Name: comparing the affinity of gtpase-binding proteins using competition assays
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This work was supported by Wellcome Trust grant 088419 to MDB.

GST etiketli GTPaz 1. Saflaştırma <ol><li> Kültür, bir E. örneğin 220 rpm&#39;de çalkalanarak 37 ° C&#39;de pGEX-Rac1 O / N ile transforme BL21 gibi E. coli soyundan, autoinduction ortam 500 ml (25 mM Na-2 HPO 4, 25 mM KH 2 PO 4, 50 mM NH4CI, 5 SO 4 mM Na 2, 2 mM MgSO 4, 2 mM CaCl2,% 0.5 gliserol,% 0.05 Glukoz,% 0.2 laktoz, 5 g tripton, 2.5 g maya ekstresi, 100 ug / ml Ampisilin). </li><li> 10.000 x g&#39;de, 4 ° C&#39;de 10 dakika için santrifüjleme ile hasat bakteri. </li><li> 20 ml protein ekstre edici reaktif, 1 x proteaz inhibitörü bakteriyel pelet yeniden süspanse edin ve inversiyon ile oda sıcaklığında 20 dakika inkübe edilir. </li><li> 30 dakika boyunca 40.000 x g&#39;de santrifüjleme ile lizat açıklığa kavuşturulması. </li><li> Fosfat tamponlu tuz ile yıkandı, 2 ml glutasyon manyetik boncuklar, ekleme (PBS: 10 mM Na-2 HPO 4, 1.8 mM KH 2 PO 4, 137 mM NaCI, 2.7 mM KCI). </li><li> 4 ° C&#39;de ters çevirme ile karıştırılması, 2 saat süre ile inkübe edilir. </li><li> Her adımda boncuk çökelmesi için bir manyetik parçacık ayırıcıyla, 10 mi, PBS ile protein yüklü boncuk dört kez yıkayın. </li><li> Gerekli olana kadar yeniden süspanse 100 ul alikotları -80 ° C &#39;de 2 ml PBS içinde boncuk ve mağaza protein yüklü. </li></ol> GTPaz bağlama proteinlerinin ekspresyonu 2. <ol><li> Şöyle gün önce deney, yeşil flüoresan proteini (GFP) kodlayan transfekte plazmidler HEK293T ayrı bir 75-cm 2 şişe içine, her GTPaz bağlayıcı proteinin sürümlerini etiketli. Nükleotid yükleme doğrulama için, transfect HEK293T üçüncü 75 cm 2 balona TrioD1 GFP etiketli. <ol><li> 100 ul içinde 1 mg / ml steril 150 mM NaCl polyethylamine seyreltin. </li><li> 223 ul azaltılmış serum medya 27 ul seyreltilmiş polyethylamine ekleyin. </li><li> 250 ul düşük serum ortamı 12 ug plazmit DNA ekleyin. </li><li> Oda sıcaklığında 2 dakika için her bir tüp inkübe edin. </li&gt; <li> Polyethylamine birleştirin ve DNA 2 dakika boyunca tek bir tüp ve vorteks karıştırır. </li><li> Oda sıcaklığında 15-20 dakika kuluçkalayın. </li><li> 5 ml taze büyütme ortamı ile% 90 konfluent HEK293T üzerindeki büyüme ortamı (Dulbecco Modified Eagle Ortam,% 10 fetal bovin serumu, 2 mM L-glutamin, antibiyotikler herhangi bir) değiştirin. </li><li> Şişeye Birleştirilen polyethylamine / DNA karışımı ekleyin ve 37 ° C&#39;de,% 5 CO2 O / N inkübe edin. </li></ol></li></ol> GTPaz bağlama proteinlerinin saflaştırılması 3. <ol><li> PBS içinde transfekte edilmiş hücrelerin şişeler durulayın ve serbest sıvı aspire, 5 dakika boyunca balon boşaltın. </li><li> 500 ul liziz tamponu içinde hücrelerini Scrape (50 mM Tris-HCl (pH 7.8),% 1 Nonidet P-40, 1 x proteaz inhibitörü) mikrofüj tüpüne. </li><li> 