This work was supported by the Lehigh University Start-up Package. We thank Dr. Walter Fast for providing the GST-PAD4 plasmid for protein expression.

1. PAD4 Trasformazione, Espressione e purificazione <ol><li> Per PAD4 trasformazione, trasformare il plasmide contenente pGEX PAD4 GST fusione in chimicamente competente E. Coli (BL21 (DE3)), le cellule per l&#39;espressione di proteine ​​utilizzando la seguente procedura. Preparare chimicamente competente (cloruro di calcio) E. Coli (BL21 (DE3)), le cellule secondo protocolli standard. <ol><li> Scongelare 50 ml di preparato in precedenza BL21 chimicamente competente (DE3) celle su ghiaccio e mescolare con 1 ml di plasmide pGEX contenente gene PAD4 in una provetta da 5 ml. Incubare la miscela in ghiaccio per 10 min, agitando delicatamente ogni 2 min. </li><li> Heat Shock cellule collocando la miscela in un bagno d&#39;acqua a 42 ° per 40 sec. Porre immediatamente la miscela di cellule-plasmide indietro su ghiaccio per 2 minuti per permettere alle cellule di recuperare. Aggiungere 1 ml di brodo LB sterile al composto e mettere in ghiaccio per 1 min. </li><li> Incubare il calore cellule scioccato a 37 ° C, agitazione a 250 rpm per 1hr. Pipettare 75 ml di cellule trasformate su una piastra di agar ampicillina resistenti e incubare a 37 ° C per 15 h. Piastra Conservare a 4 ° C. </li></ol></li><li> PAD4 Expression. <ol><li> Raccogliere 1 colonia di (DE3) cellule BL21 dalla piastra di agar ampicillina e posto in 5 ml di LB contenente ampicillina 1x. Posto in incubatrice e agitare O / N a 37 ° C. </li><li> Trasferire i 5 ml di LB (avviamento) in 1 L di sterile LB contenente ampicillina triidrato 1x (MW 403,45 g / mol). Posizionare la crescita in un incubatore agitazione 37 ° C. Monitorare l&#39;OD 600 della crescita. Quando la crescita raggiunge un diametro esterno 600 di 0,3, muovere la crescita in 16 ° C agitazione incubatore. </li><li> Dopo aver raggiunto un OD 600 di 0,6, induce le cellule con isopropylthiagalactoside 0,3 mM (IPTG, MW 238,30 g / mol). Consentono alle cellule siano scossi per 15 ore a 16 ° C. </li><li> Celle di raccolta per centrifugazione a 4000 xg per 20 minuti a 0 ° C. Eliminare il surnatante e conservare pellet a -80 ° C. </li></ol></li><li> PAD4 Purificazione <ol><li> Risospendere il pellet contenente il PAD4 espresso in BL21 (DE3) cellule in tampone 50 mM NaCl (MW 58.44 g / mol), 300 mM NaH 2 PO 4 (PM 119.98 g / mol), imidazolo 10 mM (MW 68,077 g / mol), 0,1 mM fluoruro phenylmethylsulfonyl (PMSF, MW 174,94 g / mol) e 1 mM ditiotreitolo (DTT, 154.25 g / mol), pH = 8,0. </li><li> Lisare le cellule tramite sonicazione per 15 min a 4 ° C. Dopo sonicazione, centrifugare il lisato cellulare a 20.000 xg per 20 min a 0 ° C. Eliminare il surnatante e riporlo. Batch il surnatante con il glutatione (GSH) agarosio per 30 minuti a RT. </li><li> Scolare il surnatante dal GST perline / colonna per gravità. Lavare perline con 4 x 25 ml di 1x PBS (tampone fosfato, pH = 8.0) a temperatura ambiente. </li><li> Eluire PAD4 con 2 x 10 ml di tampone di eluizione, Tris 50 mM (idrossimetil) aminometano (Tris Base, MW 121,14 g / mol), 10 mM glutatione (GSH, MW 307,32 g / mol), pH = 8,0. </li><li> Concentrato PAD4 con 100k MW cut-oprovette da centrifuga ff e centrifugare a 4000 xg per 20 minuti a 4 ° C. Aliquota di proteine ​​in 200 volumi in microlitri 1,0 ml provette da microcentrifuga e conservare a -80 ° C. </li></ol></li></ol> 2. Preparare soluzioni madre di buffer <ol><li> Pesare il cloruro di sodio (NaCl, MW 58.44 g / mol) e preparare una soluzione 2 M. Mescolare fino a quando la soluzione chiara. </li><li> Pesare Tris (idrossimetil) aminometano (Tris Base, MW 121,14 g / mol) e preparare una soluzione 2 M, pH = 8,0. Mescolare fino a quando la soluzione chiara. </li><li> Pesare diidrato cloruro di calcio (CaCl 2 2H 2 O, MW 147.01 g / mol) e preparare una soluzione 500 mM. Mescolare fino a quando la soluzione chiara. </li><li> Pesare Tris (2-carbossietil) fosfina (TCEP, MW 250,19 g / mol) e preparare una soluzione 200 mM. Mescolare fino a quando la soluzione chiara e conservare a -20 ° C. </li><li> Pesare ditiotreitolo (DTT, MW 154,25 g / mol) e preparare una soluzione 1 M. Mescolare fino a quando la soluzione chiara e conservare a -20 ° C. </li><li> Preparareuna soluzione allo 0,5% di Triton X-100. </li><li> Pesare etilendiamminotetraacetico (EDTA, MW 292,24 g / mol) e preparare una soluzione 100 mM. Mescolare fino a quando la soluzione chiara. </li><li> Pesare Z- Arg- Arg- 7- amido- 4- metilcumarina cloridrato (ZRcoum, MW 621,69 g / mol) e preparare una soluzione 10 mM in dimetilsolfossido (DMSO). </li></ol> 3. PAD4 test a 37 ° C <ol><li> Da 10 ZRcoum mM magazzino, preparare una soluzione 125 mM di ZRcoum in acqua. Questa soluzione 125 mM ZRcoum sarà Soluzione A. </li><li> Preparare un buffer di 62,5 mM NaCl, 62,5 mM Tris, 12,5 mM CaCl 2, 6,25 mM DTT, e 5 mM PAD4 (pH = 8,0). Questo sarà soluzione B. </li><li> Preparare un buffer di 62,5 mM NaCl, 62,5 mM Tris, 12,5 mM CaCl 2 e 6,25 mM DTT (pH = 8,0). Questo sarà soluzione C. </li><li> Pesare tripsina, cristallino (da pancreas bovino) e preparare 10 mg / ml in EDTA 100 mM. Mescolare fino a quando la soluzione chiara e conservare a -20° C. Questo sarà soluzione D. </li><li> Ottenere una piastra a 96 pozzetti e designare un numero di pozzi per i controlli (non PAD4) e pozzi di prova (+ PAD4). </li><li> Pipettare 160 ml di soluzione B in pozzi di prova e pipetta 160 ml di soluzione di C nei pozzetti di controllo. Incubare per 15 minuti a 37 ° C. </li><li> Pipettare 40 ml di soluzione A in tutti i pozzetti e incubare a 37 ° C per 45 min. </li><li> Pipettare 10 ml di dH 2 O a metà dei pozzetti di controllo e la metà dei pozzi di prova. Per l&#39;altra metà dei pozzetti di controllo e comandi di test, pipetta 10 ml di soluzione di D. Incubare per 10 min a 37 ° C. </li><li> Ottenere una fluorescenza lettura su un lettore multimodale con lunghezza d&#39;onda di eccitazione di 345 nm e una lunghezza d&#39;onda di emissione di 465 nm. </li></ol> 4. PAD4 test a temperatura