Siamo molto grati a Victor GJ Rodgers per preziosi consigli. Ringraziamo tutti i membri del gruppo di Liao per molto stretto lavoro di collaborazione e di aiuto con questo studio. Questo studio è stato sostenuto dal National Institutes of Health (Grant AI076504 a JL).

1. Costrutti plasmidici <ol><li> Amplificare le fasi di lettura aperte dei geni mediante PCR, e clonare i prodotti di PCR in pCRII-TOPO vettore. </li><li> Confermare i prodotti dal sequenziamento, e clonare il cDNA codificante CyPet-(pre-SUMO1)-YPet, CyPet-SUMO1, YPet e domini catalitici di SENP1 nella (b) pET28 vettore con un N-terminale tag hexahistidine. </li></ol> 2. Espressione e purificazione di proteine <ol><li> Trasformare cellule di Escherichia coli ceppo BL21 (DE3) con pET28 (b) vettori codificanti CyPet-(pre-SUMO1)-YPet, CyPet-SUMO1, YPet ed i domini catalitici di SENP1. </li><li> Coltivato i batteri trasformati in mezzo 2xYT per 3 ore a 37 ° C (agitando a 250 rpm) per raggiungere una densità ottica di 0,5 a 600 nm. </li><li> Aggiungere 100 mM isopropil-β-D-tiogalattoside (IPTG) (concentrazione finale) per indurre l&#39;espressione di proteine ​​e agitare per 16 ore a 25 ° C a 200 rpm. </li><li> Raccogliere i batteri da centrifugzione a 10.000 rpm a 4 ° C per 5 minuti e risospendere in un tampone di 20 mM Tris-HCl (pH 7,4), 50 mM NaCl, 5 mM e imidazolo. </li><li> Sonicare le cellule per 10 min a 5-sec intervalli in un livello di potenza di 25 W utilizzando MiSonics 4000 sonicatore e alla loro raccolta per centrifugazione a 35.000 xg a 4 ° C per 30 min. </li><li> Impostare la colonna con 500 ml Ni-NTA perline per 1 L cultura e trasferire il sopranatante in colonna. </li><li> Lavare la resina con tampone di 20 mM Tris-HCl (pH 7,4), 500 mM NaCl, 10 mM imidazolo e due volte. </li><li> Proteine ​​eluire con tampone di 20 mM Tris-HCl (pH 7,4), NaCl 500 mM, e 500 mM imidazolo e dialisi in un tampone di 20 mM Tris-HCl (pH 7,4), 50 mM NaCl, 1 mM ditiotreitolo (DTT) a 4 ° C per una notte. </li><li> Determinare le concentrazioni delle proteine ​​purificate dal saggio Bradford. Metodo alternativo per la misura della concentrazione di proteine ​​sarà SDS-PAGE elettroforesi su gel e quindi colorato con Coomassie blue seguita con imagingquantitativa. </li></ol> 3. Quantitativa FRET Analisi dello spettro <ol><li> La strategia generale per il saggio è basato su FRET segnalazione (Figura 1). La coppia FRET, CyPet e YPet, è stato etichettato per la N-e C-termini, rispettivamente, di pre-SUMO1. SENP1 scinde la proteina di fusione CyPet-(pre-SUMO1)-YPet al Gly-Gly del sito in SUMO1 del C-terminale e, quindi, rilascia la coda SUMO con YPet. Il segnale di FRET è interrotto, con conseguente aumento delle emissioni da CyPet e una drastica riduzione delle emissioni di YPet alla lunghezza d&#39;onda di eccitazione CyPet. </li><li> Quando eccitato dalla luce di lunghezza d&#39;onda 414 nm, l&#39;emissione totale di fluorescenza di CyPet-(pre-SUMO1)-YPet a 530 nm può essere derivato da tre fonti: emissione assoluto FRET indotta YPet, il CyPet emissione diretta e YPet emissione diretta (Figura 2). </li></ol><img alt="Equazione 1" src="/files/ftp_upload/4430/4430eq1.jpg" /> dove FL 530/414 &lt;/ Sub&gt; è l&#39;emissione totale di fluorescenza a 530 nm quando viene eccitato a 414 nm, FL FRET è l&#39;assoluto segnale di FRET, FL CyPet (continua) è l&#39;emissione CyPet diretta quando viene eccitato a 414 nm, e FL YPet (continua) è la YPet emissione diretta quando viene eccitato a 414 nm. L&#39;indice di (continua) sta per contributo. <ol start="3"><li> L&#39;emissione diretta di CyPet a 530 nm è proporzionale alla sua emissione a 475 nm quando viene