma aliquota de GST-Rac1 esferas magnéticas, preparado no passo 1. </li><li> Tomar 90 ul de esferas de GST-Rac1 e lavar três vezes com 20 mM de Tris-HCl (pH 7,6), NaCl 25 mM, DTT 0,1 mM, EDTA 4 mM, utilizando um classificador de partículas magnéticas para precipitar os grânulos em cada passo. </li><li> Aspirar tampão dos grânulos e adiciona-se 100 ul de 20 mM Tris-HCl (pH 7,6), NaCl 25 mM, DTT 0,1 mM, EDTA 4 mM. </li><li> De acordo com o PIB se, GTP ou nenhuma carga de nucleótidos é necessária para a experiência de competição, adicionar 12 ul de PIB 100 mM, 12 ul de 10 mM de guanosine 5 &#39;- [γ-tio] trifosfato (GTP) ou nenhum nucleótido a 60 ul de GST-Rac1 grânulos. </li><li> Para os controles de nucleótidos de carregamento, dividir os grânulos restantes em três alíquotas de 10 ul e adiciona-2 ul PIB 100 mM, 2 ul de 10 mM ou GTPyS não de nucleótidos para cada tubo. </li><li> Incubar as misturas de esferas durante 30 minutos a 30 ° C com agitação. </li><li> Estabilizar Rac1 ligados a nucleótidos por adição de 1 M de MgCl2: 3 ul à mistura experimental (passo 4.4), 0,5 ul de cada uma das misturas de controlo (passo 4.5). </li></ol> 5. Concorrência vinculativo. <ol><li> Configure 6 tubos de microcentrífuga, cada uma contendo: 200 ul de 50 mM Tris-HCl (pH 7,6), 20 mM de MgCl2 10 jul experimentais contas de Rac1 carregado de nucleotídeo (a partir do passo 4.7) 5 jul proteína Rac1 de ligação A (proteína de ligação constante) </li><li> Para cada tubo, adicionar 0, 1, 2.5, 5, 10 ou 20 ul de proteína de ligação a Rac1 B (proteína de ligação variável). Estes volumes assumir umaproximadamente iguais concentrações banco de proteínas de ligação constante e variável e pode precisar de ser ajustada. <ol><li> Ajustar o volume de proteínas de ligação A e B se existirem grandes diferenças nas afinidades de ligação das duas proteínas e isto deve ser determinado empiricamente através das repetições experimentais. Perfazer o volume total da mistura de ligação a 235 ul, por adição de 50 mM de Tris-HCl (pH 7,6), 20 mM de MgCl 2. </li></ol></li><li> Configurar um tubo de microcentrífuga contendo: 200 ul de 50 mM Tris-HCl (pH 7,6), 20 mM de MgCl2 10 jul experimentais contas de Rac1 carregado de nucleotídeo (a partir do passo 4.7) 10 ul de proteína Rac1 de ligação A (proteína de ligação constante) </li><li> Configure o PIB, GTPyS e sem tubos de controle de nucleotídeos: 200 ul de 50 mM Tris-HCl (pH 7,6), 20 mM de MgCl2 10 esferas de Rac1 controle ul carregado no passo 4.5 com o PIB, GTPyS ou nenhuma nucleotídeos e estabilizado na etapa 4.7. 180 ul de HEK293T GFP-TrioD1 lisado, preparado como no passo 3.6 4 ul de 1 M MgCl2 </li><li> Incubar a mistura durante 2 h, misturando por inversão a 4 ° C. </li><li> Lavar as pérolas três vezes com 50 mM de Tris-HCl (pH 7,6), 20 mM de MgCl 2. </li><li> Eluir proteínas ligadas, em 20 ul de tampão de amostra redutora (50 mM de Tris-HCl (pH 7), SDS a 5%, 20% de glicerol, 0,02 mg / ml de azul de bromofenol, 5% β-mercaptoetanol). </li></ol> 6. Análise da concorrência <ol><li> Resolver 10 ul de a proteína ligada (passo 5.6) por electroforese em dodecil sulfato de sódio poliacrilamida gel (SDS-PAGE) e transferência de Western. </li><li> Incubar a membrana a 4 ° CO / N em anticorpo anti-GFP diluído 1/1000 em tampão de bloqueio diluído em PBS 1x, 0,1% de Tween-20 para detectar ambas as proteínas de ligação a GTPase marcados. </li><li> Lava-se a membrana três vezes durante 10 min com PBS, 0,1% de Tween-20. </li><li> Incubar a membrana durante 30 minutos à temperatura ambiente em 800 DyLight-seg conjugado anti-coelhoanticorpo secundá-, diluído a 1 / 10.000 em tampão de bloqueio diluído em PBS 1x, 0,1% de Tween-20. </li><li> Lava-se a membrana três vezes durante 10 min com PBS, 0,1% de Tween-20. </li><li> Digitalizar a membrana usando um sistema de imageamento infravermelho, usando o software para medir a intensidade da banda de acordo com o protocolo do fabricante. </li><li> Traçar a intensidade da banda de cada proteína contra volume do concorrente variável (Proteína B). </li><li> Dividir o volume de competidor variável no ponto em que as linhas se cruzam pelo volume de competidor constante (Proteína A, 5 uL) para determinar a razão de competidor no qual é conseguido o equilíbrio. </li><li> Para a validação do estado de carregamento de nucleótidos, para membranas de sonda activada por p21 quinase 1 (PAK1) (um efector) e GFP-TrioD1 (um GEF), conforme descrito nas etapas 6.1-6.6. </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.

