This work was supported by a grant from the NIH. The assays shown in Figure 1 was performed by Dr. Joseph Fasolo. We thank Dr. Rui Chen for helpful comments.

1. Probe Hazırlık <ol><li> Kültür ve aşağıdaki gibi diğer proteinler ile etkileşimini incelemek için kullanılmıştır V5 füzyon kinaz probları saflaştırılması: <ol><li> Taze çizgili maya suşu Y258 kullanın (MATa pep4-3, his4-580, ura3-53, leu2-3,112) (GATEWAY vektör pYES-DEST52 ifade edilen) V5-füzyon proteini içeren. Mikrodiziler üzerinde prob olarak izole edilmiş proteini kullanın. Sentetik tam-urasil (Sc-Ura) /% 2 dekstroz / Agar maya Plate ve dondurulmuş kültürünün (-80 ° C gliserol stoku) 3 gün boyunca 30 ° C&#39;de büyütülmüştür. </li><li> Tek bir koloniden başlatıcı kültürleri (5.20 mi) aşılamak ve 30 ° C &#39;de platformun (220-250 rpm) veya tekerlek çalkalama SC-Ura /% 2 dekstroz içinde bir gece boyunca büyür. </li><li> Ertesi sabah, bir nihai OD 0.1 600 yeterli starter kültür ile Sc-Ura /% 2 rafinoz kültürünün 400 ml aşılamak. </li><li> 0.6 600 V5-kinaz fu galaktoz indüksiyon ardından OD inokulantlar büyütünyon şekilde galaktoz nihai konsantrasyonu,% 2, 3 kat endüksiyon ortamı seyreltilmesi için yeterli eklenerek,% 6 galaktoz ile takviye edilmiş 3x Maya Özü / Pepton (YEP) içindeki bir çözeltisi ilave edilerek ifade yapısı. </li><li> Bir çalkalama platformu üzerinde 6 saat boyunca 30 ° C&#39;de hücre neden. Uygun havalandırma sağlamak için 2 L Erlenmeyer şişesi kullanın. </li><li> 4 ° C&#39;de 5 dakika boyunca 1000 x g&#39;de hücre süspansiyonu 400 ml eğirme bir JA-10 (ya da eşdeğeri) bir rotor kullanılarak hasat hücreleri. </li><li> Buz, 50 ml soğuk PBS tamponu ve 50 ml konik tüp transferi ile bir kez hücreler yıkanır. Liziz tüpleri kapaklı ek ml 2 liziz ve transferi için kullanılan (deterjanlar veya diğer katkı maddeleri hariç), buz gibi soğuk PBS tamponu içinde yeniden pelet yıkayın. </li><li> Bir pelet ve bir pipet uzaklıkta tamponu, 4 ° C&#39;de 1 dakika boyunca 20,000 xg&#39;de hücreleri dönerler. </li><li> Buz üzerinde tüpler yerleştirin ve parçalama adımla devam edin. </li><li> Lyse hücreleri (250-350 ul pelet) 0 ile1: 1 .5 mm zirkonyum boncukları hücre peleti, taneler, ve fosfat tamponlu salin (PBS) içinde 1 hacim 4 ° C &#39;de 2 dakika aralıklarla tampon ve vorteks ajitasyon platformunu 3 kez kullanılarak karışımın lizis. </li><li> 4 ° C&#39;de 10 dakika boyunca masa üstü mikrofüj içinde 20,000 x g&#39;de santrifüjleyin lizat. </li><li> Pipet polikarbonat yüksek hızlı santrifüj tüpüne süpernatan ve 4 ° C&#39;de 150,000 x g&#39;de 30 dakika boyunca ulracentrufugation berrak hale getirilmelidir. </li><li> Histidin yakalamak için 4 ° C&#39;de 2 saat süreyle nutator önceden yıkanmış Ni2 + afinite reçinesi (~ 100 ul) ihtiva eden bir tüpe açıklık lizat aktarın ve inkübe (His) 6X V5-füzyon proteinini etiketli. </li><li> Yıkama Tamponu ile 4 ° C &#39;de 10 dakika süre ile, reçineyi üç defa yıkanır. 