Name: probing high-density functional protein microarrays to detect protein-protein interactions
Uploaded: 2015-08-02T12:00:00.000+00:00
Duration: 8 min 7 s
Description: Watch this Scientific Journal Video about Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions at JoVE.com

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 Vorbereitung <ol><li> Kultur und Reinigung der V5-Fusionskinase-Sonden verwendet werden, um Wechselwirkungen mit anderen Proteinen zu untersuchen, wie folgt: <ol><li> Verwenden Sie frisch ausgestrichenen Hefestamm Y258 (MATa pep4-3, his4-580, ura3-53, leu2-3,112), die V5-Fusionsprotein (von GATEWAY Vektor pYES-DEST52 ausgedrückt). Verwenden Sie das isolierte Protein als Sonde für die Mikroarrays. Platte die Hefe auf synthetischem Komplett-Uracil (SC-Ura) / 2% Dextrose / Agar und wachsen bei 30 ° C für 3 Tage aus gefrorenen Kultur (-80 ° C Glycerolstammlösung). </li><li> Impfen Starterkulturen (5-20 ml) aus einer Einzelkolonie und über Nacht wachsen in Sc-Ura / 2% Dextrose auf Schüttelplattform (220-250 rpm) oder Rad bei 30 ° C. </li><li> Am folgenden Morgen inokulieren 400 ml des Sc-Ura / 2% Raffinose Kultur mit ausreichend Starterkultur auf eine endgültige OD 600 von 0,1. </li><li> Wachsen die Impfkulturen bis zu einer OD 600 von 0,6, gefolgt von Galactose-Induktion des V5-Kinase-fusion Konstrukt-Expression durch Zugabe einer Lösung von 3x Hefeextrakt / Pepton (YEP) mit 6% Galactose ergänzt durch Zugabe von genug, um das Induktionsmittel durch einen Faktor von 3 zu verdünnen, so dass die endgültige Konzentration der Galactose beträgt 2%. </li><li> Induzieren Zellen bei 30 ° C für 6 Stunden auf eine schwankende Plattform. Verwenden Sie einen 2 l-Erlenmeyerkolben, angemessene Belüftung sicherzustellen. </li><li> Ernten der Zellen unter Verwendung eines JA-10 (oder vergleichbaren) Rotors durch Drehen mit 400 ml Zellsuspension bei 1.000 g für 5 min bei 4 ° C. </li><li> Mit 50 ml eiskaltem PBS-Puffer und in einen 50-ml konischen Röhrchen Waschen der Zellen einmal. Dann wird noch einmal das Pellet in eiskaltem PBS-Puffer (ohne Reinigungsmittel oder andere Additive) für die Lyse und Transfer zum 2 verwendet ml Röhrchen für die Lyse-Kappe einrasten. </li><li> Drehen Sie die Zellen bei 20.000 · g für 1 min bei 4 ° C zu einem Pellet und Pipette entfernt Puffer. </li><li> Zeigen Röhrchen auf Eis und füllen Lyseschritt. </li><li> Lyse der Zellen (250-350 ul Pellet) mit 00,5 mm Zirkoniumoxidkügelchen in einer 1: 1: 1 Volumen des Zellpellets, Perlen und phosphatgepufferter Kochsalzlösung (PBS) Lysepuffer und Wirbel das Gemisch unter Verwendung eines Bewegungsplattform 3 mal in 2 min Intervallen bei 4 ° C. </li><li> Zentrifugieren Sie das Lysat bei 20.000 × g in einer Tischmikrozentrifuge für 10 min bei 4 ° C. </li><li> Pipette Stand in Polycarbonat Hochgeschwindigkeitszentrifugenröhrchen und Klärung durch ulracentrufugation für 30 Minuten bei 150.000 × g bei 4 ° C. </li><li> Übertragen die geklärte Lysat in ein Röhrchen vorgewaschen Ni 2+ Affinitätsharz (~ 100 &amp; mgr; l) und Inkubieren auf einem Nutator für 2 h bei 4 ° C zu erfassen Histidin (His) 6X markierten V5-Fusionsprotein ist. </li><li> Dreimal Waschen des Harzes für 10 Minuten bei 4 ° C mit Waschpuffer. Pelletierung des Harzes unter Verwendung einer Tisch-Zentrifuge 5 min bei 1000 × g