30 dakika boyunca 4 ° C &#39;de ters çevirme ile karıştırılarak Hücreleri,. </li><li> Liziz sırasında yıkamalar arasında 2 dakika boyunca 2700 x g&#39;de 40 ul GFP-Trap boncuklar iki çok taze lizis tamponu ile üç kez, çöktürülmesi, boncuk yıkama. </li><li> 10 dakika boyunca 21.000 x g&#39;de santrifüjleme ile lizatları açıklığa kavuşturulması. </li><li> Aktarım 4 ° C de ters çevirme ile karıştırılması, yıkandı, GFP-trap boncuk ayrılması ve GFP-füzyon proteinleri, 2 saat boyunca bağlamasına izin vermek için rakip proteinin her birinin lizat açıklık. Buz üzerinde GFP-TrioD1 hücrelerinden lizat tutun. </li><li> 50 mM Tris-HCl (pH 7.8), 50 mM NaCI içinde iki kez yüklü GFP-Trap boncuk yıkayın,% 0.7 (w / v) Nonidet P-40 ve iki kez de 50 mM Tris-HCI (pH 7.6) içinde, 20 mM MgCl2 , yıkamalar arasında 2 dakika boyunca 2700 x g&#39;de boncuk çökeltildi. </li><li> 40 ul 0.2 M glisin (pH 2.5) ilave etmek ve 30 saniye süreyle aşağı ve yukarı pipetlenerek GFP füzyon proteinlerini Zehir. 4 ul 1 M Tris-HCl (pH 10.4) içeren yeni bir mikro santrifüj tüpüne 21.000 60 s için xg ve transfer sıvısının hemen tortu boncuklar. Saflaştırılmış protein zarar sınırlamak için hızla yapın. </li><li> Kantitatif Blott kullanarak göreceli verim kurmak için, bir anti-GFP antikor ile Western blot ve sonda her bir saflaştırılmış protein 1 ul analizüreticinin protokolüne uygun olarak sistemi olarak konumlandırılır. Seçenek olarak ise, bisinkoninik asit (BCA) deneyi ile protein konsantrasyonlarını belirlemek ancak proteinler, özdeş bir tarzda tahlil ile reaksiyona girmeyen ya da kirletici proteinler vardır, bu hatalar ortaya çıkarır. </li><li> 50 mM Tris-HCI (pH 7.6), 20 mM MgCl2 ilave edilerek mol protein konsantrasyonu dengeleyin. </li></ol> GTPaz 4. nükleotid yükleme <ol><li> Aşama 1 &#39;de hazırlanan GST-Rac1 manyetik boncuk, bir kısım çözülme. </li><li> Her adımda boncuk çökelmesi için bir manyetik parçacık ayırıcıyla GST-Rac1 boncuk 90 ul alın ve 20 mM Tris-HCl (pH 7.6), 25 mM NaCI, 0.1 mM DTT, 4 mM EDTA ile üç kez yıkayın. </li><li> Aspire boncuklardan tamponu ve 100 ul 20 mM Tris-HCl (pH 7.6), 25 mM NaCI, 0.1 mM DTT, 4 mM EDTA ekleyin. </li><li> GDP, GTP veya nükleotid yükleme rekabet deneyinde için gerekli olup olmadığını göre, 12 ul 100 mM GDP, 12 ul 10 mM gu eklemeanosine 5 &#39;- [γ-tiyo] trifosfat (GTP yS) ya da 60 ul GST-Rac1 boncuklar için bir nükleotid. </li><li> Nükleotid yükleme kontrolleri, üç 10-ul kısma kalan boncuk bölünmüş ve 2 ul 100 mM GSYİH, 2 ul 10 mM GTPtS veya her tüpe hiçbir nükleotid ekleyin. </li><li> Çalkalama ile 30 ° C &#39;de 30 dakika boyunca damla karışımları inkübe edin. </li><li> Deney karışımı 3 ul (aşama 4,4), kontrol karışımları (adım 4.5) her bir 0.5 ul: 1 M MgCl2 ilave edilerek nükleotid bağlı Rac1 stabilize. </li></ol> Bağlama 5. Rekabet. <ol><li> 6 mikrofüj tüpleri kurmak, her biri: 200 ul 50 mM