Cette recherche a été soutenue par des subventions de la Deutsche Forschungsgemeinschaft GraKo1121, Hu1011/2-1 et SFB940 à SH

Remarque: Les informations détaillées concernant les tampons indiquées dans le protocole est disponible dans le tableau 1. Une. Fixation des interactions protéine-protéine par formaldéhyde réticulation dans les cellules vivantes <ol><li> Pour commencer la préparation des milieux de culture, solutions mères et de tampon P1 <ol><li> Préparer 500 ml de milieu: Le milieu doit offrir des conditions qui favorisent l&#39;interaction entre les protéines membranaires de protéines appâts et proies. En outre, une expérience doit être réalisée dans des conditions où l&#39;on prévoit aucune interaction (par exemple, sans réticulation). Note: Nous comparons les interactions protéine-protéine dans des bactéries stressées et non stressées. Par conséquent, on prépare 500 ml de milieu Luria Bertani (LB) (tableau 1) que nous sommes complémentaires avec un agent inducteur de stress (par exemple NaCl 0,5 M) dans un ballon d&#39;Erlenmeyer de 2 litres. Pour le contrôle, nous utilisons milieu LB normale avec 0,17 M de NaCl (pH 7,0). </li><li> Préparer du tampon Tris (20 mM Tris-HCl, pH 8,0) et 0,1 M d&#39;acide éthylènediaminetétra-acétique (EDTA), pH 8,0, solution mère (Tableau 1). </li><li> Préparer tampon P1. Dissoudre le saccharose à une concentration finale de 0,5 M dans du tampon Tris. Stériliser tampon P1 par filtration et stocker à 4 ° C. </li></ol></li><li> Cultiver des cellules exprimant la protéine appât de la membrane avec une Strep-tag fusion C-terminale à partir d&#39;un vecteur. Induire l&#39;expression de protéines d&#39;appât de la membrane pendant une durée suffisante. Note: on induit l&#39;expression de protéines d&#39;appât de la membrane bactérienne lors de la phase précoce-log (A 600 = 0,3) par addition de 250 ul de 1 M d&#39;isopropyl-β-D-thiogalactopyranoside (IPTG) à 500 ml de milieu (concentration finale: 0,5 mM) . Afin de permettre une expression suffisante, l&#39;incubation de la bactérie jusqu&#39;à la phase logarithmique tardive (A 600 = 1,2). </li><li> Préparer pour chaque culture deux béchers de centrifugation d&#39;un volume minimum de 300 ml chacun et de les placer sur la glace. </li><li> Effectuer formaldéhyde réticulation. CAUTION: Le formaldéhyde est hautement toxique Nous recommandons de travailler sous une hotte de sécurité.. <ol><li> Transférer le récipient de culture sous une hotte de sécurité. Diviser chaque échantillon en deux échantillons, l&#39;un en omettant de réticulation (- X) et y compris le formaldéhyde une réticulation (+ X). Ajouter une solution de 4 ml de formaldéhyde à 37% à 250 ml de la culture pour parvenir à une concentration finale de 0,6%. </li></ol></li><li> Transférer les récipients de culture en arrière et cultiver des cellules pour 20 minutes supplémentaires comme avant. </li><li> Remplissez vos cultures dans les tubes de centrifugation sous une hotte de sécurité. Recueillir les cellules par centrifugation à 3000 xg pendant 30 min. </li><li> Rejeter le surnageant par pipetage avec précaution sous une hotte de sécurité. Recueillir toxique surnageant contenant du formaldéhyde et jetez-la. </li><li> Afin d&#39;atteindre un rendement optimal lors de la préparation de protéine membranaire, de préparer d&#39;abord des sphéroplastes. Ici, nous fournissons un protocole pour la formation de sphéroplastes de bactéries à Gram négatif: <ol><li> Prepare tampon P2 (tableau 1) à partir de poudre lyophilisée. Dissoudre doucement 2 mg de lysozyme dans 0,1 M d&#39;EDTA, pH 8, dans un tube de 1,5 ml. Toujours préparer fraîchement tampon P2 pour le jour de l&#39;expérience. </li><li> Préparer le tampon Tris avec un inhibiteur de la protéase (P3 tampon). A 10 ml de Tris-tampon, ajouter 0,1 ml de 1 M de fluorure de phénylméthylsulfonyle (PMSF) (tableau 1) à une concentration finale de 10 mM. Utiliser le tampon immédiatement, afin d&#39;assurer le bon fonctionnement de PMSF comme inhibiteur de protéase. </li><li> culots cellulaires d&#39;Remettre en suspension dans 10 ml de Tris-tampon avec un inhibiteur de protéase et de la solution de transfert à un tube conique de 15 ml. </li><li> Ajouter 1 ml de tampon P2 et incuber sur de la glace pendant 30 min. </li><li> Recueillir sphéroplastes par centrifugation à 3000 g pendant 30 min et éliminer le surnageant avec précaution. </li></ol></li><li> Incuber les pastilles de sphéroplastes pendant une nuit à -20 ° C. </li></ol> 2. Purification de Strep-tag Membrane Protein (Bait) <ol><li> Placez sphéroplaste pastille sur la glace. &lt;/ Li&gt; <li> Pendant le temps des pastilles de sphéroplaste dégel sur la glace, préparer 10 ml de tampon P3 pour chaque préparation sphéroplaste. Dissoudre délicatement 1 mg DNaseI dans 10 ml de Tris-tampon. Ajouter 0,1 ml de 1 M de PMSF juste avant utilisation. </li><li> Reprendre le culot dans 6 ml de P3 fraîchement préparé. Soniquer l&#39;échantillon quatre fois pendant 1 min en continu sur de la glace avec 1 min de pause entre chaque rafale, afin de perturber les sphéroplastes. </li><li> Centrifuger l&#39;échantillon à 10 000 xg pendant 10 minutes à des débris de cellules de la