eccitato a 414 nm con un rapporto costante di α. CyPet-SUMO1 è stato preparato a concentrazioni di 50, 100, 200, 500, e 750 nm e 1 mm , e le emissioni a 475 e 530 nm sono stati misurati dopo eccitazione a 414 nm per determinare α (Figura 3-1). </li><li> L&#39;emissione diretta di YPet a 530 nm in eccitazione a 414 nm è proporzionale alla sua emissione a 530 nm quando viene eccitato a 475 nm con un rapporto costante di β. YPet è stato preparato a concentrazioni di 50, 100, 200, 500, 750 And 1.000 nm e l&#39;emissione a 530 nm è stata misurata quando i campioni sono stati eccitati da lunghezze d&#39;onda di 414 e 475 nm per determinare β (Figura 3-2). </li><li> Quando CyPet-(pre-SUMO1)-YPet è stato digerito dal SENP1, la scissione rilasciato CyPet-SUMO1 e la coda SUMO1 con YPet. Quando il composto è stato eccitato a 414 nm, l&#39;emissione di fluorescenza a 530 nm (FL &#39;530/414) è diminuita ma può ancora essere divisa in tre parti come: </li></ol><img alt="Equazione 2" src="/files/ftp_upload/4430/4430eq2.jpg" /> dove FL &#39;530/414 è il totale delle emissioni di fluorescenza a 530 nm dopo la digestione quando eccitato a 414 nm, FL&#39; FRET è il restante assoluto segnale di FRET, FL &#39;CyPet (475/414) è l&#39;emissione CyPet a 475 nm dopo la digestione quando eccitato a 414 nm (in questo caso l&#39;emissione CyPet è da due parti: non digerito CyPet-(pre-SUMO1)-YPet e digerito CyPet-SUMO1), e FL YPet(530/475) è l&#39;emissione YPet quando eccitato a 475 nm, che è costante se CyPet-(pre-SUMO1)-YPet viene digerito o meno. <ol start="6"><li> Dopo digestione SENP1, il restante FRET emissione (FL &#39;FRET) è: </li></ol><img alt="Equazione 3" src="/files/ftp_upload/4430/4430eq3.jpg" /> dove C è la concentrazione totale di CyPet-(pre-SUMO1)-YPet ed x è la concentrazione di digerito CyPet-(pre-SUMO1)-YPet. <ol start="7"><li> Combinando tutti gli elementi, l&#39;emissione di fluorescenza rilevata a 530 nm in eccitazione di 414 nm (FL &#39;530/414) è: </li></ol><img alt="Equazione 4" src="/files/ftp_upload/4430/4430eq4.jpg" /> 4. FRET saggio basato Proteasi per Enzyme studio cinetico <ol><li> CyPet-(pre-SUMO1)-YPet stato incubato con il dominio catalitico di SENP1 a 37 ° C in un tampone di 20 mM Tris-HCl (pH 7,4), 50 mM NaCl, 0,1% (v /v) Tween-20 e DTT 1 mM in un volume totale di 80 ml e trasferita in piastra a 384 pozzetti. </li><li> Piste stati condotti misurando l&#39;emissione di fluorescenza a 475 e 530 nm dopo eccitazione a 414 nm in un lettore di piastra multipozzetto fluorescenza per 5 minuti con intervalli di 15 sec. </li><li> La velocità di reazione (v) è stata correlata con la variazione della quantità di substrato (S), come: </li></ol><img alt="Equazione 5" src="/files/ftp_upload/4430/4430eq5.jpg" /><ol start="4"><li> La concentrazione di prodotto aumentato esponenzialmente da 0 a [S] 0 (concentrazione del substrato originale) quando t = 0: </li></ol><img alt="Equazione 6" src="/files/ftp_upload/4430/4430eq6.jpg" /><ol start="5"><li> Quando t = 0, la velocità iniziale (V 0) è: </li></ol><img alt="Equazione 7" src="/files/ftp_upload/4430/4430eq7.jpg" /><ol start="6"><li> Il concentration di SENP1 è stato fissato, e la concentrazione di CyPet-(pre-SUMO1)-YPet stata aumentata da 100 volte superiore alla concentrazione di enzima, che è richiesta da Michaelis-Menten. </li><li> Tutte le letture di fluorescenza sono stati analizzati con il metodo di analisi quantitativa FRET e tracciata in Software GraphPad Prism V per adattarsi alla Michaelis-Menten. La regressione non lineare può essere eseguita anche con l&#39;ausilio di pacchetti software più comuni, come i programmi di fogli di calcolo (ad esempio Microsoft Excel). </li></ol> 5. Risultati rappresentativi Maturazione di pre-SUMO1 da SENP1 può essere determinata monitorando i cambiamenti nel segnale di fluorescenza a 475 e 530 nm durante il processo. Il risultato ha mostrato che la velocità di pre-SUMO1 digestione SENP1 in un modo dipendente dalla dose-substrato (Figura 4). Questo suggerisce che il dominio catalitico di SENP1 mostra un&#39;attività eccellente per la maturazione di pre-SUMO1. La reazione inizialevelocità zione sono stati calcolati dalla precedente analisi con diverse concentrazioni di substrato (Tabella 1). Il cat / K k rapporto M è generalmente utilizzato per confrontare le efficienze di differenti enzimi con un substrato o un particolare enzima con substrati diversi. K M e V max può essere ottenuta dalla equazione di Michaelis-Menten tracciando le velocità iniziali diverse, corrispondenti per le diverse concentrazioni di CyPet-(pre-SUMO1)-YPet (Figura 5) cat k è stato ottenuto come.: <img alt="Equazione 8" src="/files/ftp_upload/4430/4430eq8.jpg" /> Secondo l&#39;analisi di cui sopra, il valore calcolato per K M è stato 0,21 ± 0,04 mM, il gatto k era 6,90 ± 0,28 s-1, e il gatto / K M k rapporto era (3,2 ± 0,55) x10 7 M -1 </sup<html> &gt; S -1. <img alt="Figura 1" src="/files/ftp_upload/4430/4430fig1.jpg" /> Figura 1. Grafico di FRET saggio basato proteasi per SENP pre-Sumos maturazione. <img alt="Figura 2" src="/files/ftp_upload/4430/4430fig2.jpg" /> Figura 2. L&#39;analisi quantitativa del segnale fluorescente, come contributi del donatore accettore, e FRET. Dissezione di spettri di emissione da CyPet-(pre-SUMO1)-YPet sotto eccitazione a 414 nm. FL CyPet (530/414) è emissione CyPet di a 530 nm in eccitazione di 414 nm, FL FRET è il FRET indotta emissioni YPet a 530 nm in eccitazione di 414 nm, e FL YPet (530/414) è l&#39;emissione YPet di a 530 nm in eccitazione di 414 nm. load/4430/4430fig3.jpg &quot;/&gt; Figura 3. Calcolo del fattore di emissione α direzione e β. <img alt="Figura 4" src="/files/ftp_upload/4430/4430fig4.jpg" /> Figura 4. Analisi quantitativa di CyPet-(pre-SUMO1)-YPet digerito dai rapporti diversi del dominio catalitico di SENP1. Le reazioni sono state monitorate entro i primi 5 min. <img alt="Figura 5" src="/files/ftp_upload/4430/4430fig5.jpg" /> Figura 5. Michaelis-Menten analisi grafica di digestione CyPet-(pre-SUMO1)-YPet da parte SENP1. I dati sono stati riportati e analizzati da GraphPad Prism V e la regressione non lineare. <table border="1"><tbody><tr><td> [S] (pM) </td><td> V 0 (pM / s) </td></tr><tr><td> 0,115 </td><td> 0,0023 ± 0,00005 </td></tr&gt; <tr><td> 0,214 </td><td> 0,0028 ± 0,00004 </td></tr><tr><td> 0,407 </td><td> 0,0033 ± 0,00007 </td></tr><tr><td> 0,594 </td><td> 0,0037 ± 0,00013 </td></tr><tr><td> 0,725 </td><td> 0,0043 ± 0,00012 </td></tr><tr><td> 1,471 </td><td> 0,0051 ± 0,00036 </td></tr><tr><td> 1,899 </td><td> 0,0050 ± 0,00031 </td></tr><tr><td> 2,300 </td><td> 0,0050 ± 0,00062 </td></tr></tbody></table> Tabella 1. Iniziale determinazione velocità di maturazione pre-SUMO1 da parte SENP1. In ogni concentrazione del substrato, quattro campioni sono stati utilizzati per misurare la digestione. La deviazione standard è venuto dalle variazioni di questi quattro campioni. <table border="1"><tbody><tr><td> K M (pM) </td><td> k cat (s-1) </td><td> k cat / K M (M -1 • s-1) </td></tr><tr><td> 0,21 ± 0,04 </td><td> 6,90 ± 0,28 </td><td> 3,2 ± 0,55 × 10 7 </td></tr></tbody></table> Tabella 2. Parametri cinetici di maturazione pre-SUMO1 da parte SENP1 da quantitativa FRET analisi. La deviazione standard è venuto dai quattro campioni per ogni concentrazione del substrato.