Este protocolo é concebido para calcular as afinidades relativas dos parceiros de ligação para Rac1, sem a necessidade de conhecer a concentração exacta dos concorrentes (Figura 1). Determinação da concentração de proteína e introduz erros quando se considera a concorrência entre moléculas de uma via de sinalização não é necessária. No entanto, é importante saber que os dois competidores têm a mesma concentração molar das soluções de reserva para permitir proporções simples para ser calculada ao adicionar diferentes volumes de ensaio. 40 ul de contas de GFP-Armadilha têm uma capacidade de ligação de ~ 300 pmol de modo confluente 75 centímetros 2 frascos de altamente células que expressam irá saturar as contas, com o resultado que os preparativos das duas proteínas de ligação diferentes será semelhante antes do ajuste (Figura 2A). Se uma das proteínas fracamente expressa, este problema pode ser superado através da purificação de proteínas a partir de que mais de um frasco de células. <p claSS = &quot;jove_content&quot;&gt; A ligação da maioria dos efectores reguladores de GTPase e depende do nucleótido-carregamento da GTPase isca, de modo que é importante para testar se o carregamento tem sido bem sucedida. Carregando pode ser verificada por meio de precipitação de proteínas de ligação a partir de lisados ​​de células conhecidas. Proteínas efectoras, tais como PAK1 se ligam a GTP-Rac1 e pode ser facilmente precipitado a partir de lisados ​​e detectadas através de Western blotting 8 (Figura 2B). GEFs ligam-se preferencialmente ao nucleótido-livre GTPase para estabilizar o estado de transição. Como GEFs são de baixa abundância, normalmente inativo e freqüentemente apagar mal, é melhor para sobre-expressar uma GEF GEF ou fragmento de teste GTPase livre de nucleótido. Nós freqüentemente usam o primeiro homologia Dbl de Trio, expresso como uma fusão GFP (GFP-TrioD1 9) (Figura 2B), mas qualquer GEF iria funcionar. As proteínas que se ligam ao GTPase carregado-PIB são mais raros. Recentemente, relatou RCC2 como uma tal proteína 7, ou PIB-carregamento pode ser validado como simplesmente binding a GEF nem nem efectora. A saída a partir da experiência será uma mancha de Western que descreve os dois parceiros de ligação marcado com GFP ligados ao GTPase. Ao utilizar um único anticorpo para detectar ambas as proteínas, as concentrações em que quantidades similares de ambos os competidores se ligam podem ser determinados e, por conseguinte, as afinidades relativas inferida. Neste exemplo, a competição entre o domínio de hélice da proteína Rac1 de tráfico, coronin-1C (Rac1 de ligação de proteína A), e a proteína Rac1-sequestrante, RCC2 (Rac1 proteína de ligação B), é demonstrada (Figura 3A). Usando um volume constante de hélice coronin-1C (5 mL), e adicionando volumes crescentes de RCC2, podemos ver a partir da GFP blot que o equilíbrio é alcançado em 1,25-2,5 l de RCC2 (asterisco), demonstrando que tem um forte RCC2 afinidade para Rac1 que coronin-1C. Ao medir a intensidade das bandas utilizando transferência de Western quantitativa, e traçando os valores médios para cada competitoR, o ponto de equilíbrio pode ser calculada com precisão, identificando os volumes em que as curvas cruzam (Figura 3B). Um dos possíveis obstáculos a um ensaio de competição é bem sucedido se os parceiros de ligação se ligam uns aos outros, bem como