récolte. Transférer le surnageant à l&#39;aide d&#39;une pipette dans un tube d&#39;ultracentrifugation. </li><li> Sédimenter la fraction membranaire à 100 000 xg pendant 30 min. Laver le culot avec soin dans du tampon Tris sans dissolvant. Sécher le tube avec un mouchoir en papier (par exemple Kleenex). Ne pas perturber le culot, à tout moment. </li><li> Reprendre le culot (= membranes) avec précaution 1 ml de Tris-tampon. Utiliser une fraction aliquote de 20 ul de déterminer la concentration en protéine par dosage BCA par exemple. À cette étape, les membranes peuvent être congelés dans un choc lichique azote et conservés à -80 ° C. </li></ol> 3. Purification de Strep-tag Membrane Protein Bait et SDS-PAGE <ol><li> Normaliser la concentration en protéines de la fraction membranaire à 5 mg / ml avec du tampon Tris. Prendre 2,5 ml fraction de membrane (5 mg / ml) dans un tube d&#39;ultracentrifugation et ajouter 0,25 ml de 20% de Triton X-100 pour atteindre une concentration finale de 2%, afin de solubiliser les protéines membranaires. Ajouter une tige micro-magnétique et remuer sur de la glace pendant 1 heure. Remarque: Bien que, en général, nous avons de bons résultats en utilisant du Triton X-100 comme détergent, il peut être utile de modifier le détergent pour l&#39;optimisation. A cet égard, il faut obtenir les meilleurs résultats avec les détergents utilisés pour la purification de la protéine fonctionnelle de l&#39;appât de la membrane respective. </li><li> Tout en exécutant l&#39;étape 3.1, de préparer 50 ml de tampon B et 5 ml de tampon E (tableau 1). Remplir 10 ml 5x tampon W concentré à 50 ml et ajouter 150 ul 20% de Triton X-100. <ol><li> Remplir 1 ml 5x Buffer E concentré à 10 ml et ajouter 30 ul de 20% de Triton X-100. Equilibrer une colonne de débit 1 ml Strep-Tactin superflow gravité avec 8 ml de tampon W. Remarque: il est essentiel d&#39;ajouter le détergent utilisé pour la solubilisation dans un facteur 10 de la concentration au-dessus de la concentration micellaire critique (cmc) dans tout le tampon au cours de la procédure de purification. </li></ol></li><li> Retirer la tige de micro-magnétique à partir de l&#39;échantillon de solubilisation et par ultracentrifugation à 100000 g pendant 30 min, pour obtenir un culot de la fraction membranaire insoluble. Retirer le surnageant avec une pipette pour une purification supplémentaire. </li><li> Charger le surnageant à la colonne. Exécutez la colonne uniquement avec écoulement par gravité. Laver la colonne avec 5 ml de tampon W. Répétez cette étape de lavage 5x. </li><li> Éluer protéines appâts de la membrane avec 1 ml de tampon E. Répétez cette étape d&#39;élution 4x. </li><li> Concentrer les fractions d&#39;élution 2, 3, et 4 à 300 ul avec une unité de filtre centrifuge. </li><li> Mélanger 200 ul de chaque échantillon avec 50 pi 5x SDS-PAGE colorant de chargement. Fendez chaque préparation dans 125 aliquotes. Faire bouillir une fraction aliquote de chaque préparation pendant 20 min à 95 ° C, pour inverser formaldéhyde liaisons transversales. Laissez refroidir les échantillons à la température ambiante pendant au moins 10 min au-dessus de banc. </li><li> Charge: 30 ul de chaque échantillon à une seule voie d&#39;un gel de polyacrylamide-adapté à un immunotransfert. Utilisez un marqueur Prestained de poids moléculaire pour une meilleure orientation et exécuter SDS-PAGE 10. </li></ol> 4. Analyse par immunoblot pour confirmer interaction Partenaires <ol><li> Une fois l&#39;étape 3.8 est terminée, protéines de transfert sur ​​une membrane de nitrocellulose par exemple demi-sec. </li><li> Bloquer la membrane pour éviter l&#39;étiquetage imprécis. Préparer le tampon de blocage en pesant le sérum-albumine bovine (BSA) pour atteindre 3% en poids par volume dans une solution saline tamponnée au Tris supplémenté avec une concentration finale de 0,05% de Tween-20 (TBS-T). Utiliser un volume suffisant de tampon de blocage pour couvrir la membrane. Bloquer la membrane pendant 1 heure à température ambiante. </li><li> Diluer unend incuber le premier anticorps spécifique de la protéine proie comme d&#39;habitude. Utilisation d&#39;un anticorps HRP-lié en tant que second anticorps. </li><li> Développer l&#39;immunoblot en utilisant un kit de détection de chimioluminescence avec une grande sensibilité. Surveiller le signal en utilisant une procédure de traitement de film classique ou de l&#39;équipement d&#39;imagerie numérique. </li></ol> 5. NanoLC-ESI-MS/MS haute résolution expériences pour repérer interaction Partenaires <ol><li> Dans le cas où aucun anticorps spécifique est disponible pour la protéine proie ou partenaires d&#39;interaction inconnus doivent être identifiés, utiliser la spectrométrie de masse (MS) pour l&#39;identification. Afin d&#39;empêcher la contamination de la kératine, en utilisant des gels precasted pour la séparation des protéines. </li><li> Coloration à l&#39;argent du SDS-PAGE en utilisant un kit de coloration MS-compatible selon le protocole du fabricant. Effectuez toutes les étapes de lavage et coloration dans les réservoirs de verre. </li><li> Accise bandes respectives et analyser ceux-ci en haute résolution LC / MS 9. </li></ol>