<ol>
	<li>Johnson, E. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+modification+By+SUMO.">Protein modification By SUMO.</a> Annual Review of Biochemistry. 73, 355-382 (2004).</li><li>Gill, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO+and+ubiquitin+in+the+nucleus:+different+functions,+similar+mechanisms.">SUMO and ubiquitin in the nucleus: different functions, similar mechanisms.</a> Genes &amp; Development. 18, 2046-2059 (2004).</li><li>Hay, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO:+a+history+of+modification.">SUMO: a history of modification.</a> Molecular Cell. 18, 1-12 (2005).</li><li>M&#252;ller, S., Hoege, C., Pyrowolakis, G., Jentsch, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUMO,+ubiquitin's+mysterious+cousin.">SUMO, ubiquitin's mysterious cousin.</a> Nature. , 202-210 (2001).</li><li>Hochstrasser, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SP-RING+for+SUMO:+new+functions+bloom+for+a+ubiquitin-like+protein.">SP-RING for SUMO: new functions bloom for a ubiquitin-like protein.</a> Cell. , 5-8 (2001).</li><li>Drag, M., Salvesen, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DeSUMOylating+enzymes-SENPs.">DeSUMOylating enzymes-SENPs.</a> IUBMB Life. 60, 734-742 (2008).</li><li>Mukhopadhyay, D., Dasso, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modification+in+reverse:+the+SUMO+proteases.">Modification in reverse: the SUMO proteases.</a> Trends in Biochemical Sciences. 32, 286-295 (2007).</li><li>Reverter, D., Lima, 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=Structural+basis+for+SENP2+protease+interactions+with+SUMO+precursors+and+conjugated+substrates.">Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.</a> Nature Structural &amp; Molecular Biology. 13, 1060-1068 (2006).</li><li>Shen, 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=SUMO+protease+SENP1+induces+isomerization+of+the+scissile+peptide+bond.">SUMO protease SENP1 induces isomerization of the scissile peptide bond.</a> Nature Structural &amp; Molecular Biology. 13, 1069-1077 (2006).</li><li>Horton, R., Strachan, E., Vogel, K., Riddle, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+substrate+for+deubiquitinating+enzymes+based+on+time-resolved+fluorescence+resonance+energy+transfer+between+terbium+and+yellow+fluorescent+protein.">A substrate for deubiquitinating enzymes based on time-resolved fluorescence resonance energy transfer between terbium and yellow fluorescent protein.</a> Analytical Biochemistry. 360, 138-143 (2007).</li><li>Mikolajczyk, 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=Small+Ubiquitin-related+Modifier+(SUMO)-specific+Proteases:+PROFILING+THE+SPECIFICITIES+AND+ACTIVITIES+OF+HUMAN+SENPs.">Small Ubiquitin-related Modifier (SUMO)-specific Proteases: PROFILING THE SPECIFICITIES AND ACTIVITIES OF HUMAN SENPs.</a> Journal of Biological Chemistry. 282, 26217-26224 (2007).</li><li>Kolli, N., Mikolajczyk, J., Drag, M., Mukhopadhyay, D., Moffatt, N., Dasso, M., Salvesen, G., Wilkinson, K. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distrubition+and+paralogue+specificity+of+mammalian+deSUMOylating+enzymes.">Distrubition and paralogue specificity of mammalian deSUMOylating enzymes.</a> Biochem. J. , 335-344 (2010).</li><li>Drag, M., Mikolajczyk, J., Krishnakumar, I. M., Huang, Z., Salvesen, G. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity+profiling+of+human+deSUMOylating+enzymes+(SENPs)+with+synthetic+substrates+suggests+an+unexpected+specificity+of+two+newly+characterized+members+of+the+family.">Activity profiling of human deSUMOylating enzymes (SENPs) with synthetic substrates suggests an unexpected specificity of two newly characterized members of the family.</a> Biochemical Journal. 409, 461 (2008).</li><li>Engels, I. H., 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+time-resolved+fluorescence+resonance+energy+transfer-based+assay+for+DEN1+peptidase+activity.">A time-resolved fluorescence resonance energy transfer-based assay for DEN1 peptidase activity.</a> Analytical Biochemistry. 390, 85-87 (2009).</li><li>Martin, S., Hattersley, N., Samuel, I., Hay, R., Tatham, 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+fluorescence-resonance-energy-transfer-based+protease+activity+assay+and+its+use+to+monitor+paralog-specific+small+ubiquitin-like+modifier+processing.">A fluorescence-resonance-energy-transfer-based protease activity assay and its use to monitor paralog-specific small ubiquitin-like modifier processing.</a> Analytical Biochemistry. 363, 83-90 (2007).</li><li>Nguyen, A. W., Daugherty, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolutionary+optimization+of+fluorescent+proteins+for+intracellular+FRET.">Evolutionary optimization of fluorescent proteins for intracellular FRET.</a> Nature Biotechnology. 23, 355-360 (2005).</li></ol>