4 ° C&#39;de 1000 x g&#39;de 5 dakika boyunca masa üstü bir santrifüj kullanılarak reçine pelet ve süpernatan aspire. Her yıkama için taze yıkama tamponu ekleyin ve yıkama esnasında tüpü ajitasyon için Nutator döndürür. </li><li> Yıkama ste sonraps tamamlandı, elüsyon için yeni bir G-25 kolonuna yıkanır reçineyi uygulayın. </li><li> 9 fraksiyonların toplam 50 mm&#39;lik artışlarla 500 mM imidazol, 100 mM imidazol ile başlayan aşamalı bir şekilde elüsyon tamponu 25 ul uygulanır. </li><li> Sodyum dodesil sülfat poliakrilamid jel kullanılarak toplanan fraksiyonları deneyi (SDS-PAGE) ve deneyde kullanım için en fazla zenginleştirilmiş bölüm (ler) i tespit ve -80 ° C &#39;de% 30 ve saklamak için gliserol ekleyin Coomassie boyaması, kullanılıncaya kadar deneyi. </li></ol></li></ol> 2. Diziler Probing NOT: tahlili başlamadan önce antikor çözeltisi hazırlamak için bu bölümün aşamasını 2.6 bakınız. <ol><li> Etkileşimlerini tespit etmek için, numune tamponu içinde 260 ng / ml&#39;ye kadar V5-florofor konjuge antikor (örneğin, AlexaFluor 647) sulandırılır ve çalkalama ile iyice karıştırın. NOT: kullanımı ve nutat üzerine tüp yerleştirmek için 30 dakika kala bu antikor çözüm hazırlayında tekerlek tam karıştırma ve antikor homojen bir süspansiyon sağlamak. </li><li> 5-500 ug / ml&#39;lik bir konsantrasyon aralığı üzerinde V5-füzyon proteini probu ile seyreltilir. Not: Prob tamponu kullanılarak, her bir protein-protein etkileşimi deneyi için optimize edilmiştir. Optimizasyon tampon soruşturma daha sondalar ekleyerek içerir. Tipik olarak 10 ug / ml başlangıç ​​noktası olarak kullanılır ve sinyal gücüne göre uygun şekilde ayarlanır. </li><li> Dondurucu (-20 ° C), elde edilen protein mikrodizileri çıkarın ve kullanımdan hemen önce buzdolabında 4 ° C&#39;ye getir. </li><li> Sızmasını önlemek için parafilm ile üst protein micorarrays içeren slayt sahibine doğrudan engelleme tampon ekleyin ve kapsamaktadır. 4 ° C &#39;de bir sahne üzerinde 50 rpm&#39;de çalkalanarak 1 saat boyunca bloke edici tampon içinde dizileri bloke eder. </li><li> Bloke edildikten sonra, 4 ° C&#39;ye soğutulmuş, nemlendirilmiş bir odacıkta diziler transferi, doğrudan dizi yüzeye seyreltilmiş prob 90 ul ekle. Arr Yerleşimi1.5 saat boyunca 4 ° C&#39;de nemlendirilmiş bir haznede lekelenmiştir yükseltilmiş bir kaldırma kayma ays ve statik inkübe (bir çalkalama). </li><li> Üç 50 ml konik tüpler prob tamponunda 1 dakika her diziler 3 kere yıkayın. Tamamen slayt zarf yeterli önceden soğutulmuş prob tampon içeren konik tüplere slayt ekleyin. Kaldırıcı kayma yavaşça protein mikroarray (bu dizi yüzeyine zarar görmesine neden olabilir gibi onu zorlamayın) kapalı slayt izin verin. </li><li> Hemen önce olduğu gibi yükseltilmiş kaldırıcı kayma yıkama (adım 2.5) ve bindirme tamamladıktan sonra diziye doğrudan antikor çözümü uygulayın. Nemlendirilmiş bir odada 4 ° C&#39;de 30 dakika boyunca inkübe edin dizileri. </li><li> Oda sıcaklığında 5 dakika boyunca masa üstü santrifüjü içinde 800 xg&#39;de 50 ml konik bir tüp içinde, aynı yıkama (prob tampon maddesi içinde 3 kez 1 dakika) daha önce olduğu gibi adımı, ve spin gerçekleştirin. 647 nm dizi taramadan önce 30 dakika süreyle karanlıkta bir slayt tutucu dizileri Hava kurutun. </li></ol>