<ol>
	<li>Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predicting+transmembrane+protein+topology+with+a+hidden+markov+model:+application+to+complete+genomes.">Predicting transmembrane protein topology with a hidden markov model: application to complete genomes.</a> J. Mol. Biol. 305, 567-580 (2001).</li><li>Bakheet, T. M., Doig, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Properties+and+identification+of+human+protein+drug+targets.">Properties and identification of human protein drug targets.</a> Bioinformatics. 25, 451-457 (2009).</li><li>Yildirim, M. A., Goh, K. I., Cusick, M. E., Barabasi, A. L., Vidal, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug-target+network.">Drug-target network.</a> Nat. Biotechnol. 25, (2007).</li><li>Daley, D. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+assembly+of+membrane+proteins+into+complexes.">The assembly of membrane proteins into complexes.</a> Curr. Opin. Struct. Biol. 18, 420-424 (2008).</li><li>Jung, K., Fried, L., Behr, S., Heermann, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histidine+kinases+and+response+regulators+in+networks.">Histidine kinases and response regulators in networks.</a> Curr. Opin. Microbiol. 15, 118-124 (2012).</li><li>M&#252;ller, V. S., Jungblut, P. R., Meyer, T. F., Hunke, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane-SPINE:+An+improved+method+to+identify+protein-protein+interaction+partners+of+membrane+proteins+in+vivo.">Membrane-SPINE: An improved method to identify protein-protein interaction partners of membrane proteins in vivo.</a> Proteomics. 11, 2124-2128 (2011).</li><li>Herzberg, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SPINE:+A+method+for+the+rapid+detection+and+analysis+of+protein-protein+interactions+in+vivo.">SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo.</a> Proteomics. 7, 4032-4035 (2007).</li><li>Sutherland, B. W., Toews, J., Kast, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Utility+of+formaldehyde+cross-linking+and+mass+spectrometry+in+the+study+of+protein-protein+interactions.">Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions.</a> J. Mass Spectrom. 43, 699-715 (2008).</li><li>Hernandez, P., M&#252;ller, M., Appel, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+protein+identification+by+tandem+mass+spectrometry:+Issues+and+strategies.">Automated protein identification by tandem mass spectrometry: Issues and strategies.</a> Mass Spectrom. Rev. 25, 235-254 (2006).</li><li>Laemmli, U. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cleavage+of+structural+proteins+during+the+assembly+of+the+head+of+bacteriophage+T4.">Cleavage of structural proteins during the assembly of the head of bacteriophage T4.</a> Nature. 227, 680-685 (1970).</li><li>Hunke, S., Keller, R., M&#252;ller, V. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signal+integration+by+the+Cpx-envelope+stress+system.">Signal integration by the Cpx-envelope stress system.</a> FEMS Microbiol. Lett. 326, 12-22 (2012).</li><li>Weber, R. F., Silverman, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cpx+proteins+of+Escherichia+coli+K12+:+Structure+of+the+CpxA+polypeptide+as+an+inner+membrane+component.">The Cpx proteins of Escherichia coli K12 : Structure of the CpxA polypeptide as an inner membrane component.</a> J. Mol. Biol. 203, 467-478 (1988).</li></ol>

Nous n&#39;avons rien à communiquer.

Analyse membrane colonne vertébrale est une approche biochimique que l&#39;on permet de confirmer et d&#39;identifier à ce point inconnus partenaires d&#39;interaction de protéines membranaires. Membrane SPINE combine in vivo réticulation par le formaldéhyde à la purification d&#39;une protéine appât de membrane Strep-marqué. La combinaison avec des immuno-empreinte facilite la confirmation de partenaires d&#39;interaction prédites (Figure 2). En outre, la combinaison avec l&#39;analy...