Tris-HCl (pH 7.6), 20 mM MgCl2 (Aşama 4,7), 10 ul deney nükleotid yüklü Rac1 boncuklar 5 ul Rac1 bağlayıcı protein A (sabit bağlayıcı protein) </li><li> Her bir tüpe, 0, 1, 2.5, 5, 10 veya 20 ul Rac1 bağlayıcı protein B (değişken bağlayıcı protein) ekleyin. Bu birimler bir varsayıyorumpproximately eşit hisse sabit ve değişken bağlama proteinleri konsantrasyonları ve ayarlanması gerekebilir. <ol><li> Orada iki proteinin bağlama yakınlıkları büyük farklılıklar vardır ve bu deneysel tekrarlar yoluyla ampirik olarak tespit edilmelidir eğer bağlayıcı proteinler A hacimleri ve B ayarlayın. 50 mM Tris-HCI (pH 7.6), 20 mM MgCl2 ilave edilerek 235 ul bağlanma karışımın toplam hacmini hazırlayın. </li></ol></li><li> Içeren bir mikrofuge&#39;de tüp ayarlayın: 200 ul 50 mM Tris-HCl (pH 7.6), 20 mM MgCl2 (Aşama 4,7), 10 ul deney nükleotid yüklü Rac1 boncuklar 10 ul Rac1 bağlayıcı protein A (sabit bağlayıcı protein) </li><li> GSYİH, GTPtS ve hiçbir nükleotid kontrol tüpleri ayarlayın: 200 ul 50 mM Tris-HCl (pH 7.6), 20 mM MgCl2 10 ul kontrol Rac1 boncuk GSYİH, GTPtS veya nükleotid ile adım 4.5 yüklü ve adım 4.7 stabilize. 180 ul HAşama 3.6 gibi hazırlanmıştır EK293T GFP-TrioD1 lizatı, 4 ul 1 M MgCI2 </li><li> 4 ° C&#39;de ters çevirme ile karıştırılması, 2 saat süre ile inkübe karışımı. </li><li> 50 mM Tris-HCI (pH 7.6), 20 mM MgCl2 ile boncuk üç kez yıkayın. </li><li> Elute indirgeyici örnek tamponu 20 ul bağlı proteinleri (50 mM Tris-HCI (pH 7),% 5 SDS,% 20 gliserol, 0.02 mg / ml bromofenol mavi,% 5 β-merkaptoetanol). </li></ol> Yarışmanın 6. Analizi <ol><li> Sodyum dodesil sülfat poliakrilamid jel elektroforezi (SDS-PAGE) ve Western blot ile bağlı protein (aşama 5,6) 10 ul giderin. </li><li> 4 ° CO de membran inkübe / N anti-GFP antikorda Bloklama Tamponu içinde 1/1000 oranında seyreltilmiş PBS&#39;de 1x seyreltilmiş,% 0.1 Tween-20 isim levhası GTPaz bağlama proteinlerinin her ikisi de tespit etmek. </li><li> PBS ile 10 dakika,% 0.1 Tween-20, membran üç kez yıkayın. </li><li> 800 konjuge edilmiş anti-tavşan sek DyLight içinde oda sıcaklığında 30 dakika boyunca zarın inkübesekonder antikor Bloklama Tamponunda 1 / 10,000 seyreltilen,% 0.1 Tween-20, PBS içinde 1 x seyreltilmiştir. </li><li> PBS ile 10 dakika,% 0.1 Tween-20, membran üç kez yıkayın. </li><li> Üreticinin protokolüne göre, bant yoğunluğu ölçmek için yazılımını kullanarak, kızılötesi görüntüleme sistemi kullanılarak zar tarama. </li><li> Değişken rakip (Protein B) birim karşı her proteinin bant yoğunluğunu çiziniz. </li><li> Çizgiler, denge elde edildiği rakip oranının saptanması için sabit bir rakip (Protein A, 5 ul) hacimce kesiştiği noktada değişken yarışmacının hacmi bölün. </li><li> Adımda 6,1-6,6 tarif edildiği gibi p21-aktive edilmiş kinaz 1 (PAK1) (bir efektör) ve GFP-TrioD1 (GEF), nükleotid yükleme durumu, prob membran geçerli olabilmesi için. </li></ol>