ambiente <ol><li> Da 10 ZRcoum mM magazzino, preparare una soluzione di 50 mM di ZRcoum in acqua. Questa soluzione ZRcoum 50 micron sarà Soluzione A. </li><li> Preparare un buffer di Na 100 mMCl, Tris 100 mM, 20 mM CaCl 2, 2 TCEP mM, 0,02% Triton X-100, e 8 mM PAD4 (pH = 8,0). Questo sarà soluzione B. </li><li> Preparare un buffer di NaCl 100 mM, Tris 100 mM, 20 mM CaCl 2, 2 TCEP mM e 0,02% Triton X-100 (pH = 8,0). Questo sarà soluzione C. </li><li> Pesare tripsina, cristallino (da pancreas bovino) e preparare 10 mg / ml in EDTA 100 mM. Mescolare fino a quando la soluzione chiara e conservare a -20 ° C. Questo sarà soluzione D. </li><li> Ottenere una piastra da 384 pozzetti e designare pozzetti per i controlli (non PAD4) e pozzi di prova (+ PAD4). </li><li> Pipettare 25 ml di soluzione B in pozzi di prova e pipetta 25 ml di soluzione di C nei pozzetti di controllo. Consentire buffer con / senza PAD4 ad incubare in pozzetti per 20 minuti a RT. </li><li> Pipettare 25 ml di soluzione C in tutti i pozzetti e incubare per 45 minuti a temperatura ambiente. </li><li> Pipettare 10 ml di dH 2 O a metà dei pozzetti di controllo e la metà dei pozzi di prova. Per l&#39;altra metà dei pozzetti di controllo e comandi di test, pipette 10 ml della soluzione D. Incubare a temperatura ambiente per 10 min. </li><li> Ottenere una fluorescenza lettura su un lettore multimodale con lunghezza d&#39;onda di eccitazione di 345 nm e una lunghezza d&#39;onda di emissione di 465 nm. </li></ol> 5. PAD4 Andamento temporale saggi a 37 ° C e RT <ol><li> Da 10 ZRcoum mM magazzino, preparare una soluzione 125 mM di ZRcoum in acqua. Questa soluzione 125 mM ZRcoum sarà Soluzione A. </li><li> Preparare un buffer di 62,5 mM NaCl, 62,5 mM Tris, 12,5 mM CaCl 2, 6,25 mM DTT, e 5 mM PAD4 (pH = 8,0). Questo sarà soluzione B. </li><li> Pesare tripsina, cristallino (da pancreas bovino) e preparare 10 mg / ml in EDTA 100 mM. Mescolare fino a quando la soluzione chiara e conservare a -20 ° C. Questo sarà soluzione C. </li><li> Ottenere 2 piastre a 96 pozzetti e pipetta 160 ml di soluzione di B in # quantità di pozzi (# di pozzi dipenderà da quanti punti di tempo). </li><li> Incubare una piastra a 96 pozzetti a 37 ° C. Incubare l&#39;altra piastra da 96 pozzetti a temperatura ambiente. </li><li> Semeette 40 ml di soluzione A in tutti i pozzetti in entrambe le piastre a 96 pozzetti e subito Pipettare 10 ml di Soluzione C nelle t = 0 min pozzi. Continuare ad aggiungere 10 ml di soluzione C in punti temporali specifici prima di aver spento tutti i pozzetti. </li><li> Ottenere una fluorescenza lettura su un lettore multimodale con lunghezza d&#39;onda di eccitazione di 345 nm e una lunghezza d&#39;onda di emissione di 465 nm. </li></ol> 6. PAD4 Inibizione test a temperatura ambiente <ol><li> Da 10 ZRcoum mM magazzino, preparare una soluzione 83 mM di ZRcoum in acqua. Questa soluzione ZRcoum 83 mM sarà Soluzione A. </li><li> Pesare Cl-amidina (MW 424,8 g / mol) e preparare una soluzione madre a 100 micron. Questo sarà soluzione B. </li><li> Preparare un buffer di NaCl 100 mM, Tris 100 mM, 20 mM CaCl 2, 2 TCEP mM, 0,02% Triton X-100, e 8 mM PAD4 (pH = 8,0). Questo sarà soluzione C. </li><li> Preparare un buffer di NaCl 100 mM, Tris 100 mM, 20 mM CaCl 2, 2 TCEP mM e 0,02% Triton X-100 (pH = 8,0). Thè sarà Soluzione D. </li><li> Pesare tripsina, cristallino (da pancreas bovino) e preparare 10 mg / ml in EDTA 100 mM. Mescolare fino a quando la soluzione chiara e conservare a -20 ° C. Questo sarà Soluzione E. </li><li> Ottenere una piastra da 384 pozzetti e designare pozzi per i controlli (non PAD4), pozzi di prova (+ PAD4), e pozzi di inibizione (PAD4 + Cl-ammidinici). </li><li> Pipettare 25 ml di soluzione C in pozzi di prova e pipetta 25 ml di soluzione di D nei pozzetti di controllo. Consentire buffer con / senza PAD4 ad incubare in pozzetti per 20 minuti a RT. </li><li> Pipettare 10 ml di soluzione B nei pozzetti di inibizione e incubare per 20 minuti a Rte. </li><li> Pipettare 15 ml di soluzione A in tutti i pozzetti e incubare per 45 minuti a temperatura ambiente. </li><li> Pipettare 10 ml di soluzione E a tutti i pozzetti. Incubare a temperatura ambiente per 10 minuti. </li><li> Ottenere una fluorescenza lettura su un lettore multimodale con lunghezza d&#39;onda di eccitazione di 345 nm e una lunghezza d&#39;onda di emissione di 465 nm. </li></ol> 7. greggio lisato Assaya RT <ol><li> Dopo la raccolta delle cellule dal PAD4 1 L di crescita, risospendere le cellule in 10 ml di 50 mM Tris, 50 mM NaCl, 0.1 mM phenylmethylsulfonyl fluoruro (PMSF, MW 174,94 g / mol) e 1 mM ditiotreitolo (DTT, 154.25 g / mol), pH = 8.0. </li><li> Lisare le cellule tramite sonicazione per 15 min a 4 ° C. Centrifugare il lisato cellulare a 20.000 xg per 20 min a 0 ° C. Concentrare il surnatante limpido per la metà del volume mediante centrifugazione a 4000 rpm a 4 ° C con 100k MW provette di cut-off. </li><li> Da 10 ZRcoum mM magazzino, preparare una soluzione 250 mM di ZRcoum in acqua. Questa soluzione 250 mM ZRcoum sarà Soluzione A. </li><li> Preparare un buffer di NaCl 100 mM, Tris 100 mM, 20 mM CaCl 2, e 2 TCEP mM (pH = 8,0). Questo sarà soluzione B. </li><li> Pesare tripsina, cristallino (da pancreas bovino) e preparare 10 mg / ml in EDTA 100 mM. Mescolare fino a quando la soluzione chiara e conservare a -20 ° C. Questo sarà soluzione C. </li><li> Ottenere una piastra da 384 pozzetti nero e designmangiato pozzetti per i controlli (senza lisato cellulare) e le fonti di prova (+ lisato cellulare). </li><li> Pipettare 100 ml di soluzione B in tutti i pozzetti e le pipette 60 ml di lisato cellulare nei pozzetti di prova. Incubare per 20 minuti a RT. </li><li> Pipettare 40 ml di soluzione A in tutti i pozzetti e incubare per 45 minuti a temperatura ambiente. </li><li> Pipettare 10 ml di soluzione C a tutti i pozzetti. Incubare a temperatura ambiente per 10 minuti. </li><li> Ottenere una fluorescenza lettura sul lettore multimodale con lunghezza d&#39;onda di eccitazione di 345 nm e una lunghezza d&#39;onda di emissione di 465 nm. </li></ol>