Pour comprendre la fonction d&#39;une protéine, il est essentiel de connaître ses partenaires d&#39;interaction. Plusieurs techniques classiques sont disponibles pour l&#39;identification des partenaires d&#39;interaction de protéines solubles. Cependant, ces techniques ne sont pas facilement transférables à des protéines membranaires du fait de leur nature hydrophobe 4. Pour contourner cette limitation, nous avons développé la membrane Strep-protéine interaction expérience (Membrane-SPINE) 6. Il est basé sur la méthode de la colonne vertébrale, qui était uniquement pour les protéines solubles 7. Membrane-SPINE bénéficie de deux avantages de la formaldéhyde agent de réticulation: d&#39;abord, le formaldéhyde peuvent facilement pénétrer les membranes et donc génère un aperçu précis de l&#39;interactome d&#39;une cellule vivante 8. Deuxièmement, le formaldéhyde liaisons transversales peuvent être inversées en faisant bouillir 9. Ici, ces deux avantages sont utilisés pour identifier non seulement les IPP permanents mais aussi transitoires de prote de la membraneins 6. En bref, une Strep-tag est fusionnée à l&#39;extrémité C-terminale de la protéine appât membranaire intégrale. Les cellules exprimant la protéine appât de la membrane sont mises en incubation avec du formaldéhyde qui réticule les protéines s&#39;attaquent à la protéine appât de la membrane (Figure 1). Les modifications des protéines de la proie ne sont pas nécessaires. Ensuite, la fraction membranaire est préparée. Par conséquent, les protéines membranaires sont solubilisés par traitement avec un détergent et de l&#39;appât protéines sont co-purifiés avec ses protéines de proie en utilisant une purification par affinité. Par la suite, la liaison réticulée est inversé par ebullition, et l&#39;appât et de proie ses protéines co-éluées sont séparés par SDS-PAGE. Enfin, les protéines de proie peuvent être identifiés par une analyse par immunotransfert ou spectrométrie de masse.

<table border="0" cellpadding="0" cellspacing="0" width="878">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">37% Formaldehyde</td>
			<td style="width:128px;">Roth</td>
			<td style="width:137px;">4979.1</td>
			<td style="width:271px;">Should not be older than one year</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">DNaseI</td>
			<td style="width:128px;">Sigma</td>
			<td style="width:137px;">DN25</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">BCA protein assay kit</td>
			<td style="width:128px;">Pierce</td>
			<td style="width:137px;">23225</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Micromagnetic rod</td>
			<td style="width:128px;">Roth</td>
			<td style="width:137px;">0955.2</td>
			<td style="width:271px;">5 mm in length, 2 mm in diameter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Triton X-100</td>
			<td style="width:128px;">Roth</td>
			<td style="width:137px;">6683.1</td>
			<td style="width:271px;">standard detergent for solubilization</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">n-Dodecyl-&#946;-maltoside</td>
			<td style="width:128px;">Glycon</td>
			<td style="width:137px;">D97002-C</td>
			<td style="width:271px;">the best detergent to solubilze CpxA</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">1 ml Strep-Tactin superflow gravity flow column</td>
			<td style="width:128px;">IBA</td>
			<td style="width:137px;">2-1207-050</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Strep-tag protein purification buffer set</td>
			<td style="width:128px;">IBA</td>
			<td style="width:137px;">2-1002-001</td>
			<td style="width:271px;">Contains buffer W and buffer E</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Amicon Ultra-4 centrifugal filter</td>
			<td style="width:128px;">Millipore</td>
			<td style="width:137px;">UFC803024</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:343px;">SuperSignal West Pico Chemiluminescent substrate</td>
			<td style="width:128px;">Pierce</td>
			<td style="width:137px;">34080</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">SilverQuest Silverstaining kit</td>
			<td style="width:128px;">Invitrogen</td>
			<td style="width:137px;">LC6070</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">FireSilver Staining Kit</td>
			<td style="width:128px;">Proteome Factory</td>
			<td style="width:137px;">P-S-2001</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Ultracentrifuge</td>
			<td style="width:128px;"></td>
			<td style="width:137px;"></td>
			<td style="width:271px;"></td>
		</tr>
	</tbody>
</table>

membrane-spine: a biochemical tool to identify protein-protein interactions of membrane proteins in vivo

Les protéines membranaires sont essentielles pour la viabilité des cellules et sont donc des cibles thérapeutiques importantes 3.1. Comme ils fonctionnent dans des complexes 4, méthodes pour identifier et caractériser leurs interactions sont nécessaires 5. À cette fin, nous avons développé l&#39;expérience d&#39;interaction Strep-protéine de membrane, appelée membrane-SPINE 6. Cette technique combine in vivo de réticulation réversible à l&#39;aide du formaldéhyde agent de réticulation avec une purification par affinité de la protéine d&#39;appât de la membrane à étiquette Strep. Au cours de la procédure, les protéines de proies réticulés sont co-purifiés avec la protéine appât de la membrane et ensuite séparées par ébullition. Ainsi, deux grandes tâches peuvent être exécutées lors de l&#39;analyse des interactions protéine-protéine (IPP) de protéines membranaires en utilisant membrane-SPINE: d&#39;abord, la confirmation d&#39;un partenaire d&#39;interaction proposé par immunoblot, et d&#39;autre part, l&#39;identification de nouveaux partenaires d&#39;interaction par spectrométrie de masse . En outre, même low affinité, les IPP transitoires sont détectables par cette technique. Enfin, Membrane-SPINE est adaptable à presque n&#39;importe quel type de cellule, qu&#39;il s&#39;applique à un outil de dépistage pour identifier des IPP de protéines membranaires.

