Este projeto foi parcialmente financiado por um IOS NSF (0849230); Hatch, McIntire-Stennis (AD421 CRIS), USDA Grant Seed (2011-04375), e Sir Frederick McMaster Bolsa de Investigação para ABD.

<ol>
	<li>Georgieva, Y., Konthur, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+screening+of+M13+phage+display+cDNA+libraries.">Design and screening of M13 phage display cDNA libraries.</a> Molecules. 16, 1667-1681 (2011).</li><li>Beghetto, E., Gargano, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lambda-display:+a+powerful+tool+for+antigen+discovery.">Lambda-display: a powerful tool for antigen discovery.</a> Molecules. 16, 3089-3105 (2011).</li><li>Li, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ORF+phage+display+to+identify+cellular+proteins+with+different+functions.">ORF phage display to identify cellular proteins with different functions.</a> Methods. 58, 2-9 (2012).</li><li>Willats, W. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phage+display:+practicalities+and+prospects.">Phage display: practicalities and prospects.</a> Plant Mol. Biol. 50, 837-854 (2002).</li><li>Konthur, Z., Crameri, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+applications+of+phage+display+in+proteomic+analyses.">High-throughput applications of phage display in proteomic analyses.</a> Targets. 2, 261-270 (2003).</li><li>Chen, T., 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=Substrates+of+the+Arabidopsis+thaliana+protein+isoaspartyl+methyltransferase+1+identified+using+phage+display+and+biopanning.">Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning.</a> J. Biol. Chem. 285, 37281-37292 (2010).</li><li>Jung, S., Honegger, A., Pluckthun, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+for+improved+protein+stability+by+phage+display.">Selection for improved protein stability by phage display.</a> J. Mol. Biol. 294, 163-180 (1999).</li><li>Battaglia, M., Olvera-Carrillo, Y., Garciarrubio, A., Campos, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+enigmatic+LEA+proteins+and+other+hydrophilins.">The enigmatic LEA proteins and other hydrophilins.</a> Plant Physiol. 148, 6-24 (2008).</li><li>Egli, D. B., Bruening, W. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Source-sink+relationships,+seed+sucrose+levels+and+seed+growth+rates+in+soybean.">Source-sink relationships, seed sucrose levels and seed growth rates in soybean.</a> Ann. Botany. 88, 235-242 (2001).</li><li>Badotti, F., 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=Switching+the+mode+of+sucrose+utilization+by+Saccharomyces+cerevisiae.">Switching the mode of sucrose utilization by Saccharomyces cerevisiae.</a> Microb. Cell Fact. 7, 4 (2008).</li><li>Kushwaha, R., Lloyd, T. D., Schafermeyer, K. R., Kumar, S., Downie, A. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+Late+Embryogenesis+Abundant+(LEA)+Protein+Putative+Interactors+Using+Phage+Display.">Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display.</a> Int. J. Mol. Sci. 13, 6582-6603 (2012).</li><li>Sorensen, H. P., Mortensen, K. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soluble+expression+of+recombinant+proteins+in+the+cytoplasm+of+Escherichia+coli.">Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli.</a> Microb. Cell Fact. 4, 2859 (2005).</li><li>Gasser, B., 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=Protein+folding+and+conformational+stress+in+microbial+cells+producing+recombinant+proteins:+a+host+comparative+overview.">Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview.</a> Microb. Cell Fact. 7, 11 (2008).</li><li>Daly, R., Hearn, M. T. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Expression+of+heterologous+proteins+in+Pichia+pastoris:+a+useful+experimental+tool+in+protein+engineering+and+production.">Expression of heterologous proteins in Pichia pastoris: a useful experimental tool in protein engineering and production.</a> J. Mol. Recognit. 18, 119-138 (1002).</li><li>Davis, T. R., 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=Comparative+recombinant+protein+production+of+eight+insect+cell+lines.">Comparative recombinant protein production of eight insect cell lines.</a> In Vitro Cell Dev. Biol. Anim. 29, 388-390 (1993).</li><li>Kost, T. A., Condreay, J. P., Jarvis, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Baculovirus+as+versatile+vectors+for+protein+expression+in+insect+and+mammalian+cells.">Baculovirus as versatile vectors for protein expression in insect and mammalian cells.</a> Nat. Biotechnol. 23, 567-575 (2005).</li><li>Popescu, S. 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=Differential+binding+of+calmodulin-related+proteins+to+their+targets+revealed+through+high-density+Arabidopsis+protein+microarrays.">Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.</a> Proc. Natl. Acad. Sci. U.S.A. 104, 4730-4735 (2007).</li><li>Popescu, S. C., Snyder, M., Dinesh-Kumar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arabidopsis+protein+microarrays+for+the+high-throughput+identification+of+protein-protein+interactions.">Arabidopsis protein microarrays for the high-throughput identification of protein-protein interactions.</a> Plant Signal Behav. 2, 416-420 (2007).</li><li>Al-Fageeh, M. B., Marchant, R. J., Carden, M. J., Smales, C. 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+cold-shock+response+in+cultured+mammalian+cells:+Harnessing+the+response+for+the+improvement+of+recombinant+protein+production.">The cold-shock response in cultured mammalian cells: Harnessing the response for the improvement of recombinant protein production.</a> Biotechnol. Bioeng. 93, 829-835 (2006).</li><li>Wurm, F. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production+of+recombinant+protein+therapeutics+in+cultivated+mammalian+cells.">Production of recombinant protein therapeutics in cultivated mammalian cells.</a> Nat. Biotechnol. 22, 1393-1398 (2004).</li></ol>