Nessun conflitto di interessi dichiarati.

FRET tecnologia è stata usata per studiare la maturazione pre-SUMO1 da parte SENP1 9. CFP-YFP è stato usato come FRET coppia e analisi raziometrico, che è il rapporto tra accettore di emissioni donatori, è stato utilizzato per caratterizzare le proprietà cinetiche. Tuttavia, non vi è alcuna considerazione di donatore e accettore auto-fluorescenza nella raziometrica tradizionale analisi FRET. Il rapporto non è direttamente correlata con la quantità di substrato digerito. Qu...

<table border="1"><tbody><tr><td> Nome del reagente </td><td> Azienda </td><td> Numero di catalogo </td></tr><tr><td> PCR II TOPO Kit </td><td> Invitrogen </td><td> K466040 </td></tr><tr><td> 2xYT </td><td> Ricerca Prodotti Internationa.l Corp. </td><td> X15600 </td></tr><tr><td> Ni-NTA Agrose </td><td> Thermo Scientific </td><td> 88222 </td></tr><tr><td> Coomassie più (Bradford) Regent Assay </td><td> Thermo Scientific </td><td> 23238 </td></tr><tr><td> Piastra a 384 pozzetti (inferiore di vetro) </td><td> Greiner </td><td> 781892 </td></tr><tr><td> FlexStation II 384 lettore di piastre </td><td> Dispositivo molecolare </td><td></td></tr></tbody></table>

quantitative fret (f&#246;rster resonance energy transfer) analysis for senp1 protease kinetics determination