<ol>
	<li>Jensen, O. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interpreting+the+protein+language+using+proteomics.">Interpreting the protein language using proteomics.</a> Nat. Rev. Mol. Cell Biol. 7, 391-403 (2006).</li><li>Sims, R. J., Reinberg, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Is+there+a+code+embedded+in+proteins+that+is+based+on+post-translational+modifications.">Is there a code embedded in proteins that is based on post-translational modifications.</a> Nat. Rev. Mol. Cell Biol. 9, 815-820 (2008).</li><li>Pandey, A., Mann, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomics+to+study+genes+and+genomes.">Proteomics to study genes and genomes.</a> Nature. 405, 837-846 (2000).</li><li>Berger, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+complex+language+of+chromatin+regulation+during+transcription.">The complex language of chromatin regulation during transcription.</a> Nature. 447, 407-412 (2007).</li><li>Fischle, W., Wang, Y., Allis, C. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Binary+switches+and+modification+cassettes+in+histone+biology+and+beyond.">Binary switches and modification cassettes in histone biology and beyond.</a> Nature. 425, 475-479 (2003).</li><li>Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D., Patel, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=How+chromatin-binding+modules+interpret+histone+modifications:+lessons+from+professional+pocket+pickers.">How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.</a> Nat. Struct. Mol. Biol. 14, 1025-1040 (2007).</li><li>Seet, B. T., Dikic, I., Zhou, M. M., Pawson, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reading+protein+modifications+with+interaction+domains.">Reading protein modifications with interaction domains.</a> Nat. Rev. Mol. Cell Biol. 7, 473-483 (2006).</li><li>Strahl, B. D., Allis, C. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+language+of+covalent+histone+modifications.">The language of covalent histone modifications.</a> Nature. 403, 41-45 (2000).</li><li>Vossenaar, E. R., Zendman, A. J., van Venrooij, W. J., Pruijn, G. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PAD,+a+growing+family+of+citrullinating+enzymes:+genes,+features+and+involvement+in+disease.">PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease.</a> Bioessays. 25, 1106-1118 (2003).</li><li>Gyorgy, B., Toth, E., Tarcsa, E., Falus, A., Buzas, E. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Citrullination:+a+posttranslational+modification+in+health+and+disease.">Citrullination: a posttranslational modification in health and disease.</a> Int. J. Biochem. Cell Biol. 38, 1662-1677 (2006).</li><li>Nakashima, K., Hagiwara, T., Yamada, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+localization+of+peptidylarginine+deiminase+V+and+histone+deimination+in+granulocytes.">Nuclear localization of peptidylarginine deiminase V and histone deimination in granulocytes.</a> J. Biol. Chem. 277, 49562-49568 (2002).</li><li>Hagiwara, T., Hidaka, Y., Yamada, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deimination+of+histone+H2A+and+H4+at+arginine+3+in+HL-60+granulocytes.">Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes.</a> Biochemistry. 44, 5827-5834 (2005).</li><li>Kearney, P. L., 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=Kinetic+characterization+of+protein+arginine+deiminase+4:+a+transcriptional+corepressor+implicated+in+the+onset+and+progression+of+rheumatoid+arthritis.">Kinetic characterization of protein arginine deiminase 4: a transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis.</a> Biochemistry. 44, 10570-10582 (2005).</li><li>Christophorou, M. A., 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=Citrullination+regulates+pluripotency+and+histone+H1+binding+to+chromatin.">Citrullination regulates pluripotency and histone H1 binding to chromatin.</a> Nature. 507 (7490), 104-108 (2014).</li><li>Brinkmann, V., 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=Neutrophil+extracellular+traps+kill+bacteria.">Neutrophil extracellular traps kill bacteria.</a> Science. 303, 1532-1535 (2004).</li><li>Li, P., 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=PAD4+is+essential+for+antibacterial+innate+immunity+mediated+by+neutrophil+extracellular+traps.">PAD4 is essential for antibacterial innate immunity mediated by neutrophil extracellular traps.</a> J. Exp. Med. 207, 1853-1862 (2010).</li><li>Wang, Y., 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=Histone+hypercitrullination+mediates+chromatin+decondensation+and+neutrophil+extracellular+trap+formation.">Histone hypercitrullination mediates chromatin decondensation and neutrophil extracellular trap formation.</a> J. Cell. Biol. 184, 205-213 (2009).</li><li>Wang, S., Wang, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peptidylarginine+deiminases+in+citrullination,+gene+regulation,+health+and+pathogenesis.">Peptidylarginine deiminases in citrullination, gene regulation, health and pathogenesis.</a> Biochim. Biophys. Acta. 1829, 1126-1135 (2013).</li><li>Trouw, L. A., Mahler, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Closing+the+serological+gap:+promising+novel+biomarkers+for+the+early+diagnosis+of+rheumatoid+arthritis.">Closing the serological gap: promising novel biomarkers for the early diagnosis of rheumatoid arthritis.</a> Autoimmun. Rev. 12, 318-322 (2012).</li><li>Chang, X., Fang, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PADI4+and+tumourigenesis.">PADI4 and tumourigenesis.</a> Cancer Cell Int. 10, 7 (2010).</li><li>Wang, L., Chang, X., Yuan, G., Zhao, Y., Wang, P. <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+peptidylarginine+deiminase+type+4+in+ovarian+tumors.">Expression of peptidylarginine deiminase type 4 in ovarian tumors.