Os autores não têm nada a revelar.

Ao executar o experimento em três poços replicados, fago adquirida independentemente de a mesma ligação com a proteína de isca pode ser distinguida, mesmo se eles são o mesmo clone (isto é, não houve diferença na sequência de nucleótidos da região de CDS que foi adquirido, mas estes têm sido recuperado a partir de poços independentes). Caso contrário, a única maneira de diferenciar entre o fago que codifica para a mesma ligação com a proteína isco é, se eles são independentemente inverter r...

Por que usar de apresentação de fagos e seleção de afinidade em vez de uma miríade de outras técnicas disponíveis para descobrir e investigar as interações de proteínas com outras moléculas? Phage display pode reivindicar algumas vantagens únicas em relação a outros métodos de detecção de interações proteína-ligante 1-3 incluindo o seguinte: Muito amplo repertório de moléculas de isca A principal razão é na diversidade de moléculas capazes de actuar como isco na selecção por afinidade 4. A exibição em fagos é um meio muito poderoso para isolar fragmentos de proteínas que interagem com outras proteínas, hidratos de carbono, nucleótidos, etc 5 Essencialmente, se um polímero / molécula pode ser ligada a um suporte recuperável, que podem ser rastreados para afinidade com as proteínas apresentadas em fagos. Além disso, a molécula de isca pode ser acedido para determinar se ele retém a actividade biológica quando imobilizada 6, se as condições usadas para reduce / eliminar a sua actividade são eficazes ou 6, para introduzir as modificações pós-tradução para o isco antes da selecção de afinidade. Resistência aos fagos a fatores externos Uma segunda razão para a utilização de apresentação de fagos, é que é possível que alguns iscos pode exigir esforço ambiental (calor, altas concentrações de agente osmótico, co-factores específicos, etc.) Para capturar as proteínas que interagem com, ou as proteínas apresentadas em fagos pode necessitar ser de alguma forma alterados antes da selecção de afinidade. O factor principal a ser estudado é a interacção entre o isco e proteína, não a condição que permite a interacção ocorrer, ou se é letal para o organismo de teste. O fago T7 é particularmente bem adequada para estes estudos porque pode suportar condições experimentais agressivos tanto intacta e viável (por exemplo, o máximo térmico publicado para a viabilidade de T7 é ~ 60 ° C 7). Como um exemplo de alteração fago exibido próproteínas, ao analisar o proteoma semente Arabidopsis thaliana para substratos de proteínas da enzima de reparação, Proteína Isoaspartyl Metil Transferease (PIMT), o vírus utilizado nestes estudos foi &quot;idade&quot;, durante uma semana, antes de cada seleção afinidade rodada, para incentivar a introdução de isoaspartate (isoAsp) resíduos de proteínas suscetíveis 6 que não é possível em organismos que podem reconhecer e reparar / metabolizam essas anormalidades. Metabolicamente inerte Além disso, os fagos são geralmente resistentes aos venenos metabólicos e interferindo pequenas moléculas que, no mínimo, resultar em efeitos pleiotrópicos sobre organismos de teste metabolicamente activas. Após as lavagens de rigor, o veneno é removido antes de uma grande quantidade de bactérias são introduzidos por infecção de modo que o veneno é diluída a uma gama inócuo para a bactéria ou a replicação do fago subsequente. Ao investigar alvos da proteína do reparo PIMTenzima, de S-adenosil-metionina (AdoMet) foi usado para activar a enzima de micro-titulação de placa-bem imobilizada para permitir a captura de proteína alvo, baseando-se S-adenosil-homocisteína (AdoHcy) para inactivar a enzima e proporcionar um controlo negativo útil fixar em do conhecimento que o vírus não seria influenciada negativamente por qualquer AdoMet ou AdoHcy 6. Além disso, os membros de certas famílias Abundante embriogénese tardia (LEA), proteína investigados neste laboratório, são conhecidos para alterar a sua forma, na presença de aditivos tais como sacarose, 8, que podem atingir concentrações tão elevadas como 200 mM em sementes de soja, no ponto de maturidade fisiológica 9. O vírus não está prevista para ser influenciado pela adição de 200 mM de sacarose em cada fase de selecção de afinidade, possivelmente necessário para certas interações proteína LEA-cliente, o que não é o caso de organismos de teste de forma autônoma viáveis ​​10. Este laboratório tem se concentrado em DESCOBERTAg interações proteína-proteína em, sementes desidratadas ou germinando maduros que fundamentam o mecanismo de proteção proteoma armazenadas durante 11 desidratação ou reparação de componentes do proteoma armazenado que são suscetíveis à formação isoAsp uma vez que a semente tem absorvido 6. Assim, a produção e purificação de proteínas recombinantes exigidos como isca em um estado ativo, e garantir que eles permaneçam assim, antes e depois de serem imobilizados, embora freqüentemente difícil, é um dos pilares para o nosso trabalho. No entanto, como cada um dos cenários de produção de proteína recombinante é diferente, as condições para a optimização da produção de proteína recombinante não será abordada aqui. Os utilizadores são convidados a tentar, sempre que possível, para determinar se a proteína imobilizada é funcional (por exemplo, se se trata de uma enzima, fazer um ensaio de enzima nos poços da placa de microtitulação). Isto irá fornecer alguma confiança de que a isca é biologicamente ativo e, portanto, que todas as interações são descobertosum pouco mais propensos a ter relevância biológica.