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The authors declare that they have no competing financial interests.

Protokol başlangıçta in vivo 1&#39;de yeni kinaz etkileşim ağlarının tanımlanmasında elde edilen maya protein kinazların farklı ve ilgili ailelerdeki bağlanma aktivitesini karşılaştırmak için 85 benzersiz bir maya protein kinaz-V5 füzyon proteinleri kullanılarak gerçekleştirildi kullanarak verilmiştir. Gelişmekte olan bir proteomik profilleme teknolojisi olarak, Yüksek Çıkan (SDP) peptid kütüphaneleri ve ökaryotik ve prokaryotik model organizmaların 8,17 dayan...

Protein biyokimya ve in vivo bağlanma faaliyeti küresel analizlerini gerçekleştirmek için gerek protein-protein etkileşimlerini (PPIs) ve bütün proteomlarda 1,3-8 arasında post-translasyonel modifikasyonlar profil için yeni yöntemlerin geliştirilmesine yol açmıştır. Protein mikrodizileri antikorları 10,11 ihtiva 4-6,8,9 tam uzunlukta fonksiyonel proteinleri kullanılarak fonksiyonel bir protein mikrodizilerinin veya analitik protein mikrodizilerinin olarak imal edilir. Bunlar 12 analiz, geniş kapsamlı biyokimyasal iletmek için gereken deney koşulları çeşitli kolaylaştırmak için yüzey kimyaları çeşitli mikroskop lamları üzerine dizilmiş, proteinlerin yüksek yoğunluklu içeren tasarlanmıştır. Bu tür diğerleri 13 arasında afinite eki için His-etiketli proteinler ve glutatyon takmak için nikel şelatlı slaytlar olarak lizin veya afinite eki yöntemleri ile kimyasal bağlanması için nitroselüloz ve aldehit yüzey kimyaları. </p&gt; protein-protein etkileşimleri tespit etmek için fonksiyonel protein mikrodizilerinin kullanımı yüksek kaliteli, fonksiyonel bir protein kitaplığına 14 erişim gerektirir. S. cerevisiae yüksek verimli kromatografik saflaştırma teknikleri protein takılı yapılar yüksek kopya afinitesi eşleştirme yoluyla bu tür bir kütüphane üretilmesi için müsait olan. Maya genomunun büyük bir çoğunluğu dizilenmiştir ve neredeyse tüm proteom saflaştırma için yüksek kopya plazmid eksprese edilebilir ve biyokimyasal 12 analiz eder. Proteinler elde edilir ve 384 oyuklu formatta dizilmiş sonra, bunlar, hızlı paralel çok parametre biyokimyasal analizler ve biyoinformatik sorgulama 8,14-16 sağlayan bir mikroskop lamı üzerine basılır. Protein mikrodizileri diğer birçok uygulamalar arasında proteinler, lipidler, küçük moleküller, ve nükleik asitler ile enzimatik deney ve etkileşimleri için kullanılmıştır. proteomun yüzeyi üzerinde proteinlerin erişilebilirlikdiziler de dahil olmak üzere, analitik tespiti farklı immün afinite onları müsait hale plazmon rezonansı, floresans ve pek çok başka teknik yüzeyler. Ayrıca, in vivo yapmak zor olabilir deneysel koşul ince kontrol sağlar. Bu protokolün amacı, protein-protein etkileşimleri tespit etmek için fonksiyonel protein mikrodizilerinin uygun kullanımını göstermektir. Bu uygulama, ilgi konusu bir yüksek ölçüde saflaştırılmış analiti (protein) kullanılarak protein bağlanma faaliyetleri, yüksek verimli, paralel biyokimyasal analiz sağlar. Bir C-terminali (ucu karboksi) ilgi V5-füzyon yem proteini, protein saflaştırma için optimize edilmiş bir maya suşunda bir yüksek kopya plazmid elde edilir etiketli. C-terminali etiketleme tam boyda bir protein çevrildi sağlar. Bu çalışmada kullanılan protein His6X etiketi ile nikel afinite reçinesi kullanılarak saflaştırılır Tda1-V5 füzyon protein kinaz vardır. Tda1-V5 füzyon konstrüksiyont tahlilinde kullanım için en fazla zenginleştirilmiş fraksiyonu elüt edilmesi için bir imidazol gradyanı kullanılarak, seri elüsyon yoluyla saflaştırılır.