</a> Int. J. Biol. Sci. 6, 454-464 (2010).</li><li>Chang, X., 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=Investigating+the+pathogenic+role+of+PADI4+in+oesophageal+cancer.">Investigating the pathogenic role of PADI4 in oesophageal cancer.</a> Int. J. Biol. Sci. 7, 769-781 (2011).</li><li>Zhang, X., 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=Genome-wide+analysis+reveals+PADI4+cooperates+with+Elk-1+to+activate+c-Fos+expression+in+breast+cancer+cells.">Genome-wide analysis reveals PADI4 cooperates with Elk-1 to activate c-Fos expression in breast cancer cells.</a> PLoS Genet. 7, (2011).</li><li>Tanikawa, 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=Regulation+of+histone+modification+and+chromatin+structure+by+the+p53-PADI4+pathway.">Regulation of histone modification and chromatin structure by the p53-PADI4 pathway.</a> Nat. Commun. 3, 676 (2012).</li><li>Cui, X., 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=The+induction+of+microRNA-16+in+colon+cancer+cells+by+protein+arginine+deiminase+inhibition+causes+a+p53-dependent+cell+cycle+arrest.">The induction of microRNA-16 in colon cancer cells by protein arginine deiminase inhibition causes a p53-dependent cell cycle arrest.</a> PLos One. 8, (2013).</li><li>Jones, J. E., Causey, C. P., Knuckley, B., Slack-Noyes, J. L., Thompson, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+arginine+deiminase+4+(PAD4):+Current+understanding+and+future+therapeutic+potential.">Protein arginine deiminase 4 (PAD4): Current understanding and future therapeutic potential.</a> Curr. Opin. Drug Discov. Devel. 12, 616-627 (2009).</li><li>Li, P., 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=Regulation+of+p53+target+gene+expression+by+peptidylarginine+deiminase+4.">Regulation of p53 target gene expression by peptidylarginine deiminase 4.</a> Mol. Cell Biol. 28, 4745-4758 (2008).</li><li>Wang, Y., 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=Anticancer+peptidylarginine+deiminase+(PAD)+inhibitors+regulate+the+autophagy+flux+and+the+mammalian+target+of+rapamycin+complex+1+activity.">Anticancer peptidylarginine deiminase (PAD) inhibitors regulate the autophagy flux and the mammalian target of rapamycin complex 1 activity.</a> J. Biol. Chem. 287, 25941-25953 (2012).</li><li>Slack, J. L., Causey, C. P., Thompson, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+arginine+deiminase+4:+a+target+for+an+epigenetic+cancer+therapy.">Protein arginine deiminase 4: a target for an epigenetic cancer therapy.</a> Cell. Mol. Life Sci. 68, 709-720 (2011).</li><li>Luo, Y., Knuckley, B., Lee, Y. H., Stallcup, M. R., Thompson, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+fluoroacetamidine-based+inactivator+of+protein+arginine+deiminase+4:+design,+synthesis,+and+in+vitro+and+in+vivo+evaluation.">A fluoroacetamidine-based inactivator of protein arginine deiminase 4: design, synthesis, and in vitro and in vivo evaluation.</a> J. Am. Chem. Soc. 128, 1092-1093 (2006).</li><li>Knuckley, 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=Substrate+specificity+and+kinetic+studies+of+PADs.">Substrate specificity and kinetic studies of PADs.</a> Biochemistry. 1, 4852-4863 (2010).</li><li>Knipp, M., Vasak, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+colorimetric+96-well+microtiter+plate+assay+for+the+determination+of+enzymatically+formed+citrulline.">A colorimetric 96-well microtiter plate assay for the determination of enzymatically formed citrulline.</a> Anal. Biochem. 286, 257-264 (2000).</li><li>Knuckley, 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=A+fluopol-ABPP+HTS+assay+to+identify+PAD+inhibitors.">A fluopol-ABPP HTS assay to identify PAD inhibitors.</a> Chem. Commun. 46, 7175-7177 (2010).</li><li>Bicker, K. L., Subramanian, V., Chumanevich, A. A., Hofseth, L. J., Thompson, P. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Seeing+citrulline:+development+of+a+phenylglyoxal-based+probe+to+visualize+protein+citrullination.">Seeing citrulline: development of a phenylglyoxal-based probe to visualize protein citrullination.</a> J. Am. Chem. Soc. 134, 17015-17018 (2012).</li><li>Wang, Q., Priestman, M. A., Lawrence, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monitoring+of+protein+arginine+deiminase+activity+by+using+fluorescence+quenching:+multicolor+visualization+of+citrullination.">Monitoring of protein arginine deiminase activity by using fluorescence quenching: multicolor visualization of citrullination.</a> Angew. Chem. Int. Ed. Engl. 52, 2323-2325 (2013).</li><li>Jones, J. E., 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=Synthesis+and+screening+of+a+haloacetamidine+containing+library+to+identify+PAD4+selective+inhibitors.">Synthesis and screening of a haloacetamidine containing library to identify PAD4 selective inhibitors.</a> ACS Chem. Biol. 7, 160-165 (2012).</li><li>Dreyton, C. J., 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=.">.</a> Optimization and characterization of a pan protein arginine deiminase (PAD) inhibitor. , (2010).</li><li>Shimoyama, S., 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=Deimination+stabilizes+histone+H2A/H2B+dimers+as+revealed+by+electrospray+ionization+mass+spectrometry.">Deimination stabilizes histone H2A/H2B dimers as revealed by electrospray ionization mass spectrometry.</a> J. Mass Spectrom. 45, 900-908 (2010).</li><li>Luo, Y., 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=Inhibitors+and+inactivators+of+protein+arginine+deiminase+4:+functional+and+structural+characterization.">Inhibitors and inactivators of protein arginine deiminase 4: functional and structural characterization.</a> Biochemistry. 45, 11727-11736 (2006).</li></ol>