<table border="1">
 <tbody>
 <tr>
 <td>Name of Reagent/Material</td>
 <td>Company</td>
 <td>Catalog Number</td>
 <td>Comments</td>
 </tr>
 <tr>
 <td>Tryptone</td>
 <td>Becton Dickinson Co.</td>
 <td>211705</td>
 <td></td>
 </tr>
 <tr>
 <td>Yeast Extract</td>
 <td>Becton Dickinson</td>
 <td>212750</td>
 <td></td>
 </tr>
 <tr>
 <td>Agar</td>
 <td>Becton Dickinson</td>
 <td>214010</td>
 <td></td>
 </tr>
 <tr>
 <td>Sodium Chloride</td>
 <td>Fisher Scientific</td>
 <td>BP358-10</td>
 <td></td>
 </tr>
 <tr>
 <td>Agarose</td>
 <td>Research Products International</td>
 <td>A20090</td>
 <td></td>
 </tr>
 <tr>
 <td>Blocking Reagent</td>
 <td>EMD Chemicals Inc.</td>
 <td>69064</td>
 <td></td>
 </tr>
 <tr>
 <td>Tween 20</td>
 <td>Fisher Scientific</td>
 <td>BP337-100</td>
 <td></td>
 </tr>
 <tr>
 <td>Sodium Hydroxide</td>
 <td>Fisher Scientific</td>
 <td>BP359-212</td>
 <td></td>
 </tr>
 <tr>
 <td>Sodium Dodecyl Sulfate</td>
 <td>Fisher Scientific</td>
 <td>BP166-500</td>
 <td></td>
 </tr>
 <tr>
 <td>Tris Base</td>
 <td>Fisher Scientific</td>
 <td>BP152-5</td>
 <td></td>
 </tr>
 <tr>
 <td>Chloroform</td>
 <td>Fisher Scientific</td>
 <td>BP1145-1</td>
 <td></td>
 </tr>
 <tr>
 <td>Escherichia coli BLT5403</td>
 <td>EMD Chemicals Inc.</td>
 <td>BLT5403</td>
 <td>Genotype: F- ompT hsdSB (rB - mB -) gal dcm pAR5403 (AmpR)</td>
 </tr>
 <tr>
 <td>ampicillin, Sodium Salt</td>
 <td>Research Products International</td>
 <td>A40040</td>
 <td></td>
 </tr>
 <tr>
 <td>ethidium bromide</td>
 <td>Fisher Scientific</td>
 <td>BP102-1</td>
 <td></td>
 </tr>
 <tr>
 <td>Bovine Serum Albumin (BSA)</td>
 <td>Sigma-Aldrich Corp.</td>
 <td>A-9647</td>
 <td></td>
 </tr>
 <tr>
 <td>penta-HIS primary antibody</td>
 <td>Qiagen Inc.</td>
 <td>34660</td>
 <td></td>
 </tr>
 <tr>
 <td>Goat anti mouse alkaline phosphatise conjugate</td>
 <td>Sigma-Aldrich Corp.</td>
 <td>A-5153</td>
 <td></td>
 </tr>
 <tr>
 <td>para-nitrophenylphosphate</td>
 <td>Sigma-Aldrich Corp.</td>
 <td>N-7653</td>
 <td></td>
 </tr>
 <tr>
 <td>T7-UP primer</td>
 <td>EMD Chemicals Inc.</td>
 <td></td>
 <td>5'-GGAGCTGTCGTATTCCAGTC-3'</td>
 </tr>
 <tr>
 <td>T7-DOWN primer</td>
 <td>EMD Chemicals Inc.</td>
 <td></td>
 <td>5'-AACCCCTCAAGACCCGTTTA-3'</td>
 </tr>
 <tr>
 <td>Qiaquick PCR Purification kit</td>
 <td>Qiagen Inc.</td>
 <td>28104</td>
 <td></td>
 </tr>
 <tr>
 <td>Qiaquick Gel Extraction kit </td>
 <td>Qiagen Inc.</td>
 <td>28706</td>
 <td></td>
 </tr>
 <tr>
 <td>Big Dye Terminator v3.1 Cycle Sequencing Kit</td>
 <td>Invitrogen Life Technologies</td>
 <td>4336917</td>
 <td></td>
 </tr>
 <tr>
 <td>Heating Block</td>
 <td>Pierce Chemical Co. (Thermo Fisher Scientific Co.)</td>
 <td>18780</td>
 <td></td>
 </tr>
 <tr>
 <td>96 Well Cell Culture Plates</td>
 <td>Corning</td>
 <td>Costar 3590</td>
 <td></td>
 </tr>
 <tr>
 <td>Isotemp Incubator Oven</td>
 <td>Fisher Scientific</td>
 <td>516D</td>
 <td></td>
 </tr>
 <tr>
 <td>Pasteur Pipets, 5 &frac34;"</td>
 <td>Fisher Scientific</td>
 <td>13-678-20A</td>
 <td></td>
 </tr>
 <tr>
 <td>ChromaView Transilluminator</td>
 <td>UVP Inc.</td>
 <td>TS-15</td>
 <td></td>
 </tr>
 <tr>
 <td>UV Shield</td>
 <td>Oberon</td>
 <td>071AF</td>
 <td></td>
 </tr>
 <tr>
 <td>Gloves, Nitrile</td>
 <td>Fisher Scientific</td>
 <td>19-170-010C</td>
 <td></td>
 </tr>
 <tr>
 <td>Sterile 1.5 ml tubes</td>
 <td>USA Scientific Inc</td>
 <td>1615-5500</td>
 <td></td>
 </tr>
 <tr>
 <td>10 ml borosilicate Pipets</td>
 <td>Fisher Scientific</td>
 <td>13-678-25E</td>
 <td></td>
 </tr>
 <tr>
 <td>Borosilicate culture tubes</td>
 <td>Fisher Scientific</td>
 <td>14-961-27</td>
 <td></td>
 </tr>
 <tr>
 <td>Uniskan I, ELISA plate reader</td>
 <td>Labsystem and Flow Laboratories, Helsinki, Finland</td>
 <td>Type 362</td>
 <td></td>
 </tr>
 </tbody>
</table>