bei 4 ° C und saugt den Überstand. In frischem Waschpuffer für jeden Wasch und senden Sie das Rohr Nutatorwinkel für Agitation während der Wäsche. </li><li> Nach dem Wasch steps abgeschlossen sind, wenden die gewaschene Harz in ein frisches G-25-Säule für die Elution. </li><li> Gelten 25 ul Elutionspuffer in einer schrittartigen Weise, beginnend mit 100 mM Imidazol und 500 mM Imidazol in 50 mM Inkremente für insgesamt 9 Fraktionen. </li><li> Assay Die gesammelten Fraktionen mittels Natriumdodecylsulfat-Polyacrylamidgelelektrophorese (SDS-PAGE) und Coomassie-Färbung, um die am stärksten angereicherten Fraktion (en) zur Verwendung in dem Assay zu identifizieren und fügen Glycerin zu 30% und bei -80 ° C bis in den verwendeten Assay. </li></ol></li></ol> 2. Beobachtung der Arrays HINWEIS: Bitte beachten Sie Schritt 2.6 dieses Abschnitts, um die Antikörperlösung vor dem Test vorzubereiten. <ol><li> Um Wechselwirkungen zu erfassen, verdünnen das V5-Fluorophor konjugierten Antikörper (dh AlexaFluor 647) bis 260 ng / ml in Sondenpuffer und mischen durch Schütteln. HINWEIS: Bereiten Sie dieses Antikörperlösung 30 Minuten vor der Anwendung und legen Sie den Schlauch auf einem nutatoder oder ein Rad vollständige Vermischung und eine homogene Suspension von Antikörper zu gewährleisten. </li><li> Verdünne die V5-Fusionsprotein Sonde über einen Konzentrationsbereich von 5-500 &amp; mgr; g / ml. HINWEIS: Optimiert für jedes Protein-Protein-Interaktionsassays, mit Sondenpuffer. Optimierung beinhaltet das Hinzufügen von mehr Sonden an Puffer zu sondieren. Typischerweise 10 &amp; mgr; g / ml wird als Ausgangspunkt verwendet und angepasst basierend auf der Signalstärke. </li><li> Entfernen der Proteinarrays aus dem Tiefkühler (-20 ° C) und bringen auf 4 ° C im Kühlraum unmittelbar vor der Verwendung. </li><li> In Blocking-Puffer direkt auf die Objektträgerhalter, die die Protein micorarrays und decken den Spitzen mit Parafilm, um ein Auslaufen zu verhindern. Blockieren die Arrays in Blockierungspuffer für 1 Stunde unter Schütteln bei 50 UpM auf einer Stufe bei 4 ° C. </li><li> Nach dem Blockieren übertragen die Arrays einer befeuchteten Kammer auf 4 ° C gekühlt, und geben 90 ul der verdünnten Probe direkt auf der Array-Oberfläche. Überlagern die arrays mit einem erhöhten Schlupf Heber und Inkubation statisch (ohne Schütteln) in der feuchten Kammer bei 4 ° C für 1,5 Std. </li><li> 3 mal in drei 50 ml konische Röhrchen waschen die Arrays für jeweils 1 min in Puffer Sonde. Fügen Sie die Folie, um konische Röhrchen, die genug vorgekühlte Sondenpuffer, um die Folie vollständig umhüllen. Lassen Sie den Lifter Schlupf sanft abrutschen des Proteinmikroarray (keine Gewalt aus, da dies zu Schäden an der Array-Oberfläche zur Folge haben). </li><li> Übernehmen Sie die Antikörper-Lösung direkt auf Array sofort nach Abschluss des Wasch (Schritt 2.5) und Überlagerung mit einem erhöhten Heber Schlupf wie zuvor. Die Arrays 30 min Inkubation bei 4 ° C in der feuchten Kammer. </li><li> Führen die gleiche Waschschritt wie zuvor (3 mal 1 min in Puffer Sonde) und Spin in einem 50 ml konischen Röhrchen bei 800 x g in einer Tischzentrifuge 5 min bei Raumtemperatur. Der Luft trocknen die Arrays in einem Objektträgerhalter in der Dunkelheit für 30 Minuten vor der Anordnung bei 647 nm gescannt. </li></ol>