The authors have nothing to disclose.

Herein, a fluorescence based assay was successfully developed that monitors the activity of PAD4. The assay has proven to be incredibly robust in a number of high-throughput conditions and is also compatible with whole cell lysates37.
The affinity between the histone proteins and the DNA strands surrounding it loosens due the neutralization of the positive charge on the arginine side chain upon citrullination. It was envisioned that the neutralization of the arginine side-chain coul...

Un gran numero di proteine ​​di mammifero sono fortemente modificato dall&#39;azione di enzimi seguito della biosintesi delle proteine ​​del ribosoma. Queste modificazioni post-traduzionali (PTM) possono aumentare notevolmente la diversità funzionale del proteoma modificando le dimensioni, la carica, la struttura, e lo stato di oligomerizzazione (tra le altre caratteristiche) di proteine ​​1-3. Di conseguenza, il cambiamento della struttura di proteine ​​può portare a conseguenze fisiologiche, quali la degradazione delle proteine, differenziazione cellulare, segnalazione, la modulazione dell&#39;espressione genica, e le interazioni proteina-proteina. Mentre queste modificazioni sono prevalenti in una grande percentuale di tutte le proteine ​​umane, il terminale termina il istoni subiscono un numero insolitamente elevato di modificazioni covalenti 4. Istoni sono una famiglia di proteine ​​strutturali che facilitano la condensazione del DNA genomico. Covalenti modificazioni delle code istoniche non strutturati sono effettuate e regolate da una series di enzimi in grado di catalizzare la modifica covalente di residui (scrittori), invertire le stesse modifiche (gomme), e distinguere tra i cambiamenti che sono impresse sulle code degli istoni (lettori) 5-7. In realtà, la maggior parte dei PTM conosciute si possono osservare in questo breve segmento del istoni compresi metilazione, fosforilazione, acetilazione, sumoilazione, ubiquitinazione e citrullination 8. Citrullination comporta la conversione del peptidil-arginina al t RNA non codificato peptidil-citrullina (Figura 1A). Le proteine, responsabili di questa catena di neutralizzazione lato, sono membri del PAD (p eptide un rginine eiminase d) famiglia di proteine, che sono tutti enzimi calcio-dipendenti. 9,10. Fino ad oggi, cinque membri della famiglia PAD sono state descritte (PAD1, PAD2, PAD3, PAD4, e PAD6). Ogni membro di questa famiglia sembra indirizzare proteine ​​cellulari distinti e anche visualizza unique profili distribuzione tissutale. PAD4 è l&#39;unico membro di questa famiglia di proteine ​​note per essere localizzato all&#39;interno del nucleo tramite una sequenza di localizzazione nucleare 11. Pertanto, è stato dimostrato per deiminate un numero di bersagli nucleari, comprese le catene laterali di arginina sulle code N-terminali degli istoni H2A residuo di arginina (3 H2R3), H3 (H3R2, H3R17 e H3R26) e H4 (H4R3) 12, 13. Mentre ciascuna delle isoenzimi PAD hanno funzioni fisiologiche specifiche e critiche, PAD4 ha ricevuto molta più attenzione a causa del suo ruolo in una serie di processi umani in cellule di entrambi i malati e sani. Recentemente, PAD4 ha dimostrato di essere un membro della pluripotenza trascrizionale di rete 14. Entrambi i livelli di espressione PAD4 e l&#39;attività hanno dimostrato di essere elevata durante la riprogrammazione e la terra statali stati pluripotenti nei topi. Controllando la regolazione dei geni di cellule staminali, PAD4 può mantenere un ruolo centrale nella riprogrammazione cellulare efficienza. PAD4 è stato anche coinvolto nelformazione di trappole extracellulari dei neutrofili, che dopo il legame di agenti patogeni consentire loro liquidazione sistema. La hypercitrullination di proteine ​​istoniche da PAD4 induce decondensazione della cromatina, che serve come materiale di base per l&#39;incapsulamento di batteri patogeni da parte della trappola extracellulare, in modo da scongiurare infezioni batteriche 15,16. Inoltre, PAD4 è stata trovata a svolgere un ruolo attivo in una serie di malattie umane. È stato precedentemente dimostrato che l&#39;espressione aberrante di PAD4 è associato con l&#39;insorgenza e la gravità di artrite reumatoide, morbo di Alzheimer, morbo di Parkinson, sclerosi multipla e 17. Infatti, la presenza di anticorpi anti-proteina citrullinati è uno dei biomarcatori diagnostici e prognostici più affidabili e definitive di artrite reumatoide 18. Analogamente, l&#39;attività PAD4 disregolazione stato recentemente osservato in un certo numero di tumori umani inclusi dell&#39;ovaio, della mammella, del polmone, und tumori esofagei 19-22. Il legame tra PAD4 e il cancro ha dimostrato di essere mediata attraverso l&#39;oncogene ELK1 o tramite il tumore soppressore p53 proteina 22,23 e lavoro precedente ha suggerito che PAD4 potrebbe essere un anti-cancro nuovo bersaglio terapeutico 17,24,25. Come una prova di principio studio, l&#39;esaurimento delle PAD4 via shRNA nella linea cellulare del cancro del colon-retto HCT116 si è rivelato essere sufficiente per indurre l&#39;apoptosi e arresto del ciclo cellulare 26. Un inibitore irreversibile PAD4 recentemente sviluppato ha portato ad una riduzione del settanta per cento della massa tumorale nei topi 27. Piuttosto notevole, l&#39;inibizione PAD4 sembrava operare come una terapia mirata che ha provocato l&#39;uccisione selettiva delle cellule cancerose risparmiando cellule non trasformate. L&#39;uso di piccole molecole per disattivare la funzione di PAD4 può rivelarsi una potente strategia nuova per colpire le cellule tumorali o di aumentare chemioterapici cancro esistenti 28. Purtroppo, un potenda inibitore reversibile PAD4 deve ancora essere scoperto. Un certo numero di inibitori covalenti sono stati sviluppati utilizzando il / maniglia imidine fluoro cloro che imita il substrato arginina 27,29,30 e hanno dimostrato di essere strumenti pratici per comprendere il ruolo di PAD4 in entrambe le cellule statali sani e malati. Tuttavia, queste molecole inibiscono tutte le pastiglie attivi con potenza simile. Pertanto, la necessità di un saggio superficiale che segnala l&#39;attività di PAD4 è cruciale. Fino ad oggi, PAD4 saggi sono stati descritti che collegano il rilascio di ammoniaca dalla reazione a una lettura colorimetrica 31, utilizzare un analogo substrato chloroamidine fluorescente per fluorescenza polarizzata test 32, si basano sulla reazione acida assistita tra gliossale e citrullina 33, e coppia l&#39;attività PAD4 ad una fluorescenza dequenching passo 34. Di questi, solo il modificatore strategia haloacetamidine covalente ha dimostrato di essere compatibile con scre elevato throughputpiattaforme zare 32,35,36. Descriviamo un test basato sulla fluorescenza facile che misura in modo affidabile l&#39;attività di PAD4. Il test, che mostra un forte rapporto segnale-rumore, velocità di analisi, e la robustezza della misura, ha il potenziale per scoprire un inibitore PAD4 veramente potente e selettivo.

<table><tbody><tr><td>LB Broth, Miller (LURIA-BERTANI)</td><td>Amresco</td><td>J106-2KG</td><td>&lt;a href=&quot;http://www.amresco-inc.com/&quot;&gt;http://www.amresco-inc.com&lt;/a&gt;</td></tr><tr><td>Ampicillin Trihydrate (Off-white Powder), Fisher BioReagents</td><td>Fisher Scientific</td><td>BP902-25&amp;nbsp;</td><td>&lt;a href=&quot;http://www.fishersci.com/&quot;&gt;http://www.fishersci.com&lt;/a&gt;</td></tr><tr><td>Isopropylthiagalactonse (IPTG)</td><td>Life Technogolies</td><td>15529-019</td><td>&lt;a href=&quot;http://www.lifetechnologies.com/&quot;&gt;http://www.lifetechnologies.com&lt;/a&gt;</td></tr><tr><td>All Buffer Salts&amp;nbsp;</td><td>Fisher Scientific</td><td></td><td>Can purchase from Fisher Scieintifc; VWR; Acros; Sigma-Aldrich; etc.</td></tr><tr><td>Protino Glutathione (GSH) agarose&amp;nbsp;</td><td>Machery-Nagel</td><td>745500.10</td><td>Store at 4 &amp;deg;C; http://www.mn-net.com/</td></tr><tr><td>Chloroamidine&amp;nbsp;</td><td>Cayman Chemical&amp;nbsp;</td><td>10599</td><td>Store at -20 &amp;deg;C; https://www.caymanchem.com/app/template/Home.vm</td></tr><tr><td>Triton X-100</td><td>Sigma Aldrich</td><td>X100-100ML</td><td>&lt;a href=&quot;http://www.sigmaaldrich.com/&quot;&gt;www.sigmaaldrich.com&lt;/a&gt;</td></tr><tr><td>Corning/Nunclon MicroWell plates (96 and 384)</td><td></td><td></td><td>Purchase from Corning; Sigma-Aldrich</td></tr><tr><td>Tecan Infinite 200 / Tecan i-control microplate reader software</td><td></td><td></td><td>&lt;a href=&quot;http://www.tecan.com/&quot;&gt;www.tecan.com&lt;/a&gt;</td></tr><tr><td>Europium Ex. 340/40 Em. 475/15 filter</td><td></td><td></td><td>&lt;a href=&quot;http://www.perkinelmer.com/&quot;&gt;http://www.perkinelmer.com&lt;/a&gt;</td></tr></tbody></table>

fluorescence-based monitoring of pad4 activity via a pro-fluorescence substrate analog

Post-translational modifications may lead to altered protein functional states by increasing the covalent variations on the side chains of many protein substrates. The histone tails represent one of the most heavily modified stretches within all human proteins. Peptidyl-arginine deiminase 4 (PAD4) has been shown to convert arginine residues into the non-genetically encoded citrulline residue. Few assays described to date have been operationally facile with satisfactory sensitivity. Thus, the lack of adequate assays has likely contributed to the absence of potent non-covalent PAD4 inhibitors. Herein a novel fluorescence-based assay that allows for the monitoring of PAD4 activity is described. A pro-fluorescent substrate analog was designed to link PAD4 enzymatic activity to fluorescence liberation upon the addition of the protease trypsin. It was shown that the assay is compatible with high-throughput screening conditions and has a strong signal-to-noise ratio. Furthermore, the assay can also be performed with crude cell lysates containing over-expressed PAD4.