a protocol for phage display and affinity selection using recombinant protein baits

Usando fago recombinante como um andaime para apresentar várias porções de proteínas codificadas por uma biblioteca de cDNA direcionalmente clonado para moléculas imobilizadas isca é um meio eficiente para descobrir interações. A técnica tem sido largamente usado para detectar interacções proteína-proteína, mas a molécula do isco a ser desafiados não precisa ser restrito a proteínas. O protocolo aqui apresentado foi optimizada para permitir que um pequeno número de iscos para ser exibido em repetições para maximizar a identificação de clones independentes que apresentam a mesma proteína. Isto permite uma maior confiança de que as proteínas que interagem identificados são interagentes legítimos da molécula isca. Monitorando a título de fagos depois de cada selecção de afinidade rodada fornece informações sobre a forma como a selecção por afinidade está progredindo, bem como sobre a eficácia dos controlos negativos. Um meio de titulação do fago, e como eo que se preparar com antecedência para permitir que este processo avance de forma tão eficiente comopossível, é apresentada. Atributos de amplicões obtidos após isolamento de placas independentes são destacadas que pode ser utilizado para determinar quão bem a selecção de afinidade progrediu. Problemas técnicas para minimizar falsos positivos ou de contornar persistentemente recuperado fago tiro são explicados. Meios de reduzir a contaminação viral surto são discutidos.

Ser capaz de prejudicar a capacidade de o isco para interagir com proteínas exibidas em fagos (metabolicamente envenenando o isco) proporciona um controlo negativo potente para esta técnica. Também é aconselhável para determinar se o isco,, quando ligados à placa de microtitulação, mantém a sua função. Ambos os cheques aumentará a confiança que interagem, proteínas exibida de fagos recuperados pela isca nonpoisoned são legítimos. Amostragem de três triplicados de cada cavida...

Watch this Scientific Journal Video about A Protocol for Phage Display and Affinity Selection Using Recombinant Protein Baits at JoVE.com

A Protocol for Phage Display and Affinity Selection Using Recombinant Protein Baits

A exibição em fagos é uma técnica poderosa para captura de proteínas ou fracções de proteínas que interagem com uma molécula de interesse imobilizada. Uma vez tomada uma decisão sobre o tipo de biblioteca de cDNA de fagos para criar e tela, o protocolo descrito aqui permite a seleção de afinidade eficiente levando à identificação de interagentes.