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The authors declare that they have no competing financial interests.

Das Protokoll vorgestellt wurde ursprünglich unter Verwendung von 85 einzigartigen Hefe-Proteinkinase-V5-Fusionsproteinen die Bindungsaktivität gegenüber verschiedenen und verwandte Familien von Hefe-Proteinkinasen, was zur Identifizierung von neuen Kinase-Interaktionsnetz in vivo 1 zu vergleichen. Als aufstrebender Proteom-Profiling-Technologie, die Entwicklung von High Throughput (HTP) Screening der Proteome mit Protein-Microarrays auf Peptidbibliotheken und eukaryotischen und prokaryotischen Mo...

Die Notwendigkeit, die globale Analysen der Proteinbiochemie und Bindungsaktivität in vivo durchzuführen in der Entwicklung neuer Verfahren zum Profilieren von Protein-Protein-Wechselwirkungen (PPI) und die post-translationalen Modifikationen von ganzen Proteomen 1,3-8 geführt. Protein-Mikroarrays werden als funktionelle Protein-Microarrays mit voller Länge funktionelle Proteine ​​4-6,8,9 oder analytische Protein-Microarrays 10,11 Antikörper enthält, hergestellt. Sie sind so konstruiert, um eine hohe Dichte von Proteinen auf Mikroskop-Objektträgern mit einer Vielzahl von Oberflächenchemie angeordnet enthalten, um eine Vielzahl von zum Leiten von weitreichenden biochemischen Analysen erforderlichen 12 Versuchsbedingungen zu erleichtern. Nitrocellulose und Aldehyd Oberflächenchemie für die chemische Anbindung durch Lysin oder Affinität Befestigungsmethoden, wie beispielsweise Nickel-Chelat-Objektträger zur Befestigung His-markierte Proteine ​​und Glutathion zur Affinitäts Befestigung unter anderem 13. </p&gt; Die Verwendung von funktionellen Protein-Mikroarrays, um Protein-Protein-Interaktionen zu detektieren erfordert den Zugriff auf einen hochwertigen funktionellen Proteinbibliothek 14. S. cerevisiae ist zugänglich Herstellung einer solchen Bibliothek durch die Paarung von hoher Kopienaffinitätsmarkierten Proteinkonstrukte mit Hochdurchsatz-chromatographischen Reinigung Techniken. Die überwiegende Mehrheit des Hefegenoms sequenziert wurde und fast die gesamte Proteoms kann aus einem high-copy-Plasmid zur Reinigung exprimiert und biochemischen Analysen 12. Sobald die Proteine ​​gewonnen und in 384-Well-Format angeordnet sind, werden sie auf einen Objektträger so dass für eine schnelle parallele multiparametrischer biochemische Analytik und Bioinformatik Abfrage 8,14-16 gedruckt. Protein-Mikroarrays für enzymatische Assays und Wechselwirkungen mit Proteinen, Lipiden, kleine Moleküle und Nukleinsäuren, unter vielen anderen Anwendungen eingesetzt. Die Zugänglichkeit von Proteinen auf der Oberfläche des ProteomsAnordnungen machen, sich auf andere Arten von analytischen Nachweis einschließlich Immunaffinitäts, Oberflächenplasmonresonanz, Fluoreszenz und viele andere Techniken. Außerdem ermöglicht sie die Feinsteuerung der experimentellen Bedingungen ab, wo es schwer, in vivo tun. Ziel dieses Protokolls ist es, die angemessene Verwendung der funktionellen Protein-Microarrays, um Protein-Protein Wechselwirkungen erkennen zu demonstrieren. Diese Anwendung ermöglicht die Hochdurchsatz parallel biochemische Analyse von Protein-Bindungsaktivitäten unter Verwendung eines hoch gereinigten Analyten (Protein) von Interesse. Ein C-terminal (carboxyterminalen) Markierte V5-Fusions-Köderprotein von Interesse aus einem high-copy-Plasmid in einem Hefestamm zur Proteinreinigung optimiert produziert. C-terminalen Markierungs sichergestellt, dass das Volllängen-Protein übersetzt worden ist. Das in dieser Studie verwendete Protein ist TDA1-V5-Fusionsprotein-Kinase, die mit gereinigtem Nickel-Affinitätsharz über eine His6X tag. Die TDA1-V5-Fusions Baut wird durch serielle Elution mit einem Imidazol-Gradienten, um die am stärksten angereicherten Fraktion für den Einsatz im Assay Eluieren gereinigt.

