Name: a protein preparation method for the high-throughput identification of proteins interacting with a nuclear cofactor using lc-ms/ms analysis
Uploaded: 2017-01-24T12:30:00
Description: Watch this Scientific Journal Video about A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis at JoVE.com

This study was supported by the Astellas Foundation for Research on Metabolic Disorders (HT), the Takeda Science Foundation (HT), and by a Japan Society for the Promotion of Science Grants-in-Aid for Young Scientists (B) to HT.

1. transfection <ol><li> Ensemencer des cellules HEK293 dans des plaques de culture à 100 mm (2 x 10 6 cellules / boîte). La culture des cellules dans un milieu de Eagle modifié par Dulbecco supplémenté avec 10% de sérum de veau foetal, 100 ug / ml de streptomycine et de 100 unités / ml de pénicilline. Incuber les cellules dans un incubateur humidifié à 5% de CO 2 et 37 ° C. </li><li> Le lendemain, transfecter les cellules avec 10 pg de étiquetée FLAG ARIP4 plasmide en utilisant 40 u...

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transfection efficace est essentielle pour obtenir un bon résultat avec ce protocole. En conséquence, nous vous recommandons d&#39;utiliser l&#39;analyse Western blot pour déterminer les niveaux de protéine FLAG-tagged immunoprécipitées. Cette étape permet aux utilisateurs de vérifier que leur protéine d&#39;intérêt est correctement surexprimée et, en outre, que l&#39;adresse IP a été réalisée avec succès. les niveaux de protéine étiquetée FLAG doivent également être vérifiés avant l&#39;analyse ...

interactions protéine-protéine jouent un rôle important dans de nombreuses fonctions biologiques. Par conséquent, ces interactions ont été impliquées dans la transduction du signal; le transport de protéines à travers les membranes cellulaires; le métabolisme cellulaire; et plusieurs processus nucléaires, y compris la replication de l&#39; ADN, la réparation des dommages de l&#39; ADN, la recombinaison et la transcription 1, 2, 3, 4. L&#39;identification des protéines impliquées dans ces interactions est par conséquent essentiel de faire progresser notre compréhension de ces processus cellulaires. Immunoprécipitation (IP) est une technique utilisée pour valider l&#39;analyse des interactions protéine-protéine. Afin de faciliter l&#39;identification des protéines co-immunoprécipitation, la spectrométrie de masse est souvent utilisée 5, 6, 7, 8,9. En ciblant un élément connu d&#39;un complexe protéique avec un anticorps, il est possible d&#39;isoler le complexe de protéines et d&#39;identifier ensuite les composants inconnus par analyse par spectrométrie de masse. ARIP4 (protéine androgène-récepteur coopérant 4), un co - régulateur de la transcription, interagit avec les protéines de récepteurs nucléaires, afin d&#39;activer ou de réprimer les promoteurs cibles d&#39;une manière dépendante du contexte 9, 10. Pour mieux comprendre les mécanismes de régulation de transcription qui régissent ces facteurs nucléaires, nous décrivons une méthode complète pour purifier et identifier les protéines qui interagissent ARIP4 en utilisant le système LC-MS / MS.

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		<tr height="81">
			<td height="81" style="height:81px;width:216px;">Lipofectamine 2000 Transfection Reagent</td>
			<td style="width:71px;">Thermo Fisher Scientific</td>
			<td style="width:119px;">11668019</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:216px;">Protease Inhibitor Cocktail (EDTA free) (100x)</td>
			<td style="width:71px;">nacalai tesque</td>
			<td style="width:119px;">03969-21</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:216px;">ANTI-FLAG M2 Affinity Gel</td>
			<td style="width:71px;">Sigma-Aldrich</td>
			<td style="width:119px;">A2220</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;">Micro Bio-Spin Columns</td>
			<td style="width:71px;">BIO-RAD</td>
			<td style="width:119px;">732-6204</td>
			<td></td>
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a protein preparation method for the high-throughput identification of proteins interacting with a nuclear cofactor using lc-ms/ms analysis

Transcriptional coregulators are vital to the efficient transcriptional regulation of nuclear chromatin structure. Coregulators play a variety of roles in regulating transcription. These include the direct interaction with transcription factors, the covalent modification of histones and other proteins, and the occasional chromatin conformation alteration. Accordingly, establishing relatively quick methods for identifying proteins that interact within this network is crucial to enhancing our understanding of the underlying regulatory mechanisms. LC-MS/MS-mediated protein binding partner identification is a validated technique used to analyze protein-protein interactions. By immunoprecipitating a previously-identified member of a protein complex with an antibody (occasionally with an antibody for a tagged protein), it is possible to identify its unknown protein interactions via mass spectrometry analysis. Here, we present a method of protein preparation for the LC-MS/MS-mediated high-throughput identification of protein interactions involving nuclear cofactors and their binding partners. This method allows for a better understanding of the transcriptional regulatory mechanisms of the targeted nuclear factors.