Um protocolo para exibição Fago e Affinity Seleção Usando Iscas proteína recombinante

Using  recombinant phage as a scaffold to present various protein portions encoded by  a directionally cloned cDNA library to immobilized bait molecules ...

a-protocol-for-phage-display-affinity-selection-using-recombinant

Research

JoVE Journal

Biology

33.8K visualizações.  University of Kentucky.  A exibição em fagos é uma técnica poderosa para captura de proteínas ou fracções de proteínas que interagem com uma molécula de interesse imobilizada. Uma vez tomada uma decisão sobre o tipo de biblioteca de cDNA de fagos para criar e tela, o protocolo descrito aqui permite a seleção de afinidade eficiente levando à identificação de interagentes. 

Vídeo: A Protocol for Phage Display and Affinity Selection Using Recombinant Protein Baits

A Method For Production of Recombinant mCD1d Protein in Insect Cells.

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated heavy chains that are noncovalently associated with beta2-microglobulin. They bind lipids rather than peptides. Although their structure confirms the similarity of CD1 proteins to MHC class I and class II antigen presenting molecules, the mCD1d groove is relatively narrow, deep, and highly hydrophobic and it has two binding pockets instead of the several shallow pockets described for the classical MHC-encoded antigen-presenting molecules. Based upon their amino acid sequences, such a hydrobphobic groove provides an ideal environment for the binding of lipid antigens. The Natural Killer T (NKT) cells use their TCR to recognize glycolipids bound to or presented by CD1d. T cells reactive to lipids presented by CD1 have been involved in the protection against autoimmune and infectious diseases and in tumor rejection. Thus, the ability to identify, purify , and track the response of CD1-reactive NKT cell is of great importance . The generation of tetramers of alpha Galactosyl ceramide (a-Galcer) with CD1d has significant insight into the biology of NKT cells. Tetramers constructed from other CD1 molecules have also been generated and these new reagents have greatly expanded the knowledge of the functions of lipid-reactive T cells, with potential use in monitoring the response to lipid-based vaccines and in the diagnosis of autoimmune diseases and other treatments.

A Method to prepare Insect cells and infect them with baculovirus for the the purpose of production of recombinant mCD1d proteinand generating mCD1d tetramers.

Um método para produção de proteína recombinante em células de inseto mCD1d.

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated ...

Biologia

Using the GELFREE 8100 Fractionation System for Molecular Weight-Based Fractionation with Liquid Phase Recovery

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based fractionation. The system is comprised of single-use, 8-sample capacity cartridges and a benchtop GELFREE Fractionation Instrument. During separation, a constant voltage is applied between the anode and cathode reservoirs, and each protein mixture is electrophoretically driven from a loading chamber into a specially designed gel column gel. Proteins are concentrated into a tight band in a stacking gel, and separated based on their respective electrophoretic mobilities in a resolving gel. As proteins elute from the column, they are trapped and concentrated in liquid phase in the collection chamber, free of the gel. The instrument is then paused at specific time intervals, and fractions are collected using a pipette. This process is repeated until all desired fractions have been collected. If fewer than 8 samples are run on a cartridge, any unused chambers can be used in subsequent separations.
This novel technology facilitates the quick and simple separation of up to 8 complex protein mixtures simultaneously, and offers several advantages when compared to previously available fractionation methods. This system is capable of fractionating up to 1mg of total protein per channel, for a total of 8mg per cartridge. Intact proteins over a broad mass range are separated on the basis of molecular weight, retaining important physiochemical properties of the analyte. The liquid phase entrapment provides for high recovery while eliminating the need for band or spot cutting, making the fractionation process highly reproducible1.

The accompanying video describes the use of the GELFREE 8100 Fractionation System, which partitions complex protein samples on the basis of molecular weight and recovers the fractions in liquid phase. The video describes how the technology works, how it is used, and provides resultant data, with polyacrylamide gel electrophoresis analysis of fractionated bovine liver homogenate.

Usando o sistema de fracionamento GELFREE 8100 para Fracionamento baseada no peso molecular com Recovery Fase Líquida

The GELFREE 8100 Fractionation System is a novel protein fractionation system designed to maximize protein recovery during molecular weight based ...