<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

Hochdichte funktionelle Protein-Microarrays ~ 4.200 rekombinanten Hefe Proteine ​​enthalten, werden für Kinase-Protein-Protein-Wechselwirkungen unter Verwendung eines affinitätsgereinigten Hefe Kinase-Fusionsproteins, enthaltend ein V5-Epitop-Tag zum Auslesen sucht. Gereinigte Kinase wird durch die Kultur eines Hefestammes für eine hohe Kopienproteinproduktion, der ein Plasmid enthält eine Kinase-V5-Fusionskonstrukt unter einem GAL induzierbarer Promotor optimiert erhalten. Die Hefe wird in restriktiven Medien mit einem neutralen Kohlenstoffquelle für 6 Stunden, gefolgt von der Induktion mit 2% Galactose gezüchtet. Anschließend wird die Kultur geerntet und Kinase unter Verwendung von Standard affinitätschromatographischen Methoden, eine hoch gereinigte Protein-Kinase für die Verwendung in Assays zu erhalten, gereinigt. Die gereinigte Kinase wird mit Kinase-Puffer auf einen geeigneten Bereich für den Test verdünnt, und die Protein-Mikroarrays werden vor der Hybridisierung mit dem Protein-Mikroarray blockiert. Nach der Hybridisierung werden die Arrays mit monoklonalen V5 ANTIB sondiertody um Proteine ​​durch die Kinase-V5-Protein gebunden zu identifizieren. Schließlich werden die Arrays mit einem Standard-Microarray-Scanner abgetastet und Daten für nachgelagerte Informatik Analyse 1,2 extrahiert, um ein hohes Vertrauen Reihe von Protein-Interaktionen für Downstream-Validierung in vivo zu bestimmen.

Das Protein-Protein-Wechselwirkung-Aktivität wurde mit einem Standard-Chip-Leser zu beurteilen, die TDA1-V5 Protein-Kinase-Fusionskonstrukt als Köderprotein gegen eine Hefe funktionelle Protein-Microarray, das etwa 4.200 einzigartige S. beobachtet cerevisiae GST-Fusionsproteinen. Weitere Abfrage mit der Genepix Software ergab eine Vielzahl von Bindungsereignissen unterschiedlicher Intensität. Die Affinität wurde aus dem abgestuften Intensität des von einem monoklonalen V5-Fluorophor-konjugierten A...

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

Verwendung von Protein-Mikroarrays enthält fast die gesamte S. cerevisiae Proteom ist für schnelle unvoreingenommene Abfragetausende von Protein-Protein-Wechselwirkungen in parallel sondiert. Dieses Verfahren kann für die Protein-Kleinmolekül, posttranslationale Modifikation und andere Assays mit hohem Durchsatz verwendet werden.

Probing hoher Dichte Funktionale Protein-Microarrays, um Protein-Protein Wechselwirkungen erkennen

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

Universidad de Cartagena UDEC

Research

JoVE Journal

Biology

8.0K Aufrufe.  Stanford University.  Verwendung von Protein-Mikroarrays enthält fast die gesamte S. cerevisiae Proteom ist für schnelle unvoreingenommene Abfragetausende von Protein-Protein-Wechselwirkungen in parallel sondiert. Dieses Verfahren kann für die Protein-Kleinmolekül, posttranslationale Modifikation und andere Assays mit hohem Durchsatz verwendet werden. 

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

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.

Extrazelluläre Protein-Microarray-Technologie für hohen Durchsatz-Erkennung von geringe Affinität-Rezeptor-Ligand-Wechselwirkungen

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

Forschung

Biochemie

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.

Komparativen Ansatz, um die Landschaft von Wirt-Pathogen-Protein-Protein-Wechselwirkungen charakterisieren

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

Immunologie und Infektion

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.

In-vivo-Detektion von Protein-Protein-Interaktionen auf Micro-gemusterten Oberflächen

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

Biologie

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.

Chemisch-Antikörper blockiert Microarray für Multiplex-High-Throughput-Profiling von spezifischen Protein-Glykosylierung bei 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 ...

Discovering Protein Interactions and Characterizing Protein Function Using HaloTag Technology

Research in proteomics has exploded in recent years with advances in mass spectrometry capabilities that have led to the characterization of numerous proteomes, including those from viruses, bacteria, and yeast.&#160; In comparison, analysis of the human proteome lags behind, partially due to the sheer number of proteins which must be studied, but also the complexity of networks and interactions these present. To specifically address the challenges of understanding the human proteome, we have developed HaloTag technology for protein isolation, particularly strong for isolation of multiprotein complexes and allowing more efficient capture of weak or transient interactions and/or proteins in low abundance. &#160;HaloTag is a genetically encoded protein fusion tag, designed for covalent, specific, and rapid immobilization or labelling of proteins with various ligands. Leveraging these properties, numerous applications for mammalian cells were developed to characterize protein function and here we present methodologies including: protein pull-downs used for discovery of novel interactions or functional assays, and cellular localization. We find significant advantages in the speed, specificity, and covalent capture of fusion proteins to surfaces for proteomic analysis as compared to other traditional non-covalent approaches. We demonstrate these and the broad utility of the technology using two important epigenetic proteins as examples, the human bromodomain protein BRD4, and histone deacetylase HDAC1.&#160; These examples demonstrate the power of this technology in enabling &#160;the discovery of novel interactions and characterizing cellular localization in eukaryotes, which will together further understanding of human functional proteomics. &#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;