Inizialmente, è stato dimostrato che ZRcoum può riferire sull&#39;attività di PAD4 in un formato di piastra da 96 pozzetti. Wells sono stati incubati con il substrato ZRcoum e in presenza / assenza di PAD4. Dopo un periodo di incubazione di 45 min a 37 ° C, la fluorescenza è stata misurata con un 340/40 - 475/15 nm filtro (Figura 2A). Come previsto, i livelli di fluorescenza sono rimasti bassi come fluoroforo entro ZRcoum (o il citrullinato <strong...

Watch this Scientific Journal Video about Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog at JoVE.com

Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog

PAD4 is an enzyme responsible for the conversion of peptidyl-arginine to peptidyl-citrulline. Dysregulation of PAD4 has been implicated in a number of human diseases. A facile and high-throughput compatible fluorescence based PAD4 assay is described.

Basato sulla fluorescenza Monitoraggio dei PAD4 attività tramite un substrato Analog Pro-fluorescenza

Post-translational modifications may lead to altered protein functional states by increasing the covalent variations on the side chains of many protein ...

fluorescence-based-monitoring-pad4-activity-via-pro-fluorescence

Universidad San Sebastian

Research

JoVE Journal

Chemistry

9.8K Views.  Lehigh University. PAD4 is an enzyme responsible for the conversion of peptidyl-arginine to peptidyl-citrulline. Dysregulation of PAD4 has been implicated in a number of human diseases. A facile and high-throughput compatible fluorescence based PAD4 assay is described.

Video: Fluorescence-based Monitoring of PAD4 Activity via a Pro-fluorescence Substrate Analog

Fluorescence detection methods for microfluidic droplet platforms

The development of microfluidic platforms for performing chemistry and biology has in large part been driven by a range of potential benefits that accompany system miniaturisation. Advantages include the ability to efficiently process nano- to femoto- liter volumes of sample, facile integration of functional components, an intrinsic predisposition towards large-scale multiplexing, enhanced analytical throughput, improved control and reduced instrumental footprints.1
In recent years much interest has focussed on the development of droplet-based (or segmented flow) microfluidic systems and their potential as platforms in high-throughput experimentation.2-4 Here water-in-oil emulsions are made to spontaneously form in microfluidic channels as a result of capillary instabilities between the two immiscible phases. Importantly, microdroplets of precisely defined volumes and compositions can be generated at frequencies of several kHz. Furthermore, by encapsulating reagents of interest within isolated compartments separated by a continuous immiscible phase, both sample cross-talk and dispersion (diffusion- and Taylor-based) can be eliminated, which leads to minimal cross-contamination and the ability to time analytical processes with great accuracy. Additionally, since there is no contact between the contents of the droplets and the channel walls (which are wetted by the continuous phase) absorption and loss of reagents on the channel walls is prevented.
Once droplets of this kind have been generated and processed, it is necessary to extract the required analytical information. In this respect the detection method of choice should be rapid, provide high-sensitivity and low limits of detection, be applicable to a range of molecular species, be non-destructive and be able to be integrated with microfluidic devices in a facile manner. To address this need we have developed a suite of experimental tools and protocols that enable the extraction of large amounts of photophysical information from small-volume environments, and are applicable to the analysis of a wide range of physical, chemical and biological parameters. Herein two examples of these methods are presented and applied to the detection of single cells and the mapping of mixing processes inside picoliter-volume droplets. We report the entire experimental process including microfluidic chip fabrication, the optical setup and the process of droplet generation and detection.

Droplet-based microfluidic platforms are promising candidates for high throughput experimentation since they are able to generate picoliter, self-compartmentalized vessels inexpensively at kHz rates. Through integration with fast, sensitive and high resolution fluorescence spectroscopic methods, the large amounts of information generated within these systems can be efficiently extracted, harnessed and utilized.

Metodi di rilevamento a fluorescenza per piattaforme goccia microfluidica

The development of microfluidic platforms for performing chemistry and biology has in large part been driven by a range of potential benefits that ...

Ricerca

Bioingegneria

An Optimized Single-Molecule Pull-Down Assay for Quantification of Protein Phosphorylation

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to measure protein phosphorylation cannot preserve the heterogeneity in phosphorylation across individual proteins. The single-molecule pull-down (SiMPull) assay was developed to investigate the composition of macromolecular complexes via immunoprecipitation of proteins on a glass coverslip followed by single-molecule imaging. The current technique is an adaptation of SiMPull that provides robust quantification of the phosphorylation state of full-length membrane receptors at the single-molecule level. Imaging thousands of individual receptors in this way allows for quantifying protein phosphorylation patterns. The present protocol details the optimized SiMPull procedure, from sample preparation to imaging. Optimization of glass preparation and antibody fixation protocols further enhances data quality. The current protocol provides code for the single-molecule data analysis that calculates the fraction of receptors phosphorylated within a sample. While this work focuses on phosphorylation of the epidermal growth factor receptor (EGFR), the protocol can be generalized to other membrane receptors and cytosolic signaling molecules.

The present protocol describes sample preparation and data analysis to quantify protein phosphorylation using an improved single-molecule pull-down (SiMPull) assay.

Un test di pull-down a singola molecola ottimizzato per la quantificazione della fosforilazione delle proteine

Phosphorylation is a necessary posttranslational modification that regulates protein function and directs cell signaling outcomes. Current methods to ...

Biochimica

Analisi cAMP con cADDis: screening da singola cellula a alto rendimento

Real-Time cAMP Dynamics in Live Cells Using the Fluorescent cAMP Difference Detector In Situ

cAMP Difference Detector In Situ (cADDis) is a novel biosensor that allows for the continuous measurement of cAMP levels in living cells. The biosensor is created from a circularly permuted fluorescent protein linked to the hinge region of Epac2. This creates a single fluorophore biosensor that displays either increased or decreased fluorescence upon binding of cAMP. The biosensor exists in red and green upward versions, as well as green downward versions, and several red and green versions targeted to subcellular locations. To illustrate the effectiveness of the biosensor, the green downward version, which decreases in fluorescence upon cAMP binding, was used. Two protocols using this sensor are demonstrated: one utilizing a 96-well plate reading spectrophotometer&#160;compatible with high-throughput screening and another utilizing single-cell imaging on a fluorescent microscope. On the plate reader, HEK-293 cells cultured in 96-well plates were stimulated with 10 &#181;M forskolin or 10 nM isoproterenol, which induced rapid and large decreases in fluorescence in the green downward version. The biosensor was used to measure cAMP levels in individual human airway smooth muscle (HASM) cells monitored under a fluorescent microscope. The green downward biosensor displayed similar responses to populations of cells when stimulated with forskolin or isoproterenol. This single-cell assay allows visualization of the biosensor location at 20x and 40x magnification. Thus, this cAMP biosensor is sensitive and flexible, allowing real-time measurement of cAMP in both immortalized and primary cells, and with single cells or populations of cells. These attributes make cADDis a valuable tool for studying cAMP signaling dynamics in living cells.