Nous avons identifié un signal fort de ARIP4, environ 160 kDa, ainsi que ceux d&#39;un contrôle de l&#39; échantillon mock et plusieurs autres protéines inconnues (Figure 1). Analyse LC-MS / MS a identifié deux peptides ARIP4 complexes et les cofacteurs de peptides potentiels dans la fraction de billes de pavillon (tableau 1). p62 (Sequestosome1), un cofacteur ARIP4 connu 11 a été identifié dans l&#39;analyse (tabl...

Watch this Scientific Journal Video about A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis at JoVE.com

A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis

Nous avons établi un procédé pour la purification des protéines d&#39;interaction co-régulation utilisant le système LC-MS / MS.

Une protéine Méthode de préparation pour le haut-débit Identification des protéines interagissant avec un cofacteur nucléaire utilisant LC-MS / MS Analysis

Transcriptional coregulators are vital to the efficient transcriptional regulation of nuclear chromatin structure. Coregulators play a variety of roles in ...

Overall goal of this procedure is to identify proteins interacting with a Nuclear Cofactor using LC-MS/MS Analysis. This method can help answer key questions related to transcriptional mechanisms in the gene regulation field. The main advantage of this technique is that we can identify the proteins interacting with a nuclear cofactor.Moreover, this method allows us to better understand the transcriptional regulatory mechanisms of the targeted nuclear factors. Harvest HEK 293 cells expressing flag-tagged ARIP4 36 hours after transvection by washing the cell sheet with ice cold PBS and collecting the cells with a cell scrapper. Transfer the cells into a 1.5 milliliter tube and then centrifuge at 8000g for two minutes at four degrees Celsius.Aspirate the supernatant and re-suspend the cell pellet in five times the pellet volume of High Salt Buffer. Rotate the mixture for 20 minutes at four degrees Celsius. After 20 minutes of rotation, centrifuge the tube at 17, 700g for 10 minutes at four degrees Celsius.Next, transfer the supernatants to a new two milliliter tube and add Dilution buffer to three times the volume of supernatant. Perform another cetrifugation and then transfer the supernatant to a new two milliliter tube. During the 10 minute centrifugation wash 50 microliters of anti-flag beads with PBS.Then centrifuge the tube at 2000g for one minute at four degrees Celsius. Remove the supernatant and repeat wash steps first with 1 molar glycine hydrochloride and then with one molar tris hydrochloride. Then wash twice with Low salt buffer.Next, mix 50 microliters of washed beads with whole-cell extracts. Gently rotate the mixture for four hours at two to four degrees Celsius. Then use a blunted tip to transfer the sample into a micro spin column and allow the solution to drip through into a 1.5 milliliter tube.Snap freeze the flow through in liquid nitrogen and store at minus 80 degrees Celsius. Next, wash the flag beads with Low salt buffer five times. To elute, place the column into a 1.5 milliliter tube and centrifuge at 2000g for one minute to dry the beads.Cap the bottom of the column and then add 50 microliters of 1 molar glycine hydrochloride. Gently shake the mixture for 10 minutes at room temperature. After 10 minutes, place the column into a new 1.5 milliliter tube and centrifuge at 2000g for one minute.Neutralize the eluted solution with 10 microliters of one molar tris hydrochloride and mix well by pipetting and vortexing. Add 50 microliters of 100 millimolar ammonium bicarbonate. 10 microliters of acetonitrile, two microliters of dithiothreitol and 50 microliters of neutralized sample.Incubate for 30 minutes at 56 degrees Celsius. After incubation, leave the sample at room temperature for 10 minutes. Then add 10 microliters of 333 millimolar iodoacetamide to the sample and incubate in the dark for 30 minutes at 37 degrees C.Add 10 microliters of trypsin to the mixture and incubate overnight at 37 degrees Celsius.The next day transport the final product to an LC-MS/MS facility or to a third party mass spectrometry lab for analysis. This image shows silver staining of flag epitope tagged ARIP4 expressed in HEK 293 cells after immunal precipitation with a flag specific antibody and separation by electrophoresis. As a control, a mock purification was performed on HEK 293 cells that did not express exogenous proteins.Using our method, it is possible to identify putative nuclear cofactors via their transcriptional factor of interest and further enhance our understanding of transcriptional regulatory mechanisms.

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