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Yazarlar ifşa hiçbir şey yok.

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.

Bu protokol, rakip hassas konsantrasyonunu bilinmesi gereken (Şekil 1) olmadan Rac1 için bağlayıcı ortaklar nispi afiniteler hesaplamak için tasarlanmıştır. Protein konsantrasyonunun saptanması hatalar oluşturan bir sinyal yolunun, moleküller arasındaki rekabeti söz konusu olduğunda gerekli değildir. Ancak, iki yarışmacı tahlil farklı hacimleri eklerken basit oranları hesaplandı izin vermek için stok solüsyonları aynı molar konsantrasyona sahip olduğunu bilmek önemlidir. GFP-Trap boncuk 40 ul 300 pmol yani birleşik 75 cm yüksek iki farklı bağlama proteinleri preparatları düzenlenmesinden önce benzer olacaktır ve bunun sonucunda, boncuk doyuracak olan ifade eden hücrelerin 2 şişeler ~ bir bağlama kapasitesine sahip (Şekil 2A). Proteinlerin bir zor ifade ederse, bu sorun, hücrelerin birden çok şişeden bu proteinin saflaştırılması ile aşılabilir. <p class = &quot;jove_content&quot;&gt; en GTPaz efektörlerinin ve düzenleyici bağlanma yem GTPaz nükleotid yükleme bağlıdır, bu yüzden yük başarılı olup olmadığını test etmek için önemlidir. Yükleme hücresi lizatları bilinen bağlanma proteinleri çökeltme ile doğrulanabilir. Örneğin GTP Rac1 ve PAK1 bağ olarak efektör proteinler kolayca lizatları çökeltildi ve Western blot 8 (Şekil 2B) ile tespit edilebilir. Geçiş durumunu stabilize etmek GTPaz ücretsiz nükleotid tercihen bağlamak GEFS. GEFS genellikle inaktif düşük bolluk, vardır ve sık sık kötü leke gibi, deney nükleotid serbest GTPaz bir GEF veya GEF fragmanı aşın daha iyidir. Biz sık sık Trio&#39;nun ilk İKO benzerlik kullanmak, bir GFP füzyon (GFP-TrioD1 9) (Şekil 2B) olarak ifade ancak herhangi GEF çalışmaya devam eder. GSYİH yüklü GTPaz bağlanan proteinler nadirdir. Bindi basitçe valide edilebilir böyle bir protein 7 veya GSYİH yükleme gibi Biz son zamanlarda RCC2 bildirdiNe GEF&#39;ten de efektör ng. Deney çıkış GTPaz bağlanan iki GFP etiketli bağlama partnerleri gösteren bir Western blot olacaktır. Her iki proteini tespit etmek için, tek bir antikor kullanarak, her iki rakip içindeki miktarlarda bağlanan hangi konsantrasyonları belirlenebilir ve bu nedenle göreceli afıniteleri anlaşılmaktadır. Rac1 kaçakçılığı protein pervane etki alanı arasındaki bu örnek yarışmada, Koronin-1C (protein A Rac1-bağlama) ve Rac1-ayırıcı protein, RCC2 (protein B Rac1-bağlama), (Şekil 3A) gösterilmiştir. Koronin-1C pervane (5 ul) sabit bir hacim kullanılarak ve RCC2 artan miktarlarda ekleyerek, RCC2 güçlü olduğunu gösteren, GFP arasından bu denge RCC2 (yıldız) 1,25-2,5 ul ulaşılır leke görebilir Koronin-1C daha Rac1 için afinite. Her competito için ortalama değerler kantitatif Batı lekelenmesi kullanılarak bantların yoğunluğunu ölçen ve komplo iler, denge noktası hacimleri hangi eğrileri (Şekil 3B) kesişir belirleyerek doğru hesaplanabilir. Bağlanma eşleri birbirine olarak Rac1 bağlanma ile bağlanması halinde başarılı bir rekabet deneyinde mümkün engellerden biri. Şekil 3A + B biz oldukça tam uzunlukta Koronin-1C daha RCC2 ve Koronin-1C pervane etki alanı arasındaki rekabeti, gösterir. Kesik Koronin kullanılmasının nedeni Koronin-1C, aynı zamanda kuyruk alanı üzerinden RCC2 bağlanması anlamına gelir. Tam uzunlukta Koronin-1C RCC2 karşı titre edildiğinde, her iki proteinin bağlanması nedeniyle üçlü kompleks oluşumu yerine rekabet (Şekil 3C) için tespit edilir. Yarışma oluşup ise, bir proteininin diğer düşüşler olurken artacak ve toplam bağlı GFP-füzyon sabit kalacaktır. Durumlarda üçlü bir kompleksi, GTPaz bağlayıcı proteinin bir kesecek için gerekli olan formları burada böylece competitors artık etkileşim. <img alt="figür 1" src="/files/ftp_upload/53254/53254fig1.jpg" /> Şekil 1. İş Akışı. Yarışma analizleri kullanılarak GTPaz-bağlayıcı proteinlerin afinite belirlemek için iş akışı şematik. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig1large.jpg" target="_blank">Bu rakamın büyük halini görmek için lütfen buraya tıklayınız.</a> <img alt="Şekil 2," src="/files/ftp_upload/53254/53254fig2.jpg" /> Saflaştırılmış proteinlerin Şekil 2. Doğrulama. (A) saflaştınldı GFP etiketli iki proteinin nispi verimi belirlemek için, anti-GFP ile sondalama Western blot ile analiz bağlayıcı proteinlerin Rac1. Deney sırasında dengeleme Bu tür da bağlanma deneyinde eşleşecek şekilde iki protein konsantrasyonu ayarlanmasına olanak tanır. (B) GDP, GTPtS ve hiçbir nükleotid yüklü GST-Rac1 endojen PAK1 veya aşırı GFP-TrioD1 için komplo tespit proteinleri GFP-TrioD1 ifade HEK293T gelen lizat ile inkübe ve bağlıydı. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig2large.jpg" target="_blank">Bu rakamın büyük halini görmek için lütfen buraya tıklayınız.</a> <img alt="Şekil 3," src="/files/ftp_upload/53254/53254fig3.jpg" /> Görece protein Şekil 3. Western Blot analizi ile yapışma. Örnek çıktıları yarışması bağlayıcı tahlillerinden. (A) Rac1 5 ul GFP Koronin-1C pervaneli alanı ile karıştırılmış ve titre edildi GFP-RCC2, gittikçe artan miktarlarda edildi GDP-yüklendi. Tarafından GFP için Western blotting bağlanmış proteinler, iki proteinin diferansiyel tayinle belirlenmesine ile ilgili sorunlar önlenir ve GFP sinyali iki füzyon proteinleri arasındaki molar oranı bildirir. Yıldız eithe rekabet oranlarını gösterirdenge noktasının r tarafında. (B), üç bağımsız deneyin ilişkili bağlantı GFP füzyon proteinlerinin Bant yoğunlukları, dengeye ulaşmak için gerekli olan fluorofor-konjuge sekonder antikor ve ortalamalar RCC2 miktarını hesaplamak için çizilen kullanılarak niceliksel Western blot ile ölçüldü. (Cı Rac1 bağlayıcı proteinler rekabet etmek yerine birbirine bağlanan ve üçlü bir kompleks oluşturur bir deney) Örnek çıktı. GDP-yüklü Rac1 5 ul GFP RCC2 ile karıştırıldı ve GFP-Koronin-1C tam boyda, gittikçe artan miktarlarda edildi titre edilmiştir. Bağlanmış GFP Koronin-1C&#39;de artış bağlanmış GFP RCC2 kaybı olmadan üçlü kompleks oluşumunu gösterir. <a href="https://www.jove.com/files/ftp_upload/53254/53254fig3large.jpg" target="_blank">Lütfen Bu rakamın büyük halini görmek için buraya tıklayın.</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.