Primer-Free Aptamer Selection Using A Random DNA Library

Aptamers are highly structured oligonucleotides (DNA or RNA) that can bind to targets with affinities comparable to antibodies 1. They are identified through an in vitro selection process called Systematic Evolution of Ligands by EXponential enrichment (SELEX) to recognize a wide variety of targets, from small molecules to proteins and other macromolecules 2-4. Aptamers have properties that are well suited for in vivo diagnostic and/or therapeutic applications: Besides good specificity and affinity, they are easily synthesized, survive more rigorous processing conditions, they are poorly immunogenic, and their relatively small size can result in facile penetration of tissues.
Aptamers that are identified through the standard SELEX process usually comprise ~80 nucleotides (nt), since they are typically selected from nucleic acid libraries with ~40 nt long randomized regions plus fixed primer sites of ~20 nt on each side. The fixed primer sequences thus can comprise nearly ~50% of the library sequences, and therefore may positively or negatively compromise identification of aptamers in the selection process 3, although bioinformatics approaches suggest that the fixed sequences do not contribute significantly to aptamer structure after selection 5. To address these potential problems, primer sequences have been blocked by complementary oligonucleotides or switched to different sequences midway during the rounds of SELEX 6, or they have been trimmed to 6-9 nt 7, 8. Wen and Gray 9 designed a primer-free genomic SELEX method, in which the primer sequences were completely removed from the library before selection and were then regenerated to allow amplification of the selected genomic fragments. However, to employ the technique, a unique genomic library has to be constructed, which possesses limited diversity, and regeneration after rounds of selection relies on a linear reamplification step. Alternatively, efforts to circumvent problems caused by fixed primer sequences using high efficiency partitioning are met with problems regarding PCR amplification 10.
We have developed a primer-free (PF) selection method that significantly simplifies SELEX procedures and effectively eliminates primer-interference problems 11, 12. The protocols work in a straightforward manner. The central random region of the library is purified without extraneous flanking sequences and is bound to a suitable target (for example to a purified protein or complex mixtures such as cell lines). Then the bound sequences are obtained, reunited with flanking sequences, and re-amplified to generate selected sub-libraries. As an example, here we selected aptamers to S100B, a protein marker for melanoma. Binding assays showed Kd s in the 10-7 - 10-8 M range after a few rounds of selection, and we demonstrate that the aptamers function effectively in a sandwich binding format.

SELEX protocols comprise multiple rounds of selection, each of which require regeneration of bound ligands, which in turn require fixed primer sequences flanking the random library regions. These fixed primer sequences can interfere with the selection process (false positives and negatives). Here we present a primer-free protocol.

Primer-Free Seleção Aptamer usando uma biblioteca de DNA Aleatório

Aptamers are highly structured oligonucleotides (DNA or RNA) that can bind to targets with affinities comparable to antibodies 1. They are identified ...

Peptides from Phage Display Library Modulate Gene Expression in Mesenchymal Cells and Potentiate Osteogenesis in Unicortical Bone Defects

Two novel synthetic peptides accelerate bone formation and can be delivered using a collagen matrix. The aim of this study was to investigate the effects on bone repair in a unicortical defect model. Treatment of mesenchymal cells produced an increase in alkaline phosphatase activity, showed nodule formation by the cells, and increased the expression of genes for runx2, osterix, bone sialoprotein, and osteocalcin. A collagen sponge soaked with peptide promoted repair of bone defects, whereas the control was less effective. The results from this study demonstrated that mesenchymal cells treated with peptide in vitro differentiate towards osteogenesis, and, that peptides delivered in vivo using a collagen sponge promote the repair of unicortical defects.

A phage display library was used to identify peptide sequences that target bone. The objective was to investigate the effect of these peptides on mesenchymal cell differentiation and to determine their effect on bone regeneration.

Peptídeos de Phage Biblioteca Mostrar modular a expressão de genes em células mesenquimais e potenciar a osteogênese em defeitos ósseos unicorticais

Two novel synthetic peptides accelerate bone formation and can be delivered using a collagen matrix. The aim of this study was to investigate the effects ...

Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification.
HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media should be employed for future, more exhaustive optimization experiments and protein purification runs 4.
The specific protein being purified here is recombinant green fluorescent protein (GFP); however, the approach may be adapted for purifying other proteins with one or more hydrophobic surface regions. GFP serves as a useful model protein, due to its stability, unique light absorbance peak at 397 nm, and fluorescence when exposed to UV light 5. Bacterial lysate containing wild type GFP was prepared in a high-salt buffer, loaded into a Bio-Rad DuoFlow medium pressure liquid chromatography system, and adsorbed to HiTrap HIC columns containing different HIC media. The protein was eluted from the columns and analyzed by in-line and post-run detection methods. Buffer blending, dynamic sample loop injection, sequential column selection, multi-wavelength analysis, and split fraction eluate collection increased the functionality of the system and reproducibility of the experimental approach.

An automated method for identifying suitable hydrophobic interaction chromatography (HIC) media to be used in the process of protein purification is presented. The method utilizes a medium-pressure liquid chromatography system including automated buffer blending, dynamic sample loop injection, sequential column selection, multi-wavelength analysis, and split fraction eluate collection.

Automated interação hidrofóbica Seleção coluna de cromatografia para uso na purificação de proteínas

In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction ...