Autore in primo piano: Avanzamento del rilevamento cAMP in tempo reale nelle cellule utilizzando il biosensore cADDis

The protocol presented in this study illustrates the effectiveness of the cAMP Difference Detector In Situ in measuring cAMP through two methods. One method utilizes a 96-well plate reading spectrophotometer with HEK-293 cells. The other method demonstrates individual HASM cells under a fluorescent microscope.

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

cAMP Difference Detector In Situ (cADDis) is a novel biosensor that allows for the continuous measurement of cAMP levels in living cells. The biosensor is ...

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

Two electrode voltage clamp electrophysiology (TEVC) is a powerful tool to investigate the mechanism of ion transport1 for a wide variety of membrane proteins including ion channels2, ion pumps3, and transporters4. Recent developments have combined site-specific fluorophore labeling alongside TEVC to 
concurrently examine the conformational dynamics at specific residues and function of these proteins on the surface of single cells.
We will describe a method to study the conformational dynamics of membrane proteins by simultaneously monitoring fluorescence and current changes using voltage-clamp fluorometry. This approach can be used to examine the molecular motion of membrane proteins site-specifically following cysteine replacement and site-directed fluorophore labeling5,6. Furthermore, this method provides an approach to determine distance constraints between specific residues7,8. 
This is achieved by selectively attaching donor and acceptor fluorophores to two mutated cysteine residues of interest.
In brief, these experiments are performed following functional expression of the desired protein on the surface of Xenopus leavis oocytes. The large surface area of these oocytes enables facile functional measurements and a robust fluorescence signal5. It is also possible to readily change the extracellular conditions such as pH, ligand or cations/anions, which can provide further information on the mechanism of membrane proteins4. Finally, recent developments 
have also enabled the manipulation of select internal ions following co-expression with a second protein9.
Our protocol is described in multiple parts. First, cysteine scanning mutagenesis proceeded by fluorophore labeling is completed at residues located at the interface of the transmembrane and extracellular domains. Subsequent experiments are designed to identify residues which demonstrate large changes in fluorescence intensity (&lt;5%)3 upon a conformational change of the protein. Second, these changes in fluorescence intensity are compared to the kinetic parameters of 
the membrane protein in order to correlate the conformational dynamics to the function of the protein10. This enables a rigorous biophysical analysis of the molecular motion of the target protein. Lastly, two residues of the holoenzyme can be labeled with a donor and acceptor fluorophore in order to determine distance constraints using donor photodestruction methods. It is also possible to monitor the relative movement of protein subunits following labeling with a donor and acceptor fluorophore.

Examining the Conformational Dynamics of Membrane Proteins in situ with Site-directed Fluorescence Labeling

We will describe a method which measures the kinetics of ion transport of membrane proteins alongside site-specific analysis of conformational changes using fluorescence on single cells. This technique is adaptable to ion channels, transporters and ion pumps and can be utilized to determine distance constraints between protein subunits.

Esaminando la dinamica conformazionale delle proteine ​​di membrana In situ Con il sito-diretta Etichettatura fluorescenza

Two electrode voltage clamp electrophysiology (TEVC) is a powerful tool to investigate the mechanism of ion transport1 for a wide variety of membrane ...

Biologia

Monitoring Kinase and Phosphatase Activities Through the Cell Cycle by Ratiometric FRET

F&ouml;rster resonance energy transfer (FRET)-based reporters1 allow the assessment of endogenous kinase and phosphatase activities in living cells. Such probes typically consist of variants of CFP and YFP, intervened by a phosphorylatable sequence and a phospho-binding domain. Upon phosphorylation, the probe changes conformation, which results in a change of the distance or orientation between CFP and YFP, leading to a change in FRET efficiency (Fig 1). Several probes have been published during the last decade, monitoring the activity balance of multiple kinases and phosphatases, including reporters of PKA2, PKB3, PKC4, PKD5, ERK6, JNK7, Cdk18, Aurora B9 and Plk19. Given the modular design, additional probes are likely to emerge in the near future10. 
Progression through the cell cycle is affected by stress signaling pathways 11. Notably, the cell cycle is regulated differently during unperturbed growth compared to when cells are recovering from stress12.Time-lapse imaging of cells through the cell cycle therefore requires particular caution. This becomes a problem particularly when employing ratiometric imaging, since two images with a high signal to noise ratio are required to correctly interpret the results. Ratiometric FRET imaging of cell cycle dependent changes in kinase and phosphatase activities has predominately been restricted to sub-sections of the cell cycle8,9,13,14.
Here, we discuss a method to monitor FRET-based probes using ratiometric imaging throughout the human cell cycle. The method relies on equipment that is available to many researchers in life sciences and does not require expert knowledge of microscopy or image processing.

FRET-based reporters are increasingly used to monitor kinase and phosphatase activities in live cells. Here we describe a method on how to use FRET-based reporters to assess cell cycle-dependent changes in target phosphorylation.

Monitoraggio Attività chinasi e fosfatasi attraverso il ciclo cellulare da raziometrica FRET

F&ouml;rster resonance energy transfer (FRET)-based reporters1 allow the assessment of endogenous kinase and phosphatase activities in living cells. Such ...

FRET Microscopy for Real-time Monitoring of Signaling Events in Live Cells Using Unimolecular Biosensors

F&ouml;rster resonance energy transfer (FRET) microscopy continues to gain increasing interest as a technique for real-time monitoring of biochemical and signaling events in live cells and tissues. Compared to classical biochemical methods, this novel technology is characterized by high temporal and spatial resolution. FRET experiments use various genetically-encoded biosensors which can be expressed and imaged over time in situ or in vivo1-2. Typical biosensors can either report protein-protein interactions by measuring FRET between a fluorophore-tagged pair of proteins or conformational changes in a single protein which harbors donor and acceptor fluorophores interconnected with a binding moiety for a molecule of interest3-4. Bimolecular biosensors for protein-protein interactions include, for example, constructs designed to monitor G-protein activation in cells5, while the unimolecular sensors measuring conformational changes are widely used to image second messengers such as calcium6, cAMP7-8, inositol phosphates9 and cGMP10-11. Here we describe how to build a customized epifluorescence FRET imaging system from single commercially available components and how to control the whole setup using the Micro-Manager freeware. This simple but powerful instrument is designed for routine or more sophisticated FRET measurements in live cells. Acquired images are processed using self-written plug-ins to visualize changes in FRET ratio in real-time during any experiments before being stored in a graphics format compatible with the build-in ImageJ freeware used for subsequent data analysis. This low-cost system is characterized by high flexibility and can be successfully used to monitor various biochemical events and signaling molecules by a plethora of available FRET biosensors in live cells and tissues. As an example, we demonstrate how to use this imaging system to perform real-time monitoring of cAMP in live 293A cells upon stimulation with a &beta;-adrenergic receptor agonist and blocker.