<table><tbody><tr><td>Petri Dishes</td><td>VWR</td><td>NC-10747</td><td>or comparable</td></tr><tr><td>Bacto yeast extract</td><td>Difco</td><td>0217-17</td><td></td></tr><tr><td>Bacto peptone</td><td>Difco</td><td>0118-17</td><td></td></tr><tr><td>Bacto agar</td><td>Difco</td><td>0140-01</td><td></td></tr><tr><td>Dextrose</td><td>Sigma</td><td>D9434</td><td></td></tr><tr><td>Raffinose</td><td>Sigma</td><td>R0514</td><td></td></tr><tr><td>Galactose</td><td>Sigma</td><td>G0750</td><td></td></tr><tr><td>Sc-Ura drop out media</td><td>MP Bio</td><td>114410622</td><td></td></tr><tr><td>Small Culture tubes</td><td>VWR/Fisher</td><td></td><td></td></tr><tr><td>Large Erlenmeyer Flask</td><td>VWR/Fisher</td><td></td><td></td></tr><tr><td>Centrifuge JA-10 rotor</td><td></td><td></td><td></td></tr><tr><td>Centrifuge tubes (500 ml)</td><td></td><td></td><td></td></tr><tr><td>Falcon tube (50 ml)</td><td>VWR/Fisher</td><td>21008-951</td><td></td></tr><tr><td>PBS Tablets</td><td>Sigma</td><td>P4417</td><td></td></tr><tr><td>FastPrep Tubes (2 ml screw cap tube)</td><td></td><td></td><td></td></tr><tr><td>FastPrep Machine</td><td>MP Biomedicals</td><td>116004500</td><td></td></tr><tr><td>Zircon Beads</td><td>BioSpec</td><td>11079105</td><td></td></tr><tr><td>Triton X100</td><td>Sigma</td><td>P4417</td><td></td></tr><tr><td>DTT</td><td>Sigma</td><td>D9779</td><td></td></tr><tr><td>MgCl&lt;sub&gt;2&lt;/sub&gt;</td><td>Sigma</td><td>M8266&amp;nbsp;</td><td></td></tr><tr><td>NaCl</td><td>Sigma</td><td>S3014&amp;nbsp;</td><td></td></tr><tr><td>Imidazole (pH = 7.4)</td><td>Sigma</td><td>I5513&amp;nbsp;</td><td></td></tr><tr><td>PMSF</td><td>Sigma</td><td>93482</td><td></td></tr><tr><td>Complete Inhibitor Cocktail (EDTA Free)</td><td>Roche</td><td>11873580001</td><td></td></tr><tr><td>Phosphatase inhibitor cocktail 1</td><td>sigma</td><td>P2850</td><td></td></tr><tr><td>BSA</td><td>Sigma</td><td>A2153&amp;nbsp;</td><td></td></tr><tr><td>Tween-20</td><td>Sigma</td><td>P1379&amp;nbsp;</td><td></td></tr><tr><td>ATP</td><td>Sigma</td><td>A1852&amp;nbsp;</td><td></td></tr><tr><td>Shaking Incubator (30 &amp;deg;C)</td><td></td><td></td><td></td></tr><tr><td>Nickel Affinity Resin</td><td>Life Technologies</td><td>R901-01</td><td></td></tr><tr><td>G25 column</td><td>GE life sciences</td><td>27-5325-01&amp;nbsp;</td><td></td></tr><tr><td>Nutator</td><td>VWR/Fisher</td><td></td><td></td></tr><tr><td>SDS-PAGE Gel (NuPage)</td><td>Life Technologies</td><td></td><td></td></tr><tr><td>Coomassie Blue Stain</td><td>Life Technologies</td><td></td><td></td></tr><tr><td>Monoclonal V5 Antibody</td><td>Life Technologies</td><td>R960-25</td><td></td></tr><tr><td>Alexa647 Tagged monoclonal V5 Antibody</td><td>Life Technologies</td><td>451098</td><td></td></tr><tr><td>Protein Microarrays Kit</td><td>Life Technologies</td><td>PAH0525013</td><td></td></tr><tr><td>Genepix Scanner</td><td>Molecular Devices</td><td></td><td></td></tr><tr><td>Lifter Slips</td><td>Thomas Scientific</td><td></td><td>http://www.thomassci.com/Supplies/Microscope-Cover-Glass/_/LIFTER-SLIPS/</td></tr><tr><td>Lysis Buffer: 0.1% Triton X-100, 0.5 mM DTT,&lt;br/&gt; 2 mM MgCl&lt;sub&gt;2&lt;/sub&gt;, 500 mM NaCl, 50 mM imidazole (pH 7.4), Complete protease inhibitor cocktail &amp;ndash; EDTA-free, Phosphatase inhibitor Cocktail 1, 1 mM PMSF&amp;nbsp; (add just prior to use)</td><td></td><td></td><td>Add the reagents to 1x PBS (0.01 M phosphate buffer, 0.0027 M potassium chloride, 0.137 M sodium chloride; pH 7.4) to obtain the desired volume of lysis solution</td></tr><tr><td>Blocking Buffer: 1% bovine serum albumin (BSA), 0.1% Tween-20</td><td></td><td></td><td>Add the reagents to 1x PBS to obtain the desired volume of blocking buffer</td></tr><tr><td>Probe Buffer: 2 mM MgCl&lt;sub&gt;2&lt;/sub&gt;, 0.5 mM DTT, 0.05% Triton X-100, 50 mM NaCl, 500 &amp;mu;M ATP (for kinases), 1% BSA</td><td></td><td></td><td>Add the reagent to 1x PBS to obtain desired volume of probe buffer</td></tr><tr><td>Wash Buffer: 0.1% Triton X-100, 500 mM NaCl, 0.5 mM DTT, 50 mM imidazole (pH 7.4),2 mM MgCl&lt;sub&gt;2&lt;/sub&gt;</td><td></td><td></td><td>Add the reagent to 1x PBS to obtain desired volume of probe buffer</td></tr><tr><td>Elution Buffer: 0.1% Triton X-100, 0.5 mM DTT, 2 mM MgCl&lt;sub&gt;2&lt;/sub&gt;, 500 mM NaCl, 50 &amp;ndash; 500 mM imidazole (pH 7.4), Complete protease inhibitor cocktail &amp;ndash; EDTA-free, Phosphatase inhibitor Cocktail 1, 1 mM PMSF (add just prior to use)</td><td></td><td></td><td>Before you begin, it is important to note the concentration gradient of imidazole (50 &amp;ndash; 500 mM) and to create separate tubes for each concentration (it is advisable to create the interval using 50 mM increments). Add the reagent to 1x PBS to obtain desired volume of probe buffer</td></tr><tr><td>3x YEP +6% galactose: Dissolve 30 g of yeast extract and&amp;nbsp; 60 g of peptone in 700 ml of H2O, and autoclave. Add 300 ml of filter sterilized 20% galactose (wt/vol)</td><td></td><td></td><td>&amp;nbsp;Galactose should not be autoclaved</td></tr></tbody></table>

probing high-density functional protein microarrays to detect protein-protein interactions