a ligação a Rac1. Na Figura 3A + B demonstramos concorrência entre RCC2 eo domínio hélice de coronin-1C, em vez de full-length coronin-1C. A razão para o uso do coronin truncado que é coronin-1C, também se liga RCC2 através do domínio da cauda. Quando full-length coronin-1C é titulada contra RCC2, a ligação de ambas as proteínas for detectada, devido à formação de complexo ternário, em detrimento da concorrência (Figura 3C). Se a concorrência está ocorrendo, a ligação de uma proteína irá aumentar, enquanto o outro diminui, e total ligada GFP-fusão permanecerá constante. Nos casos em que um complexo ternário forma que é necessário para truncar uma das proteínas de ligação de modo a que a GTPase competitors não interagem. <img alt="figura 1" src="/files/ftp_upload/53254/53254fig1.jpg" /> Figura 1. Fluxo de Trabalho. Representação esquemática do fluxo de trabalho para determinar a afinidade de proteínas de ligação GTPase usando ensaios de competição. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig1large.jpg" target="_blank">Por favor clique aqui para ver uma versão maior desta figura.</a> <img alt="Figura 2" src="/files/ftp_upload/53254/53254fig2.jpg" /> Figura 2. Validação de proteínas purificadas. (A) purificada Rac1 proteínas analisadas por Western blot de ligação, sondagem com anti-GFP para determinar o rendimento relativo das duas proteínas GFP. Este tipo de equalização durante a experiência permite que a concentração das duas proteínas de ser ajustada de modo a que eles correspondem na experiência de ligação. (B) GDP, GTPyS e não carregado de nucleotídeo GST-Rac1 foi incubado com ligado de HEK293T expressando GFP-TrioD1 e proteínas detectadas por conspirar para PAK1 endógena ou overexpressed GFP-TrioD1 obrigado. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig2large.jpg" target="_blank">Por favor clique aqui para ver uma versão maior desta figura.</a> <img alt="Figura 3" src="/files/ftp_upload/53254/53254fig3.jpg" /> Figura 3. Análise de Western blot de proteínas em relação vinculativa. Saídas Exemplo de ensaios de ligação da concorrência. (A) GDP-carregado Rac1 foi misturado com 5 jul GFP-coronin-1C domínio hélice e volumes crescentes de GFP-RCC2 foram titulados. Por proteínas ligadas Western blotting para GFP, problemas com a detecção diferencial das duas proteínas são evitados e o sinal GFP relata a proporção molar entre as duas proteínas de fusão. Os asteriscos indicam as relações de concorrência no eithelado r do ponto de equilíbrio. (B) intensidades das bandas de proteínas de fusão GFP encadernados de três experimentos independentes foram medidos por Western blot quantitativa, utilizando anticorpos e médias secundárias fluoróforos conspiraram para calcular a quantidade de RCC2 necessário para alcançar o equilíbrio. (C ) Exemplo de saída a partir de uma experiência em que as proteínas de ligação a Rac1 ligar uma à outra e formam um complexo ternário, em vez de competir. Rac1 foi misturado com 5 jul GFP-RCC2 e volumes crescentes de GFP-coronin-1C full-length carregado PIB foram titulados. O aumento no limite GFP-coronin-1C sem perda de limite GFP-RCC2 indica a formação do complexo ternário. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig3large.jpg" target="_blank">Por favor, clique aqui para ver uma versão maior desta figura.</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.