A Protocol for Computer-Based Protein Structure and Function Prediction

Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function to improve the understanding of their biological role. Although experimental methods can provide detailed information for a small fraction of these proteins, computational modeling is needed for the majority of protein molecules which are experimentally uncharacterized. The I-TASSER server is an on-line workbench for high-resolution modeling of protein structure and function. Given a protein sequence, a typical output from the I-TASSER server includes secondary structure prediction, predicted solvent accessibility of each residue, homologous template proteins detected by threading and structure alignments, up to five full-length tertiary structural models, and structure-based functional annotations for enzyme classification, Gene Ontology terms and protein-ligand binding sites. All the predictions are tagged with a confidence score which tells how accurate the predictions are without knowing the experimental data. To facilitate the special requests of end users, the server provides channels to accept user-specified inter-residue distance and contact maps to interactively change the I-TASSER modeling; it also allows users to specify any proteins as template, or to exclude any template proteins during the structure assembly simulations. The structural information could be collected by the users based on experimental evidences or biological insights with the purpose of improving the quality of I-TASSER predictions. The server was evaluated as the best programs for protein structure and function predictions in the recent community-wide CASP experiments. There are currently &gt;20,000 registered scientists from over 100 countries who are using the on-line I-TASSER server.

Guidelines for computer based structural and functional characterization of protein using the I-TASSER pipeline is described. Starting from query protein sequence, 3D models are generated using multiple threading alignments and iterative structural assembly simulations. Functional inferences are thereafter drawn based on matches to proteins with known structure and functions.

Um protocolo para Computer-Based Estrutura de Proteínas e de Previsão de Função

Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function to improve the ...

Identification of Protein Interacting Partners Using Tandem Affinity Purification

A critical and often limiting step in understanding the function of host and viral proteins is the identification of interacting cellular or viral protein partners. There are many approaches that allow the identification of interacting partners, including the yeast two hybrid system, as well as pull down assays using recombinant proteins and immunoprecipitation of endogenous proteins followed by mass spectrometry identification1. Recent studies have highlighted the utility of double-affinity tag mediated purification, coupled with two specific elution steps in the identification of interacting proteins. This approach, termed Tandem Affinity Purification (TAP), was initially used in yeast2,3 but more recently has been adapted to use in mammalian cells4-8.
As proof-of-concept we have established a tandem affinity purification (TAP) method using the well-characterized eukaryotic translation initiation factor eIF4E9,10.The cellular translation factor eIF4E is a critical component of the cellular eIF4F complex involved in cap-dependent translation initiation10. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence8. To forgo the need for the generation of clonal cell lines, we developed a rapid system that relies on the expression of the TAP-tagged bait protein from an episomally maintained plasmid based on pMEP4 (Invitrogen). Expression of tagged murine eIF4E from this plasmid was controlled using the cadmium chloride inducible metallothionein promoter.
Lysis of the expressing cells and subsequent affinity purification via binding to rabbit IgG agarose, TEV protease cleavage, binding to streptavidin linked agarose and subsequent biotin elution identified numerous proteins apparently specific to the eIF4E pull-down (when compared to control cell lines expressing the TAP tag alone). The identities of the proteins were obtained by excision of the bands from 1D SDS-PAGE and subsequent tandem mass spectrometry. The identified components included the known eIF4E binding proteins eIF4G and 4EBP-1. In addition, other components of the eIF4F complex, of which eIF4E is a component were identified, namely eIF4A and Poly-A binding protein. The ability to identify not only known direct binding partners as well as secondary interacting proteins, further highlights the utility of this approach in the characterization of proteins of unknown function.

Tandem affinity purification is a robust approach for the identification of protein binding partners. As proof of concept, this methodology was applied to the well-characterized translation initiation factor eIF4E to co-precipitate the host cell factors involved in translation initiation. This method is easily adapted to any cellular or viral protein.

Identificação de parceiros de proteína Interagir utilizando Tandem purificação por afinidade

A critical and often limiting step in understanding the function of host and viral proteins is the identification of interacting cellular or viral protein ...

A Liquid Phase Affinity Capture Assay Using Magnetic Beads to Study Protein-Protein Interaction: The Poliovirus-Nanobody Example

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein labeled, this method can be implemented for the investigation of protein-protein interactions. It is based on one hand on the recognition of the tagged protein by cobalt coated magnetic beads and on the other hand on the interaction between the tagged protein and a second specific protein that is labeled. First, the labeled and tagged proteins are mixed and incubated at room temperature. The magnetic beads, that recognize the tag, are added and the bound fraction of labeled protein is separated from the unbound fraction using magnets. The amount of labeled protein that is captured can be determined in an indirect way by measuring the signal of the labeled protein remained in the unbound fraction. The described liquid phase affinity assay is extremely useful when conformational conversion sensitive proteins are assayed. The development and application of the assay is demonstrated for the interaction between poliovirus and poliovirus recognizing nanobodies1. Since poliovirus is sensitive to conformational conversion2 when attached to a solid surface (unpublished results), the use of ELISA is limited and a liquid phase based system should therefore be preferred. An example of a liquid phase based system often used in polioresearch3,4 is the micro protein A-immunoprecipitation test5. Even though this test has proven its applicability, it requires an Fc-structure, which is absent in the nanobodies6,7. However, as another opportunity, these interesting and stable single-domain antibodies8 can be easily engineered with different tags. The widely used (His)6-tag shows affinity for bivalent ions such as nickel or cobalt, which can on their turn be easily coated on magnetic beads. We therefore developed this simple quantitative affinity capture assay based on cobalt coated magnetic beads. Poliovirus was labeled with 35S to enable unhindered interaction with the nanobodies and to make a quantitative detection feasible. The method is easy to perform and can be established with a low cost, which is further supported by the possibility of effectively regenerating the magnetic beads.