Analyse membrane RACHIS permet la co-purification des protéines membranaires et interagissant de manière transitoire partenaires protéiques. La co-purification est réalisée en utilisant l&#39;agent formaldéhyde transversale de liaison. Deux paramètres sont critiques pour éviter des liaisons transversales non spécifiques: la concentration en formaldéhyde et le temps de réticulation. L&#39;utilisation suffisante, mais non excessive de formaldéhyde peut être facilement contrôlé par immuno. Complexes protéiq...

Watch this Scientific Journal Video about Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo at JoVE.com

Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

Une approche biochimique est décrite in vivo pour identifier les interactions protéine-protéine dans (PPI) de protéines membranaires. Le procédé combine la réticulation des protéines, purification par affinité et la spectrométrie de masse, et peut être adapté à presque n&#39;importe quel type de cellule ou un organisme. Avec cette approche, même l&#39;identification des IPP transitoires devient possible.

Membrane-SPINE: un outil biochimique pour identifier les interactions protéine-protéine de protéines membranaires<em&gt; In Vivo</em

Membrane proteins are essential for cell viability and are therefore important therapeutic targets1-3. Since they function in complexes4, methods to ...

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Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

13.6K vues.  Universität Osnabrück.  Une approche biochimique est décrite in vivo pour identifier les interactions protéine-protéine dans (PPI) de protéines membranaires. Le procédé combine la réticulation des protéines, purification par affinité et la spectrométrie de masse, et peut être adapté à presque n'importe quel type de cellule ou un organisme. Avec cette approche, même l'identification des IPP transitoires devient possible. 

Vidéo: Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

Fabrication of Electrochemical-DNA Biosensors for the Reagentless Detection of Nucleic Acids, Proteins and Small Molecules

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. Many patients would be better served by rapid, bedside tests. To this end our laboratory and others have developed a versatile, reagentless 
biosensor platform that supports the quantitative, reagentless, electrochemical detection of nucleic acids (DNA, RNA), proteins (including antibodies) and small 
molecules analytes directly in unprocessed clinical and environmental samples. In this video, we demonstrate the preparation and use of several biosensors in this 
"E-DNA" class. In particular, we fabricate and demonstrate sensors for the detection of a target DNA sequence in a polymerase chain reaction mixture, an HIV-specific antibody and the drug cocaine. The preparation procedure requires only three hours of hands-on effort followed by an overnight incubation, and their use requires only minutes.

"E-DNA" sensors, reagentless, electrochemical biosensors that perform well even when challenged directly in blood and other complex matrices, have been adapted to the detection of a wide range of nucleic acid, protein and small molecule analytes. Here we present a general procedure for the fabrication and use of such sensors.

La fabrication des électrochimique de l&#39;ADN des Biocapteurs pour la détection sans réactif d&#39;acides nucléiques, protéines et petites molécules

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. ...

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Bio-ingénierie

Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural biology 1. In recent years, this method has achieved great success in studying structures of proteins and macromolecular complexes 2, 3. Compared with electron cryomicroscopy (cryoEM), in which frozen hydrated protein samples are embedded in a thin layer of vitreous ice 4, negative staining is a simpler sample preparation method in which protein samples are embedded in a thin layer of dried heavy metal salt to increase specimen contrast 5. The enhanced contrast of negative stain EM allows examination of relatively small biological samples. In addition to determining three-dimensional (3D) structure of purified proteins or protein complexes 6, this method can be used for much broader purposes. For example, negative stain EM can be easily used to visualize purified protein samples, obtaining information such as homogeneity/heterogeneity of the sample, formation of protein complexes or large assemblies, or simply to evaluate the quality of a protein preparation.
In this video article, we present a complete protocol for using an EM to observe negatively stained protein sample, from preparing carbon coated grids for negative stain EM to acquiring images of negatively stained sample in an electron microscope operated at 120kV accelerating voltage. These protocols have been used in our laboratory routinely and can be easily followed by novice users.

Visualizing protein samples by negative stain electron microscopy (EM) has become a popular structural analysis method. It is useful for quantitative structural analysis, such as calculating a 3D reconstruction of the molecules being studied, and also for qualitative examination of the quality of protein preparations. In this article we present detailed protocols for preparing the EM grids, staining the sample and visualizing the sample in an electron microscope. Novice users can follow these protocols easily and to utilize negative stain EM as a routine assay, in addition to other biochemical assays, for evaluating their protein samples.

Visualisation protéines et de complexes macromoléculaires par EM négatif Tache: de la préparation de grille pour l&#39;acquisition d&#39;images

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural ...