Reversibili modificazioni post-traduzionali di proteine ​​con proteine ​​ubiquitina o ubiquitina-like (Ubls) sono ampiamente utilizzati per regolare in modo dinamico l&#39;attività della proteina e hanno ruoli diversi in molti processi biologici. Ad esempio, SUMO modifica covalentemente un numero grande o proteine ​​con un ruolo importante in molti processi cellulari, tra cui cellule-regolazione del ciclo, la sopravvivenza cellulare e la morte, danno la risposta del DNA e risposta allo stress 1-5. SENP, come SUMO-specifiche proteasi, funziona come un endopeptidasi nella maturazione dei precursori SUMO o come isopeptidase per rimuovere SUMO dalle sue proteine ​​bersaglio e aggiornare il ciclo sumoilazione 1,3,6,7. L&#39;efficienza catalitica o specificità di un enzima è meglio caratterizzato dal rapporto delle costanti cinetiche, k cat / K M. In diversi studi, i parametri cinetici di SUMO-SENP coppie sono state determinate con vari metodi, tra cui gel di poliacrilammide-based western blot, radIOActive-marcato substrato, composto fluorescente o proteina marcata substrato 8-13. Tuttavia, le poliacrilammide-gel a base di tecniche, che hanno utilizzato i &quot;nativi&quot;, ma le proteine ​​sono laboriosi e tecnicamente impegnativo, che non si prestano ad una dettagliata analisi quantitativa. Il ottenuta k cat / K M da studi usando tetrapeptidi o proteine ​​con ACC (7-ammino-4-carbamoylmetylcoumarin) o AMC (7-ammino-4-metil) fluoroforo erano o fino a due ordini di grandezza inferiore ai substrati naturali o non può chiaramente distinguere le iso-e attività di endopeptidasi SENPs. Saggi della proteasi Recentemente, FRET-based sono stati utilizzati per studiare gli enzimi deubiquitinating (Dubs) o SENPs con il FRET coppia di proteina fluorescente ciano (PCP) e giallo proteina fluorescente (YFP) 9,10,14,15. Il rapporto di emissione dell&#39;accettore di emissione del donatore è stato utilizzato come parametro quantitativo per FRET segnale monitor per proteasi acproduttività determinazione. Tuttavia, questo metodo ignorato segnale contaminazioni crociate al accettore e lunghezze d&#39;onda di emissione del donatore e accettore da donatore auto-fluorescenza e quindi non era accurata. Abbiamo sviluppato un nuovo altamente sensibile e quantitativa FRET saggio basato proteasi per determinare i parametri cinetici di pre-SUMO1 maturazione da SENP1. Un multistrato FRET CyPet coppia e YPet con significativamente migliorato FRET efficienza e resa quantica di fluorescenza, sono stati utilizzati per generare il CyPet-(pre-SUMO1)-YPet substrato 16. Abbiamo differenziato e quantificato assoluti segnali di fluorescenza fornite dal donatore e accettore FRET e alle lunghezze d&#39;onda di emissione e accettori, rispettivamente. Il valore di k cat / K M è stato ottenuto come (3,2 ± 0,55) x10 7 M -1 s -1 SENP1 verso di pre-SUMO1, che è in accordo con i parametri generali cinetica enzimatica. Pertanto, questo metodo è valido e può essere utilizzato unsa generale approccio per caratterizzare proteasi anche altri.

Watch this Scientific Journal Video about Quantitative FRET FÃ¶rster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination at JoVE.com

Quantitative FRET F&amp;#246;rster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination

Un nuovo metodo che utilizza l&#39;analisi quantitativa di FRET (Förster Resonance Energy Transfer) segnali è descritto per lo studio di cinetica enzimatica.<em&gt; K<sub&gt; M</sub</em&gt; E<em&gt; K<sub&gt; Cat</sub</em&gt; Sono stati ottenuti per l&#39;idrolisi del dominio catalitico di SENP1 (SUMO / Sentrin specifica proteasi 1) di controllare la validità SUMO1 (Small ubiquitina-like Modifier). I principi generali della presente quantitativa-FRET-based studio cinetico proteasi può essere applicato ad altre proteasi.

Quantitativa FRET (Förster Resonance Energy Transfer) analisi per la determinazione della proteasi SENP1 Cinetica

Reversible posttranslational modifications of proteins with ubiquitin or ubiquitin-like proteins (Ubls) are widely used to dynamically regulate protein ...