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. It is a reliable technique based on the interaction between magnetic beads and tagged proteins (e.g. nanobodies) on one hand and the affinity between the tagged protein and a second, labeled protein (e.g. poliovirus) on the other.

A fase líquida ensaio de captura de afinidade usando pérolas magnéticas para estudar interação proteína-proteína: O Exemplo Poliovírus Nanobody-

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein ...

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in current research and a plethora of methods for their investigation is available1. Protein-protein interactions often are highly dynamic and may depend on subcellular localization, post-translational modifications and the local protein environment2. Therefore, they should be investigated in their natural environment, for which co-immunoprecipitation approaches are the method of choice3. Co-precipitated interaction partners are identified either by immunoblotting in a targeted approach, or by mass spectrometry (LC-MS/MS) in an untargeted way. The latter strategy often is adversely affected by a large number of false positive discoveries, mainly derived from the high sensitivity of modern mass spectrometers that confidently detect traces of unspecifically precipitating proteins. A recent approach to overcome this problem is based on the idea that reduced amounts of specific interaction partners will co-precipitate with a given target protein whose cellular concentration is reduced by RNAi, while the amounts of unspecifically precipitating proteins should be unaffected. This approach, termed QUICK for QUantitative Immunoprecipitation Combined with Knockdown4, employs Stable Isotope Labeling of Amino acids in Cell culture (SILAC)5 and MS to quantify the amounts of proteins immunoprecipitated from wild-type and knock-down strains. Proteins found in a 1:1 ratio can be considered as contaminants, those enriched in precipitates from the wild type as specific interaction partners of the target protein. Although innovative, QUICK bears some limitations: first, SILAC is cost-intensive and limited to organisms that ideally are auxotrophic for arginine and/or lysine. Moreover, when heavy arginine is fed, arginine-to-proline interconversion results in additional mass shifts for each proline in a peptide and slightly dilutes heavy with light arginine, which makes quantification more tedious and less accurate5,6. Second, QUICK requires that antibodies are titrated such that they do not become saturated with target protein in extracts from knock-down mutants.
Here we introduce a modified QUICK protocol which overcomes the abovementioned limitations of QUICK by replacing SILAC for 15N metabolic labeling and by replacing RNAi-mediated knock-down for affinity modulation of protein-protein interactions. We demonstrate the applicability of this protocol using the unicellular green alga Chlamydomonas reinhardtii as model organism and the chloroplast HSP70B chaperone as target protein7 (Figure 1). HSP70s are known to interact with specific co-chaperones and substrates only in the ADP state8. We exploit this property as a means to verify the specific interaction of HSP70B with its nucleotide exchange factor CGE19.

A Protocol for the Identification of Protein-protein Interactions Based on 15N Metabolic Labeling, Immunoprecipitation, Quantitative Mass Spectrometry and Affinity Modulation

We present a variation of the QUICK (QUantitative Immunoprecipitation Combined with Knockdown) approach that was introduced previously to distinguish between true and false protein-protein interactions. Our approach is based on 15N metabolic labeling, the modulation of affinities of protein-protein interactions by the presence/absence of ATP, immunoprecipitation, and quantitative mass spectrometry.

Um protocolo para a identificação de interações proteína-proteína Baseado<sup&gt; 15</sup&gt; Etiquetagem N Metabólica, imunoprecipitação, Quantitativa Espectrometria de Massa e Affinity Modulação

Protein-protein interactions are fundamental for many biological processes in the cell. Therefore, their characterization plays an important role in ...

High-throughput Purification of Affinity-tagged Recombinant Proteins

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity.
In order to attribute the different phenotypes to the nature of the mutation - rather than to fluctuating experimental conditions - it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates1-5.
Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex6-8. TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase9-11. This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase4. Altogether, we generated, purified and analysed 381 mutants - a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results.
This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins.

We describe a method for the affinity-tagged purification of recombinant proteins using liquid-handling robotics. This method is generally applicable to the small-scale purification of soluble His-tagged proteins in a high-throughput format.

De alto rendimento de purificação de afinidade com tag Proteínas Recombinantes

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further ...