~ 4200 rekombinant maya proteinleri içeren yüksek yoğunluklu fonksiyonel bir protein mikrodizileri okuması için V5-epitop etiketi ihtiva eden bir afinite saflaştınldı maya kinaz füzyon proteini kullanılarak kinaz, protein-protein etkileşimleri için incelenir. Saflaştırılmış kinaz bir kinaz-V5 füzyon GAL uyarımlı promotör altında yapıyı içeren bir plazmid yüksek kopya protein üretimi için optimize edilmiş bir maya suşu kültürü ile elde edilir. maya,% 2 galaktoz ile endüksiyon ile, ardından 6 saat boyunca nötr bir karbon kaynağı ile kısıtlayıcı ortamda yetiştirilir. Daha sonra, kültür hasat edilir ve kinaz deneyinde kullanılmak için yüksek ölçüde saflaştırılmış protein kinaz elde etmek üzere standart afinite kromatografik teknikleri kullanılarak saflaştırılır. Saflaştırılmış kinaz deneyi için uygun bir aralığı, kinaz tamponu ile seyreltilir ve protein mikro-dizileri, protein önce mikroarray ile hibridizasyon için bloke edilir. Hibritlemeden sonra, diziler monoklonal V5 antib ile sondalandıODY kinaz-V5 proteiniyle bağlanmış proteinleri belirlemek için. Son olarak, diziler, standart bir mikrodizi tarayıcısı kullanılarak tarandı ve veriler, in vivo aşağı doğru doğrulama için protein etkileşimleri belirlenen yüksek bir güven belirlemek için alt bilişim analiz 1,2 ekstre edilir.

Protein-protein etkileşimi aktivitesi Tda1-V5 protein kinaz füzyon yaklaşık 4,200 özgü S. ihtiva eden bir maya fonksiyonel bir protein mikrodizi karşı bir yem protein olarak inşa değerlendirmek için standart bir çipli okuyucu kullanılarak gözlenmiştir cerevisiae GST-füzyon proteinleri. GenePix yazılımı ile ayrıntılı sorgulama değişen şiddetlerde olayları bağlayıcı bir sürü gösterdi. afinite hedefine (V5-kinaz) bağlı bir monoklonal V5-Florofor konjuge antikor türetilen...

Watch this Scientific Journal Video about Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions at JoVE.com

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Neredeyse tüm S. içeren protein mikrodiziler kullanarak cerevisiae proteom paralel protein-protein etkileşimleri, binlerce hızlı tarafsız sorgulama için incelenir. Bu yöntem, protein-küçük molekül, translasyon sonrası modifikasyon ve yüksek verimlilik Diğer tahliller için kullanılabilecektir.

Yüksek yoğunluklu Fonksiyonel Protein mikrodizileri Probing Protein-protein Etkileşimleri Algılama

High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an ...

probing-high-density-functional-protein-microarrays-to-detect-protein

Research

JoVE Journal

Biology

8.0K Görüntüleme.  Stanford University.  Neredeyse tüm S. içeren protein mikrodiziler kullanarak cerevisiae proteom paralel protein-protein etkileşimleri, binlerce hızlı tarafsız sorgulama için incelenir. Bu yöntem, protein-küçük molekül, translasyon sonrası modifikasyon ve yüksek verimlilik Diğer tahliller için kullanılabilecektir. 

Video: Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological processes. Affinity purification coupled to mass spectrometry (AP-MS) has become the method of choice for identifying protein-protein interactions. However, conventional AP-MS studies provide information on protein interactions, but the organizational information is lost. To address this issue, we developed a strategy to unravel the distinct functional assemblies a protein might be involved in, by resolving affinity-purified protein complexes prior to their characterization by mass spectrometry. Protein complexes isolated through affinity purification of a bait protein using an epitope tag and competitive elution are separated through blue native electrophoresis. Comparison of protein migration profiles through correlation profiling using quantitative mass spectrometry allows assignment of interacting proteins to distinct molecular entities. This method is able to resolve protein complexes of close molecular weights that might not be resolved by traditional chromatographic techniques such as gel filtration. With little more work than conventional AP-geLC-MS/MS, we demonstrate this strategy may in many cases be adequate for obtaining protein complex topological information concomitantly to identifying protein interactions.

Here we present protocols for affinity purification of protein complexes and their separation by blue native PAGE, followed by protein correlation profiling using label free quantitative mass spectrometry. This method is useful to resolve interactomes into distinct protein complexes.

Mavi Yerli PAGE ve Protein İlişkisi Profil Yöntemi ile Affinity Saf protein Kompleksler çözümleniyor

Most proteins act in association with others; hence, it is crucial to characterize these functional units in order to fully understand biological ...

Biyokimya

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

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

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

Hücre dışı Protein Mikroarray teknoloji yüksek işlem hacmi düşük benzeşme reseptör-Ligand etkileşimleri algılanması için

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

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Significant efforts were gathered to generate large-scale comprehensive protein-protein interaction network maps. This is instrumental to understand the pathogen-host relationships and was essentially performed by genetic screenings in yeast two-hybrid systems. The recent improvement of protein-protein interaction detection by a Gaussia luciferase-based fragment complementation assay now offers the opportunity to develop integrative comparative interactomic approaches necessary to rigorously compare interaction profiles of proteins from different pathogen strain variants against a common set of cellular factors.
This paper specifically focuses on the utility of combining two orthogonal methods to generate protein-protein interaction datasets: yeast two-hybrid (Y2H) and a new assay, high-throughput Gaussia princeps protein complementation assay (HT-GPCA) performed in mammalian cells.
A large-scale identification of cellular partners of a pathogen protein is performed by mating-based yeast two-hybrid screenings of cDNA libraries using multiple pathogen strain variants. A subset of interacting partners selected on a high-confidence statistical scoring is further validated in mammalian cells for pair-wise interactions with the whole set of pathogen variants proteins using HT-GPCA. This combination of two complementary methods improves the robustness of the interaction dataset, and allows the performance of a stringent comparative interaction analysis. Such comparative interactomics constitute a reliable and powerful strategy to decipher any pathogen-host interplays.