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Quantitative FRET (F&#246;rster Resonance Energy Transfer) Analysis for SENP1 Protease Kinetics Determination

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18.9K Views.  University of California, Riverside. Un nuovo metodo che utilizza l'analisi quantitativa di FRET (Förster Resonance Energy Transfer) segnali è descritto per lo studio di cinetica enzimatica. K M

Video: Quantitative FRET F&#246;rster Resonance Energy Transfer Analysis for SENP1 Protease Kinetics Determination

Improved Visualization and Quantitative Analysis of Drug Effects Using Micropatterned Cells

To date, most HCA (High Content Analysis) studies are carried out with adherent cell lines grown on a homogenous substrate in tissue-culture treated micro-plates. Under these conditions, cells spread and divide in all directions resulting in an inherent variability in cell shape, morphology and behavior. The high cell-to-cell variance of the overall population impedes the success of HCA, especially for drug development. The ability of micropatterns to normalize the shape and internal polarity of every individual cell provides a tremendous opportunity for solving this critical bottleneck 1-2.
To facilitate access and use of the micropatterning technology, CYTOO has developed a range of ready to use micropatterns, available in coverslip and microwell formats. In this video article, we provide detailed protocols of all the procedures from cell seeding on CYTOOchip micropatterns, drug treatment, fixation and staining to automated acquisition, automated image processing and final data analysis. With this example, we illustrate how micropatterns can facilitate cell-based assays. Alterations of the cell cytoskeleton are difficult to quantify in cells cultured on homogenous substrates, but culturing cells on micropatterns results in a reproducible organization of the actin meshwork due to systematic positioning of the cell adhesion contacts in every cell. Such normalization of the intracellular architecture allows quantification of even small effects on the actin cytoskeleton as demonstrated in these set of protocols using blebbistatin, an inhibitor of the actin-myosin interaction.

Adhesive micropatterns that normalize cellular architecture can be used to increase sensitivity in the detection of drug effects, improve reproducibility and simplify automated image acquisition and analysis. Such technology will benefit drug/siRNA screening assays, performed on conventional cell culture supports and consequently suffering from excessive cell-to-cell variability.

Una migliore visualizzazione e analisi quantitativa degli effetti del farmaco utilizzando cellule Micropatterned

To date, most HCA (High Content Analysis) studies are carried out with adherent cell lines grown on a homogenous substrate in tissue-culture treated ...

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Adhesion Frequency Assay for In Situ Kinetics Analysis of Cross-Junctional Molecular Interactions at the Cell-Cell Interface

The micropipette adhesion assay was developed in 1998 to measure two-dimensional (2D) receptor-ligand binding kinetics1. The assay uses a human red blood cell (RBC) as adhesion sensor and presenting cell for one of the interacting molecules. It employs micromanipulation to bring the RBC into contact with another cell that expresses the other interacting molecule with precisely controlled area and time to enable bond formation. The adhesion event is detected as RBC elongation upon pulling the two cells apart. By controlling the density of the ligands immobilized on the RBC surface, the probability of adhesion is kept in mid-range between 0 and 1. The adhesion probability is estimated from the frequency of adhesion events in a sequence of repeated contact cycles between the two cells for a given contact time. Varying the contact time generates a binding curve. Fitting a probabilistic model for receptor-ligand reaction kinetics1 to the binding curve returns the 2D affinity and off-rate.
The assay has been validated using interactions of Fc&gamma; receptors with IgG Fc1-6, selectins with glycoconjugate ligands6-9, integrins with ligands10-13, homotypical cadherin binding14, T cell receptor and coreceptor with peptide-major histocompatibility complexes15-19.
The method has been used to quantify regulations of 2D kinetics by biophysical factors, such as the membrane microtopology5, membrane anchor2, molecular orientation and length6, carrier stiffness9, curvature20, and impingement force20, as well as biochemical factors, such as modulators of the cytoskeleton and membrane microenvironment where the interacting molecules reside and the surface organization of these molecules15,17,19.
The method has also been used to study the concurrent binding of dual receptor-ligand species3,4, and trimolecular interactions19 using a modified model21.
The major advantage of the method is that it allows study of receptors in their native membrane environment. The results could be very different from those obtained using purified receptors17. It also allows study of the receptor-ligand interactions in a sub-second timescale with temporal resolution well beyond the typical biochemical methods.
To illustrate the micropipette adhesion frequency method, we show kinetics measurement of intercellular adhesion molecule 1 (ICAM-1) functionalized on RBCs binding to integrin &alpha;L&beta;2 on neutrophils with dimeric E-selectin in the solution to activate &alpha;L&beta;2.