HaloTag technology is a multifunctional technology which has shown significant success in isolation of both small and large protein complexes from mammalian cells.&#160; Here we highlight the advantages of this technology compared to existing alternatives and demonstrate its utility to study numerous aspects of protein function inside eukaryotic cells.

Die Entdeckung und Charakterisierung von Protein-Wechselwirkungen Protein-Funktion Mit HaloTag Technologie

Research in proteomics has exploded in recent years with advances in mass spectrometry capabilities that have led to the characterization of numerous ...

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.

Ermittlung von Protein-Protein-Interaktionsstellen unter Verwendung von Peptid-Arrays

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).

Genomweite Protein-Protein-Wechselwirkungen durch Screening Protein-Fragment Komplementierungsassay (PKA) in lebenden Zellen

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

Hochempfindliche Detektion der Compound-Protein-Bindung mittels Fluoreszenz

Detection of CD40 Protein-Umbelliferone Interaction via Differential Scanning Fluorescence

The investigation of interactions between different molecules is a crucial aspect of understanding disease pathogenesis and screening for drug targets. Umbelliferone, an active ingredient in Tibetan medicine Vicatia thibetica, exhibits an immunomodulatory effect with an unknown mechanism. The CD40 protein is a key target in the immune response. Therefore, this study employs the principle of differential scanning fluorescence technology to analyze the interactions between CD40 protein and umbelliferone using fluorescent enzyme markers. Initially, the stability of the protein fluorescent orange dye was experimentally verified, and the optimal dilution ratio of 1:500 was determined. Subsequently, it was observed that the temperature melting (Tm) value of CD40 protein tended to decrease with an increase in concentration. Interestingly, the interaction between CD40 protein and umbelliferone was found to enhance the thermal stability of CD40 protein. This study represents the first attempt to detect the binding potential of small molecule compounds and proteins using fluorescence microplates and fluorescent dyes. The technique is characterized by high sensitivity and accuracy, promising advancements in the fields of protein stability, protein structure, and protein-ligand interactions, thus facilitating further research and exploration.

Autor im Rampenlicht: Rationalisierung von PCR-Methoden für verbesserte Zugänglichkeit und Effizienz

This protocol describes a unique method for detecting the binding between compounds and protein molecules, offering the advantages of minimal protein sample loss and high data accuracy.

Nachweis der CD40-Protein-Umbelliferon-Wechselwirkung mittels dynamischer Differenzialfluoreszenz

The investigation of interactions between different molecules is a crucial aspect of understanding disease pathogenesis and screening for drug targets. ...

Probing hoher Dichte Funktionale Protein-Microarrays, um Protein-Protein Wechselwirkungen erkennen

Zusammenfassung

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Extrazelluläre Protein-Microarray-Technologie für hohen Durchsatz-Erkennung von geringe Affinität-Rezeptor-Ligand-Wechselwirkungen

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In-vivo-Detektion von Protein-Protein-Interaktionen auf Micro-gemusterten Oberflächen

Chemisch-Antikörper blockiert Microarray für Multiplex-High-Throughput-Profiling von spezifischen Protein-Glykosylierung bei Complex Samples

Die Entdeckung und Charakterisierung von Protein-Wechselwirkungen Protein-Funktion Mit HaloTag Technologie

Ermittlung von Protein-Protein-Interaktionsstellen unter Verwendung von Peptid-Arrays

Genomweite Protein-Protein-Wechselwirkungen durch Screening Protein-Fragment Komplementierungsassay (PKA) in lebenden Zellen

Nachweis der CD40-Protein-Umbelliferon-Wechselwirkung mittels dynamischer Differenzialfluoreszenz

Nachweis der CD40-Protein-Umbelliferon-Wechselwirkung mittels dynamischer Differenzialfluoreszenz

Nachweis der CD40-Protein-Umbelliferon-Wechselwirkung mittels dynamischer Differenzialfluoreszenz