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic valve leaflets are composed of interstitial cells suspended within an extracellular matrix (ECM) and are lined with an endothelial cell monolayer. The valve withstands a harsh, dynamic environment and is constantly exposed to shear, flexion, tension, and compression. Research has shown calcific lesions in diseased valves occur in areas of high mechanical stress as a result of endothelial disruption or interstitial matrix damage1-3. Hence, it is not surprising that epidemiological studies have shown high blood pressure to be a leading risk factor in the onset of aortic valve disease4. 
The only treatment option currently available for valve disease is surgical replacement of the diseased valve with a bioprosthetic or mechanical valve5. Improved understanding of valve biology in response to physical stresses would help elucidate the mechanisms of valve pathogenesis. In turn, this could help in the development of non-invasive therapies such as pharmaceutical intervention or prevention. Several bioreactors have been previously developed to study the mechanobiology of native or engineered heart valves6-9. Pulsatile bioreactors have also been developed to study a range of tissues including cartilage10, bone11 and bladder12. The aim of this work was to develop a cyclic pressure system that could be used to elucidate the biological response of aortic valve leaflets to increased pressure loads. 
The system consisted of an acrylic chamber in which to place samples and produce cyclic pressure, viton diaphragm solenoid valves to control the timing of the pressure cycle, and a computer to control electrical devices. The pressure was monitored using a pressure transducer, and the signal was conditioned using a load cell conditioner. A LabVIEW program regulated the pressure using an analog device to pump compressed air into the system at the appropriate rate. The system mimicked the dynamic transvalvular pressure levels associated with the aortic valve; a saw tooth wave produced a gradual increase in pressure, typical of the transvalvular pressure gradient that is present across the valve during diastole, followed by a sharp pressure drop depicting valve opening in systole. The LabVIEW program allowed users to control the magnitude and frequency of cyclic pressure. The system was able to subject tissue samples to physiological and pathological pressure conditions. This device can be used to increase our understanding of how heart valves respond to changes in the local mechanical environment.

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

A cyclic pressure bioreactor capable of subjecting heart valve tissue to physiological and pathological pressure conditions has been designed. A LabVIEW program allows users to control pressure magnitude, amplitude and frequency. This device can be used to study the mechanobiology of heart valve tissue or isolated cells.

Conception d&#39;un bioréacteur pour la pression cyclique Ex Vivo Étude des valves cardiaques aortiques

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic ...

Determination of the Transport Rate of Xenobiotics and Nanomaterials Across the Placenta using the ex vivo Human Placental Perfusion Model

Decades ago the human placenta was thought to be an impenetrable barrier between mother and unborn child. However, the discovery of thalidomide-induced birth defects and many later studies afterwards proved the opposite. Today several harmful xenobiotics like nicotine, heroin, methadone or drugs as well as environmental pollutants were described to overcome this barrier. With the growing use of nanotechnology, the placenta is likely to come into contact with novel nanoparticles either accidentally through exposure or intentionally in the case of potential nanomedical applications. Data from animal experiments cannot be extrapolated to humans because the placenta is the most species-specific mammalian organ 1. Therefore, the ex vivo dual recirculating human placental perfusion, developed by Panigel et al. in 1967 2 and continuously modified by Schneider et al. in 1972 3, can serve as an excellent model to study the transfer of xenobiotics or particles.
Here, we focus on the ex vivo dual recirculating human placental perfusion protocol and its further development to acquire reproducible results.
The placentae were obtained after informed consent of the mothers from uncomplicated term pregnancies undergoing caesarean delivery. The fetal and maternal vessels of an intact cotyledon were cannulated and perfused at least for five hours. As a model particle fluorescently labelled polystyrene particles with sizes of 80 and 500 nm in diameter were added to the maternal circuit. The 80 nm particles were able to cross the placental barrier and provide a perfect example for a substance which is transferred across the placenta to the fetus while the 500 nm particles were retained in the placental tissue or maternal circuit. The ex vivo human placental perfusion model is one of few models providing reliable information about the transport behavior of xenobiotics at an important tissue barrier which delivers predictive and clinical relevant data.

Determination of the Transport Rate of Xenobiotics and Nanomaterials Across the Placenta using the ex vivo Human Placental Perfusion Model

The ex vivo dual recirculating human placental perfusion model can be used to investigate the transfer of xenobiotics and nanoparticles across the human placenta. In this video protocol we describe the equipment and techniques required for a successful execution of a placenta perfusion.

Détermination de la vitesse de transport des xénobiotiques et des nanomatériaux à travers le placenta en utilisant l&#39;<em&gt; Ex vivo</em&gt; Human perfusion placentaire modèle

Decades ago the human placenta was thought to be an impenetrable barrier between mother and unborn child. However, the discovery of thalidomide-induced ...

Isolation and Characterization Of Chimeric Human Fc-expressing Proteins Using Protein A Membrane Adsorbers And A Streamlined Workflow