This article focuses on the identification of high-confident interaction datasets between host and pathogen proteins using a combination of two orthogonal methods: yeast two-hybrid followed by a high-throughput interaction assay in mammalian cells called HT-GPCA.

Ana-Patojen protein-protein etkileşimleri ve Peyzaj karakterize etmek Karşılaştırmalı Bir Yaklaşım

Significant efforts were gathered to generate  large-scale comprehensive protein-protein interaction network maps. This is  instrumental to understand the ...

İmmünoloji ve Enfeksiyon

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic interactions among multiple proteins in a protein interaction network is technically difficult. Here, we present a protocol for Quantitative Multiplex Immunoprecipitation (QMI), which allows quantitative assessment of fold changes in protein interactions based on relative fluorescence measurements of Proteins in Shared Complexes detected by Exposed Surface epitopes (PiSCES). In QMI, protein complexes from cell lysates are immunoprecipitated onto microspheres, and then probed with a labeled antibody for a different protein in order to quantify the abundance of PiSCES. Immunoprecipitation antibodies are conjugated to different MagBead spectral regions, which allows a flow cytometer to differentiate multiple parallel immunoprecipitations and simultaneously quantify the amount of probe antibody associated with each. QMI does not require genetic tagging and can be performed using minimal biomaterial compared to other immunoprecipitation methods. QMI can be adapted for any defined group of interacting proteins, and has thus far been used to characterize signaling networks in T cells and neuronal glutamate synapses. Results have led to new hypothesis generation with potential diagnostic and therapeutic applications. This protocol includes instructions to perform QMI, from the initial antibody panel selection through to running assays and analyzing data. The initial assembly of a QMI assay involves screening antibodies to generate a panel, and empirically determining an appropriate lysis buffer. The subsequent reagent preparation includes covalently coupling immunoprecipitation antibodies to MagBeads, and biotinylating probe antibodies so they can be labeled by a streptavidin-conjugated fluorophore. To run the assay, lysate is mixed with MagBeads overnight, and then beads are divided and incubated with different probe antibodies, and then a fluorophore label, and read by flow cytometry. Two statistical tests are performed to identify PiSCES that differ significantly between experimental conditions, and results are visualized using heatmaps or node-edge diagrams.

Quantitative Multiplex Immunoprecipitation (QMI) uses flow cytometry for sensitive detection of differences in the abundance of targeted protein-protein interactions between two samples. QMI can be performed using a small amount of biomaterial, does not require genetically engineered tags, and can be adapted for any previously defined protein interaction network.

Multipleksed Co-İmmünopreyağış Kullanarak Protein Etkileşim Ağı Dinamiğinin Ölçülmesi

Dynamic protein-protein interactions control cellular behavior, from motility to DNA replication to signal transduction. However, monitoring dynamic ...

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

Unraveling the interaction network of molecules in-vivo is key to understanding the mechanisms that regulate cell function and metabolism. A multitude of methodological options for addressing molecular interactions in cells have been developed, but most of these methods suffer from being rather indirect and therefore hardly quantitative. On the contrary, a few high-end quantitative approaches were introduced, which however are difficult to extend to high throughput. To combine high throughput capabilities with the possibility to extract quantitative information, we recently developed a new concept for identifying protein-protein interactions (Schwarzenbacher et al., 2008). Here, we describe a detailed protocol for the design and the construction of this system which allows for analyzing interactions between a fluorophore-labeled protein ("prey") and a membrane protein ("bait") in-vivo. Cells are plated on micropatterned surfaces functionalized with antibodies against the bait exoplasmic domain. Bait-prey interactions are assayed via the redistribution of the fluorescent prey. The method is characterized by high sensitivity down to the level of single molecules, the capability to detect weak interactions, and high throughput capability, making it applicable as screening tool.

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

This video shows experiments with subsequent analysis of protein-protein interactions by the use of micro-patterned surfaces. The approach offers the possibility to detect protein interactions in living cells and combines high throughput capabilities with the possibility to extract quantitative information.

Mikro desenli Yüzeyler, protein-protein etkileşimleri-vivo Algılama

Unraveling the interaction network of molecules in-vivo is key to understanding the mechanisms that regulate cell function and metabolism. A multitude of ...