F&#246;rster resonance energy transfer (FRET) microscopy is a powerful technique for real-time monitoring of signaling events in live cells using various biosensors as reporters. Here we describe how to build a customized epifluorescence FRET imaging system from commercially available components and how to use it for FRET experiments.

FRET Microscopia per Monitoraggio in tempo reale di segnalazione di eventi in cellule vive Uso Biosensori unimolecolare

F&ouml;rster resonance energy transfer (FRET) microscopy  continues to gain increasing interest as a technique for real-time monitoring  of biochemical ...

Simultaneous Multicolor Imaging of Biological Structures with Fluorescence Photoactivation Localization Microscopy

Localization-based super resolution microscopy can be applied to obtain a spatial map (image) of the distribution of individual fluorescently labeled single molecules within a sample with a spatial resolution of tens of nanometers. Using either photoactivatable (PAFP) or&#160;photoswitchable (PSFP) fluorescent proteins fused to proteins of interest, or organic dyes conjugated to antibodies or other molecules of interest, fluorescence photoactivation localization microscopy (FPALM) can simultaneously image multiple species of molecules within single cells. By using the following approach, populations of large numbers (thousands to hundreds of thousands) of individual molecules are imaged in single cells and localized with a precision of ~10-30 nm. Data obtained can be applied to understanding the nanoscale spatial distributions of multiple protein types within a cell. One primary advantage of this technique is the dramatic increase in spatial resolution: while diffraction limits resolution to ~200-250 nm in conventional light microscopy, FPALM can image length scales more than an order of magnitude smaller. As many biological hypotheses concern the spatial relationships among different biomolecules, the improved resolution of FPALM can provide insight into questions of cellular organization which have previously been inaccessible to conventional fluorescence microscopy. In addition to detailing the methods for sample preparation and data acquisition, we here describe the optical setup for FPALM. One additional consideration for researchers wishing to do super-resolution microscopy is cost: in-house setups are significantly cheaper than most commercially available imaging machines. Limitations of this technique include the need for optimizing the labeling of molecules of interest within cell samples, and the need for post-processing software to visualize results. We here describe the use of PAFP and PSFP expression to image two protein species in fixed cells. Extension of the technique to living cells is also described.

We demonstrate the use of fluorescence photo activation localization microscopy (FPALM) to simultaneously image multiple types of fluorescently labeled molecules&#160;within cells. The techniques described yield the localization of thousands to hundreds of thousands of individual fluorescent labeled proteins, with a precision of tens of nanometers&#160;within single cells.

Localization-based super resolution microscopy can be applied to obtain a spatial map (image) of the distribution of individual fluorescently labeled ...

Utilizing pHluorin-tagged Receptors to Monitor Subcellular Localization and Trafficking

Understanding membrane protein trafficking, assembly, and expression requires an approach that differentiates between those residing in intracellular organelles and those localized on the plasma membrane. Traditional fluorescence-based measurements lack the capability to distinguish membrane proteins residing in different organelles. Cutting edge methodologies transcend traditional methods by coupling pH-sensitive fluorophores with total internal reflection fluorescence microscopy (TIRFM). TIRF illumination excites the sample up to approximately 150 nm from the glass-sample interface, thus decreasing background, increasing the signal to noise ratio, and enhancing resolution. The excitation volume in TIRFM encompasses the plasma membrane and nearby organelles such as the peripheral ER. Superecliptic pHluorin (SEP) is a pH sensitive version of GFP. Genetically encoding SEP into the extracellular domain of a membrane protein of interest positions the fluorophore on the luminal side of the ER and in the extracellular region of the cell. SEP is fluorescent when the pH is greater than 6, but remains in an off state at lower pH values. Therefore, receptors tagged with SEP fluoresce when residing in the endoplasmic reticulum (ER) or upon insertion in the plasma membrane (PM) but not when confined to a trafficking vesicle or other organelles such as the Golgi. The extracellular pH can be adjusted to dictate the fluorescence of receptors on the plasma membrane. The difference in fluorescence between TIRF images at neutral and acidic extracellular pH for the same cell corresponds to a relative number of receptors on the plasma membrane. This allows a simultaneous measurement of intracellular and plasma membrane resident receptors. Single vesicle insertion events can also be measured when the extracellular pH is neutral, corresponding to a low pH trafficking vesicle fusing with the plasma membrane and transitioning into a fluorescent state. This versatile technique can be exploited to study localization, expression, and trafficking of membrane proteins.

Labeling the extracellular domain of a membrane protein with a pH sensitive fluorophore, superecliptic pHluorin (SEP), allows subcellular localization, expression, and trafficking to be determined. Imaging SEP-labeled proteins with total internal reflection fluorescence microscopy (TIRFM) enables the quantification of protein levels in the peripheral ER and plasma membrane.

Utilizzando Recettori pHluorin-tag per il monitoraggio subcellulare localizzazione e il traffico

Understanding membrane protein trafficking, assembly, and expression requires an approach that differentiates between those residing in intracellular ...

Basato sulla fluorescenza Monitoraggio dei PAD4 attività tramite un substrato Analog Pro-fluorescenza

Riepilogo

Esplora Altri Video

Capitoli in questo video

Metodi di rilevamento a fluorescenza per piattaforme goccia microfluidica

Un test di pull-down a singola molecola ottimizzato per la quantificazione della fosforilazione delle proteine

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

Esaminando la dinamica conformazionale delle proteine di membrana In situ Con il sito-diretta Etichettatura fluorescenza

Monitoraggio Attività chinasi e fosfatasi attraverso il ciclo cellulare da raziometrica FRET

FRET Microscopia per Monitoraggio in tempo reale di segnalazione di eventi in cellule vive Uso Biosensori unimolecolare

Simultaneous Multicolor Imaging of Biological Structures with Fluorescence Photoactivation Localization Microscopy

Utilizzando Recettori pHluorin-tag per il monitoraggio subcellulare localizzazione e il traffico

Basato sulla fluorescenza Monitoraggio dei PAD4 attività tramite un substrato Analog Pro-fluorescenza

Riepilogo

Esplora Altri Video

Capitoli in questo video

Metodi di rilevamento a fluorescenza per piattaforme goccia microfluidica

Un test di pull-down a singola molecola ottimizzato per la quantificazione della fosforilazione delle proteine

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

Dinamica del cAMP in tempo reale in cellule vive utilizzando il rivelatore di differenza fluorescente cAMP in situ

Esaminando la dinamica conformazionale delle proteine ​​di membrana In situ Con il sito-diretta Etichettatura fluorescenza

Monitoraggio Attività chinasi e fosfatasi attraverso il ciclo cellulare da raziometrica FRET

FRET Microscopia per Monitoraggio in tempo reale di segnalazione di eventi in cellule vive Uso Biosensori unimolecolare

Simultaneous Multicolor Imaging of Biological Structures with Fluorescence Photoactivation Localization Microscopy

Utilizzando Recettori pHluorin-tag per il monitoraggio subcellulare localizzazione e il traffico

Esaminando la dinamica conformazionale delle proteine di membrana In situ Con il sito-diretta Etichettatura fluorescenza