Laboratory scale to industrial scale purification of biomolecules from cell culture supernatants and lysed cell solutions can be accomplished using affinity chromatography.&#160;While affinity chromatography using porous protein A agarose beads packed in columns is arguably the most common method of laboratory scale isolation of antibodies and recombinant proteins expressing Fc fragments of IgG, it can be a time consuming and expensive process.&#160;Time and financial constraints are especially daunting in small basic science labs that must recover hundreds of micrograms to milligram quantities of protein from dilute solutions, yet lack access to high pressure liquid delivery systems and/or personnel with expertise in bioseparations. Moreover, product quantification and characterization may also excessively lengthen processing time over several workdays and inflate expenses (consumables, wages, etc.).&#160;Therefore, a fast, inexpensive, yet effective protocol is needed for laboratory scale isolation and characterization of antibodies and other proteins possessing an Fc fragment.&#160;To this end, we have devised a protocol that can be completed by limited-experience technical staff in less than 9 hr (roughly one workday) and as quickly as 4 hr, as opposed to traditional methods that demand 20+ work hours. Most required equipment is readily available in standard biomedical science, biochemistry, and (bio)chemical engineering labs, and all reagents are commercially available.&#160;To demonstrate this protocol, representative results are presented in which chimeric&#160;murine galectin-1 fused to human Fc (Gal-1hFc) from cell culture supernatant was isolated using a protein A membrane adsorber.&#160;Purified Gal-1hFc was quantified using an expedited Western blotting analysis procedure and characterized using flow cytometry. The streamlined workflow can be modified for other Fc-expressing proteins, such as antibodies, and/or altered to incorporate alternative quantification and characterization methods.

Compared with traditional affinity chromatography using protein A agarose bead-packed columns, protein A membrane adsorbers can significantly speed laboratory-scale isolation of antibodies and other Fc fragment-expressing proteins.&#160;Appropriate analysis and quantification methods can further accelerate protein processing, allowing isolation/characterization to be completed in one workday, instead of 20+ work hours.

Isolation et caractérisation de protéines humaines chimériques exprimant fc à l’aide d’adsorbeurs membranaires de protéine a et d’un flux de travail rationalisé

Laboratory scale to industrial scale purification of biomolecules from cell culture supernatants and lysed cell solutions can be accomplished using ...

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range of 10-100 &#197;. By measuring the distances under various ligated conditions, conformational changes of the protein can be easily assessed. With LRET, a lanthanide, most often chelated terbium, is used as the donor fluorophore, affording advantages such as a longer donor-only emission lifetime, the flexibility to use multiple acceptor fluorophores, and the opportunity to detect sensitized acceptor emission as an easy way to measure energy transfer without the risk of also detecting donor-only signal. Here, we describe a method to use LRET on membrane proteins expressed and assayed on the surface of intact mammalian cells. We introduce a protease cleavage site between the LRET fluorophore pair. After obtaining the original LRET signal, cleavage at that site removes the specific LRET signal from the protein of interest allowing us to quantitatively subtract the background signal that remains after cleavage. This method allows for more physiologically relevant measurements to be made without the need for purification of protein.

We describe here an improved Luminescence Resonance Energy Transfer (LRET) method where we introduce a protease cleavage site between the donor and acceptor fluorophore sites. This modification allows us to obtain specific LRET signals arising from membrane proteins of interest, allowing for the study of membrane proteins without protein purification.

Luminescence Resonance Energy Transfer pour étudier les changements conformationnels dans des protéines membranaires exprimés dans les cellules de mammifères

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range ...

Fluorescence-quenching of a Liposomal-encapsulated Near-infrared Fluorophore as a Tool for In Vivo Optical Imaging

Optical imaging offers a wide range of diagnostic modalities and has attracted a lot of interest as a tool for biomedical imaging. Despite the enormous number of imaging techniques currently available and the progress in instrumentation, there is still a need for highly sensitive probes that are suitable for in vivo imaging. One typical problem of available preclinical fluorescent probes is their rapid clearance in vivo, which reduces their imaging sensitivity. To circumvent rapid clearance, increase number of dye molecules at the target site, and thereby reduce background autofluorescence, encapsulation of the near-infrared fluorescent dye, DY-676-COOH in liposomes and verification of its potential for in vivo imaging of inflammation was done. DY-676 is known for its ability to self-quench at high concentrations. We first determined the concentration suitable for self-quenching, and then encapsulated this quenching concentration into the aqueous interior of PEGylated liposomes. To substantiate the quenching and activation potential of the liposomes we use a harsh freezing method which leads to damage of liposomal membranes without affecting the encapsulated dye. The liposomes characterized by a high level of fluorescence quenching were termed Lip-Q. We show by experiments with different cell lines that uptake of Lip-Q is predominantly by phagocytosis which in turn enabled the characterization of its potential as a tool for in vivo imaging of inflammation in mice models. Furthermore, we use a zymosan-induced edema model in mice to substantiate the potential of Lip-Q in optical imaging of inflammation in vivo. Considering possible uptake due to inflammation-induced enhanced permeability and retention (EPR) effect, an always-on liposome formulation with low, non-quenched concentration of DY-676-COOH (termed Lip-dQ) and the free DY-676-COOH were compared with Lip-Q in animal trials.

Fluorescence-quenching of a Liposomal-encapsulated Near-infrared Fluorophore as a Tool for In Vivo Optical Imaging

The use of fluorophores for in vivo imaging can be greatly limited by opsonization, rapid clearance, low detection sensitivity and cytotoxic effects on the host. Encapsulation of fluorophores in liposomes by film hydration and extrusion leads to fluorescence quenching and protection which enables in vivo imaging with high detection sensitivity.