Biyoloji

Chemically-blocked Antibody Microarray for Multiplexed High-throughput Profiling of Specific Protein Glycosylation in Complex Samples

In this study, we describe an effective protocol for use in a multiplexed high-throughput antibody microarray with glycan binding protein detection that allows for the glycosylation profiling of specific proteins. Glycosylation of proteins is the most prevalent post-translational modification found on proteins, and leads diversified modifications of the physical, chemical, and biological properties of proteins. Because the glycosylation machinery is particularly susceptible to disease progression and malignant transformation, aberrant glycosylation has been recognized as early detection biomarkers for cancer and other diseases. However, current methods to study protein glycosylation typically are too complicated or expensive for use in most normal laboratory or clinical settings and a more practical method to study protein glycosylation is needed. The new protocol described in this study makes use of a chemically blocked antibody microarray with glycan-binding protein (GBP) detection and significantly reduces the time, cost, and lab equipment requirements needed to study protein glycosylation. In this method, multiple immobilized glycoprotein-specific antibodies are printed directly onto the microarray slides and the N-glycans on the antibodies are blocked. The blocked, immobilized glycoprotein-specific antibodies are able to capture and isolate glycoproteins from a complex sample that is applied directly onto the microarray slides. Glycan detection then can be performed by the application of biotinylated lectins and other GBPs to the microarray slide, while binding levels can be determined using Dylight 549-Streptavidin. Through the use of an antibody panel and probing with multiple biotinylated lectins, this method allows for an effective glycosylation profile of the different proteins found in a given human or animal sample to be developed.
Introduction
Glycosylation of protein, which is the most ubiquitous post-translational modification on proteins, modifies the physical, chemical, and biological properties of a protein, and plays a fundamental role in various biological processes1-6. Because the glycosylation machinery is particularly susceptible to disease progression and malignant transformation, aberrant glycosylation has been recognized as early detection biomarkers for cancer and other diseases 7-12. In fact, most current cancer biomarkers, such as the L3 fraction of &alpha;-1 fetoprotein (AFP) for hepatocellular carcinoma 13-15, and CA199 for pancreatic cancer 16, 17 are all aberrant glycan moieties on glycoproteins. However, methods to study protein glycosylation have been complicated, and not suitable for routine laboratory and clinical settings. Chen et al. has recently invented a chemically blocked antibody microarray with a glycan-binding protein (GBP) detection method for high-throughput and multiplexed profile glycosylation of native glycoproteins in a complex sample 18. In this affinity based microarray method, multiple immobilized glycoprotein-specific antibodies capture and isolate glycoproteins from the complex mixture directly on the microarray slide, and the glycans on each individual captured protein are measured by GBPs. Because all normal antibodies contain N-glycans which could be recognized by most GBPs, the critical step of this method is to chemically block the glycans on the antibodies from binding to GBP. In the procedure, the cis-diol groups of the glycans on the antibodies were first oxidized to aldehyde groups by using NaIO4 in sodium acetate buffer avoiding light. The aldehyde groups were then conjugated to the hydrazide group of a cross-linker, 4-(4-N-MaleimidoPhenyl)butyric acid Hydrazide HCl (MPBH), followed by the conjugation of a dipeptide, Cys-Gly, to the maleimide group of the MPBH. Thus, the cis-diol groups on glycans of antibodies were converted into bulky none hydroxyl groups, which hindered the lectins and other GBPs bindings to the capture antibodies. This blocking procedure makes the GBPs and lectins bind only to the glycans of captured proteins. After this chemically blocking, serum samples were incubated with the antibody microarray, followed by the glycans detection by using different biotinylated lectins and GBPs, and visualized with Cy3-streptavidin. The parallel use of an antibody panel and multiple lectin probing provides discrete glycosylation profiles of multiple proteins in a given sample 18-20. This method has been used successfully in multiple different labs 1, 7, 13, 19-31. However, stability of MPBH and Cys-Gly, complicated and extended procedure in this method affect the reproducibility, effectiveness and efficiency of the method. In this new protocol, we replaced both MPBH and Cys-Gly with one much more stable reagent glutamic acid hydrazide (Glu-hydrazide), which significantly improved the reproducibility of the method, simplified and shorten the whole procedure so that the it can be completed within one working day. In this new protocol, we describe the detailed procedure of the protocol which can be readily adopted by normal labs for routine protein glycosylation study and techniques which are necessary to obtain reproducible and repeatable results.

In this study, we describe an improved protocol for a multiplexed high-throughput antibody microarray with lectin detection method that can be used in glycosylation profiling of specific proteins. This protocol features new reliable reagents and significantly reduces the time, cost, and lab equipment requirements as compared to the previous procedure.

Kompleks Örnekleri spesifik protein Glikozilasyon arasında Multiplexed Yüksek verim Profilleme için Kimyasal-bloke Antikor Mikroarray

 In this study, we describe an effective protocol for use in a multiplexed high-throughput antibody microarray with glycan binding protein detection that ...

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants. Low affinity interactions can be preserved through the use of less-stringent buffer conditions and remain readily identifiable. This protocol discusses the labeling of tissue culture cells with stable isotope labeled amino acids, transfection and immunoprecipitation of an affinity tagged protein of interest, followed by the preparation for submission to a mass spectrometry facility. This protocol then discusses how to analyze and interpret the data returned from the mass spectrometer in order to identify cellular partners interacting with a protein of interest. As an example this technique is applied to identify proteins binding to the eukaryotic translation initiation factors: eIF4AI and eIF4AII.