Comparando-se a afinidade de proteínas de ligação utilizando ensaios de competição de GTPase

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

9.2K visualizações.  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.

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

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating these studies, reincorporation of detergent-solubilized membrane proteins into liposomes is a stochastic process where protein topology is impossible to enforce. This paper offers an alternative method to these challenging techniques that utilizes a liposome-based scaffold. Protein solubility is enhanced by deletion of the transmembrane domain, and these amino acids are replaced with a tethering moiety, such as a His-tag. This tether interacts with an anchoring group (Ni2+ coordinated by nitrilotriacetic acid (NTA(Ni2+)) for His-tagged proteins), which enforces a uniform protein topology at the surface of the liposome. An example is presented wherein the interaction between Dynamin-related protein 1 (Drp1) with an integral membrane protein, Mitochondrial Fission Factor (Mff), was investigated using this scaffold liposome method. In this work, we have demonstrated the ability of Mff to efficiently recruit soluble Drp1 to the surface of liposomes, which stimulated its GTPase activity. Moreover, Drp1 was able to tubulate the Mff-decorated lipid template in the presence of specific lipids. This example demonstrates the effectiveness of scaffold liposomes using structural and functional assays and highlights the role of Mff in regulating Drp1 activity.

Using Scaffold Liposomes to Reconstitute Lipid-proximal Protein-protein Interactions In Vitro

This paper describes a method for assessing the interactions and assemblies of integral membrane proteins in vitro with various partner factors in a lipid-proximal environment.

Usando andaime lipossomas para reconstituir interações proteína-proteína Lipid-proximal<em&gt; In Vitro</em

Studies of integral membrane proteins in vitro are frequently complicated by the presence of a hydrophobic transmembrane domain. Further complicating ...

Bioquímica

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.

Medição da sinalização do receptor acoplado à proteína G via ligação GTP marcada com rádio

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

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.

Medir a ligação da proteína à actina F por co-sedimentação

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

Biotinylated Cell-penetrating Peptides to Study Intracellular Protein-protein Interactions

Here we present a protocol to study intracellular protein-protein interactions that is based on the widely used biotin-avidin pull-down system. The modification presented includes the combination of this technique with cell-penetrating sequences. We propose to design cell-penetrating baits that can be incubated with living cells instead of cell lysates and therefore the interactions found will reflect those that occur within the intracellular context. Connexin43 (Cx43), a protein that forms gap junction channels and hemichannels is down-regulated in high-grade gliomas. The Cx43 region comprising amino acids 266-283 is responsible for the inhibition of the oncogenic activity of c-Src in glioma cells. Here we use TAT as the cell-penetrating sequence, biotin as the pull-down tag and the region of Cx43 comprised between amino acids 266-283 as the target to find intracellular interactions in the hard-to-transfect human glioma stem cells. One of the limitations of the proposed method is that the molecule used as bait could fail to fold properly and, consequently, the interactions found could not be associated with the effect. However, this method can be especially interesting for the interactions involved in signal transduction pathways because they are usually carried out by intrinsically disordered regions and, therefore, they do not require an ordered folding. In addition, one of the advantages of the proposed method is that the relevance of each residue on the interaction can be easily studied. This is a modular system; therefore, other cell-penetrating sequences, other tags, and other intracellular targets can be employed. Finally, the scope of this protocol is far beyond protein-protein interaction because this system can be applied to other bioactive cargoes such as RNA sequences, nanoparticles, viruses or any molecule that can be transduced with cell-penetrating sequences and fused to pull-down tags to study their intracellular mechanism of action.

This is a protocol to study intracellular protein-protein interactions based on the biotin-avidin pull-down system with the novelty of combining cell-penetrating sequences. The main advantage is that the target sequence is incubated with living cells instead of cell lysates and therefore the interactions will occur within the cellular context.

Peptídeos biotinylated célula-penetrante para estudar interações da proteína-proteína intracelular

Here we present a protocol to study intracellular protein-protein interactions that is based on the widely used biotin-avidin pull-down system. The ...

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.

Deteção de pequena GTPase Prenilação e GTP ligação usando o fracionamento de membrana e ensaio de imunoabsorção ligada de GTPase

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.

Uma adaptação semi-high-throughput do ensaio ATPase NADH-acoplado para a seleção de inibidores pequenos da molécula

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.

Interrogatório paralelo de β-Arrestin2 Recrutamento para Triagem de Ligand em escala GPCR usando ensaio PRESTO-Tango

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 Assay Activation GTPase

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

Biologia

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.

Afinidade Precipitação do Active Rho-GEFs Usando um GST-marcado Mutant proteína Rho (GST-RhoA (G17A)) a partir de lisados ​​de células epiteliais

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

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.

Determinação de interacções proteína-ligante Usando Differential Scanning Fluorimetria

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

Comparando-se a afinidade de proteínas de ligação utilizando ensaios de competição de GTPase

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