Fluorescence-trempe d&#39;un proche infrarouge fluorophore encapsulée dans des liposomes comme outil de<em&gt; In Vivo</em&gt; Imagerie optique

Optical imaging offers a wide range of diagnostic modalities and has attracted a lot of interest as a tool for biomedical imaging. Despite the enormous ...

Sandwich-like Microenvironments to Harness Cell/Material Interactions

Cell culture has been traditionally carried out on bi-dimensional (2D) substrates where cells adhere using ventral receptors to the biomaterial surface. However in vivo, most of the cells are completely surrounded by the extracellular matrix (ECM), resulting in a three-dimensional (3D) distribution of receptors. This may trigger differences in the outside-in signaling pathways and thus in cell behavior.
This article shows that stimulating the dorsal receptors of cells already adhered to a 2D substrate by overlaying a film of a new material (a sandwich-like culture) triggers important changes with respect to standard 2D cultures. Furthermore, the simultaneous excitation of ventral and dorsal receptors shifts cell behavior closer to that found in 3D environments. Additionally, due to the nature of the system, a sandwich-like culture is a versatile tool that allows the study of different parameters in cell/material interactions, e.g., topography, stiffness and different protein coatings at both the ventral and dorsal sides. Finally, since sandwich-like cultures are based on 2D substrates, several analysis procedures already developed for standard 2D cultures can be used normally, overcoming more complex procedures needed for 3D systems.

The following protocol describes the procedure to assemble sandwich-like cultures to be used as an intermediate stage between bi-dimensional (2D) and three-dimensional (3D) cellular environments. The engineered systems can have applications in microscopy, biomechanics, biochemistry and cell biology assays.

Microenvironnements sandwich à exploiter cellulaires / Interactions matérielles

Cell culture has been traditionally carried out on bi-dimensional (2D) substrates where cells adhere using ventral receptors to the biomaterial surface. ...

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Historically, most cellular processes have been studied in only 2 dimensions. While these studies have been informative about general cell signaling mechanisms, they neglect important cellular cues received from the structural and mechanical properties of the local microenvironment and extracellular matrix (ECM). To understand how cells interact within a physiological ECM, it is important to study them in the context of 3 dimensional assays. Cell migration, cell differentiation, and cell proliferation are only a few processes that have been shown to be impacted by local changes in the mechanical properties of a 3-dimensional ECM. Collagen I, a core fibrillar component of the ECM, is more than a simple structural element of a tissue. Under normal conditions, mechanical cues from the collagen network direct morphogenesis and maintain cellular structures. In diseased microenvironments, such as the tumor microenvironment, the collagen network is often dramatically remodeled, demonstrating altered composition, enhanced deposition and altered fiber organization. In breast cancer, the degree of fiber alignment is important, as an increase in aligned fibers perpendicular to the tumor boundary has been correlated to poorer patient prognosis1. Aligned collagen matrices result in increased dissemination of tumor cells via persistent migration2,3. The following is a simple protocol for embedding cells within a 3-dimensional, fibrillar collagen hydrogel. This protocol is readily adaptable to many platforms, and can reproducibly generate both aligned and random collagen matrices for investigation of cell migration, cell division, and other cellular processes in a tunable, 3-dimensional, physiological microenvironment.

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Collagen is a core component of the ECM, and provides essential cues for several cellular processes ranging from migration to differentiation and proliferation. Provided here is a protocol for embedding cells within 3D collagen hydrogels, and a more advanced technique for generating randomized or aligned collagen matrices using PDMS microchannels.

Préparation de la 3D collagène Gels et microcanaux pour l&#39;étude des interactions 3D<em&gt; In Vivo</em

Historically, most cellular processes have been studied in only 2 dimensions.  While these studies have been informative about general cell signaling ...

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes. This underlying principle is prevalent in nature (e.g., in cells or tissues), minimizing the high molecular content and thereby facilitating diffusive or active transport. Due to their biological implications and potential technological applications in biocompatible hydrogels, semiflexible polymers have been subject to considerable study. However, comprehensible investigations remained challenging since they relied on natural polymers, such as actin filaments, which are not freely tunable. Despite these limitations and due to the lack of synthetic, mechanically tunable, and semiflexible polymers, actin filaments were established as the common model system. A major limitation is that the central quantity lp cannot be freely tuned to study its impact on macroscopic bulk structures. This limitation was resolved by employing structurally programmable DNA nanotubes, enabling controlled alteration of the filament stiffness. They are formed through tile-based designs, where a discrete set of partially complementary strands hybridize in a ring structure with a discrete circumference. These rings feature sticky ends, enabling the effective polymerization into filaments several microns in length, and display similar polymerization kinetics as natural biopolymers. Due to their programmable mechanics, these tubes are versatile, novel tools to study the impact of lp on the single-molecule as well as the bulk scale. In contrast to actin filaments, they remain stable over weeks, without notable degeneration, and their handling is comparably straightforward.

Semiflexible polymers display unique mechanical properties that are extensively applied by living systems. However, systematic studies on biopolymers are limited since properties such as polymer rigidity are inaccessible. This manuscript describes how this limitation is circumvented by programmable DNA nanotubes, enabling experimental studies on the impact of filament rigidity.

Nanotubes d’ADN comme un outil polyvalent pour l’étude des polymères semi-flexibles

Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of ...