SILAC immunoprecipitation experiments represent a powerful means for discovering novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants, and low affinity interactions preserved through use of less-stringent buffer conditions.

SILAC-immunoprecipitation Kantitatif PROTEOMİK kullanma Memeli Hücrelerde Protein Etkileşim Ortakların Kimlik

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel ...

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may result in disease, making protein interactions important drug targets. It is thus highly important to understand these interactions at the molecular level. Protein interactions are studied using a variety of techniques ranging from cellular and biochemical assays to quantitative biophysical assays, and these may be performed either with full-length proteins, with protein domains or with peptides. Peptides serve as excellent tools to study protein interactions since peptides can be easily synthesized and allow the focusing on specific interaction sites. Peptide arrays enable the identification of the interaction sites between two proteins as well as screening for peptides that bind the target protein for therapeutic purposes. They also allow high throughput SAR studies. For identification of binding sites, a typical peptide array usually contains partly overlapping 10-20 residues peptides derived from the full sequences of one or more partner proteins of the desired target protein. Screening the array for binding the target protein reveals the binding peptides, corresponding to the binding sites in the partner proteins, in an easy and fast method using only small amount of protein.
In this article we describe a protocol for screening peptide arrays for mapping the interaction sites between a target protein and its partners. The peptide array is designed based on the sequences of the partner proteins taking into account their secondary structures. The arrays used in this protocol were Celluspots arrays prepared by INTAVIS Bioanalytical Instruments. The array is blocked to prevent unspecific binding and then incubated with the studied protein. Detection using an antibody reveals the binding peptides corresponding to the specific interaction sites between the proteins.

Peptide array screening is a high throughput assay for identifying protein-protein interaction sites. This allows mapping multiple interactions of a target protein and can serve as a method for identifying sites for inhibitors that target a protein. Here we describe a protocol for screening and analyzing peptide arrays.

Peptit Diziler protein-protein etkileşim Siteleri belirlenmesi

Protein-protein interactions mediate most of the processes in the living cell and control homeostasis of the organism. Impaired protein interactions may ...

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Proteins are the building blocks, effectors and signal mediators of cellular processes. A protein&#8217;s function, regulation and localization often depend on its interactions with other proteins. Here, we describe a protocol for the yeast protein-fragment complementation assay (PCA), a powerful method to detect direct and proximal associations between proteins in living cells. The interaction between two proteins, each fused to a dihydrofolate reductase (DHFR) protein fragment, translates into growth of yeast strains in presence of the drug methotrexate (MTX). Differential fitness, resulting from different amounts of reconstituted DHFR enzyme, can be quantified on high-density colony arrays, allowing to differentiate interacting from non-interacting bait-prey pairs. The high-throughput protocol presented here is performed using a robotic platform that parallelizes mating of bait and prey strains carrying complementary DHFR-fragment fusion proteins and the survival assay on MTX. This protocol allows to systematically test for thousands of protein-protein interactions (PPIs) involving bait proteins of interest and offers several advantages over other PPI detection assays, including the study of proteins expressed from their endogenous promoters without the need for modifying protein localization and for the assembly of complex reporter constructs.

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Proteins interact with each other and these interactions determine in a large part their functions. Protein interaction partners can be identified at high-throughput in vivo using a yeast fitness assay based on the dihydrofolate reductase protein-fragment complementation assay (DHFR-PCA).

Yaşayan Hücrelerde Protein-fragmanı tamamlama Assay (PCA) ile genom Protein-protein etkileşimi Eleme

Proteins are the building blocks, effectors and signal mediators of cellular processes. A protein&#8217;s function, regulation and localization often ...

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism&#39;s survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide chain or string.
Various computational and biochemical methods are used to study protein interfaces. Laboratory methods, such as affinity purification, mass spectrometry, and protein microarrays, can be used to identify new interactions. Co-immunoprecipitation of proteins and yeast two-hybrid screening are widely used to provide evidence on whether two proteins interact in vitro.&#160; Computer programs can predict PPIs based on similar interactions found in other proteins by comparing protein sequences and three-dimensional structures. Other computational approaches, such as phylogenetic profiling, predict PPIs based on the coevolution of binding partners. Additionally, gene fusion analysis is used to predict interaction partners by finding protein pairs that are fused in the genome of other organisms.&#160;
Proteins typically interact with multiple partners either at the same or different times, and they may contain more than one interaction interface.&#160; Many proteins form large complexes that perform specific functions that can only be carried out by the complete complex. In some cases, these protein interactions are regulated; that is, a protein may interact with different partners based on cellular needs. Further computational and statistical analyses sort such interactions into networks, which are curated in online interactome databases. These searchable databases enable users to study specific protein interactions, as well as design drugs that can enhance or disrupt interactions at the interface.

Protein Complexes and Protein-Protein Interactions

Protein-protein Arayüzleri

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism&#39;s survival. Most PPIs ...