Rekabet tahlilleri kullanılarak GTPaz bağlayıcı proteinlerin afinitesini

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 Görüntüleme.  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.

Video: 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.

Radyo-etiketli GTP Bağlanması vasıtasıyla G-protein ile birleşmiş Reseptör Sinyalizasyonunun Ölçümü

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

Biyokimya

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.

Ko-çöktürme yoluyla F-aktine Bağlı Proteinin Ölçülmesi

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.

Küçük GTPazlar prenilasyon ve bağlayıcı kullanarak membran ayırma ve GTPazlar bağlı Immunosorbent Assay GTP tespiti

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.

Küçük Molekül Inhibitörlerinin Taranması için NADH-Coupled ATPase Tsay'ın Yarı-Yüksek İş-İşLenme Adaptasyonu

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.

Β-Arrestin2 Ligand Tarama için PRESTO-Tango Tetkik ini Kullanarak GPCR-Geniş Ölçekte İşe Alımın Paralel Sorgulaması

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 GTPaz Etkinleştirme Testi

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

Biyoloji

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.

Epitel Hücre lizatları bir GST-etiketli Mutant Rho Protein (GST-RhoA (G17A)) Kullanarak Active Rho-gefs ve Affinity Yağış

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).

Bir floresan bazlı Kalsiyum Mobilizasyon Deneyi G proteini ile birleştirilmiş alıcıların karakterizasyonu

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.

Diferansiyel Taramalı florimetri Kullanarak Protein-ligand Etkileşimleri belirlenmesi

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).