Adhesion Frequency Assay for In Situ Kinetics Analysis of Cross-Junctional Molecular Interactions at the Cell-Cell Interface

An adhesion frequency assay for measuring receptor-ligand interaction kinetics when both molecules are anchored on the surfaces of the interacting cells is described. This mechanically-based assay is exemplified using a micropipette-pressurized human red blood cell as adhesion sensor and integrin &alpha;L&beta;2 and intercellular adhesion molecule-1 as interacting receptors and ligands.

Adesione saggio di frequenza per In Situ Analisi cinetica delle interazioni molecolari incrociati giunzionale alla cellula-cellula di interfaccia

The micropipette adhesion assay was developed in 1998 to measure two-dimensional (2D) receptor-ligand binding kinetics1. The assay uses a human red blood ...

Microfluidic-based Electrotaxis for On-demand Quantitative Analysis of Caenorhabditis elegans' Locomotion

The nematode Caenorhabditis elegans is a versatile model organism for biomedical research because of its conservation of disease-related genes and pathways as well as its ease of cultivation. Several C. elegans disease models have been reported, including neurodegenerative disorders such as Parkinson's disease (PD), which involves the degeneration of dopaminergic (DA) neurons 1. Both transgenes and neurotoxic chemicals have been used to induce DA neurodegeneration and consequent movement defects in worms, allowing for investigations into the basis of neurodegeneration and screens for neuroprotective genes and compounds 2,3.
Screens in lower eukaryotes like C. elegans provide an efficient and economical means to identify compounds and genes affecting neuronal signaling. Conventional screens are typically performed manually and scored by visual inspection; consequently, they are time-consuming and prone to human errors. Additionally, most focus on cellular level analysis while ignoring locomotion, which is an especially important parameter for movement disorders.
We have developed a novel microfluidic screening system (Figure 1) that controls and quantifies C. elegans' locomotion using electric field stimuli inside microchannels. We have shown that a Direct Current (DC) field can robustly induce on-demand locomotion towards the cathode ("electrotaxis") 4. Reversing the field's polarity causes the worm to quickly reverse its direction as well. We have also shown that defects in dopaminergic and other sensory neurons alter the swimming response 5. Therefore, abnormalities in neuronal signaling can be determined using locomotion as a read-out. The movement response can be accurately quantified using a range of parameters such as swimming speed, body bending frequency and reversal time.
Our work has revealed that the electrotactic response varies with age. Specifically, young adults respond to a lower range of electric fields and move faster compared to larvae 4. These findings led us to design a new microfluidic device to passively sort worms by age and phenotype 6.
We have also tested the response of worms to pulsed DC and Alternating Current (AC) electric fields. Pulsed DC fields of various duty cycles effectively generated electrotaxis in both C. elegans and its cousin C. briggsae 7. In another experiment, symmetrical AC fields with frequencies ranging from 1 Hz to 3 KHz immobilized worms inside the channel 8.
Implementation of the electric field in a microfluidic environment enables rapid and automated execution of the electrotaxis assay. This approach promises to facilitate high-throughput genetic and chemical screens for factors affecting neuronal function and viability.

Microfluidic-based Electrotaxis for On-demand Quantitative Analysis of Caenorhabditis elegans&#039; Locomotion

A semi-automated micro-electro-fluidic method to induce on-demand locomotion in Caenorhabditis elegans is described. This method is based on the neurophysiologic phenomenon of worms responding to mild electric fields (&#x201C;electrotaxis&#x201D;) inside microfluidic channels. Microfluidic electrotaxis serves as a rapid, sensitive, low-cost, and scalable technique to screen for factors affecting neuronal health.

Electrotaxis microfluidica-based per On-demand analisi quantitativa della<em&gt; Caenorhabditis elegans</em&gt; &#39;Locomotion

The nematode Caenorhabditis elegans is a versatile model organism for biomedical research because of its conservation of disease-related genes and ...

Drug-induced Sensitization of Adenylyl Cyclase: Assay Streamlining and Miniaturization for Small Molecule and siRNA Screening Applications

Sensitization of adenylyl cyclase (AC) signaling has been implicated in a variety of neuropsychiatric and neurologic disorders including substance abuse and Parkinson&#39;s disease. Acute activation of G&#945;i/o-linked receptors inhibits AC activity, whereas persistent activation of these receptors results in heterologous sensitization of AC and increased levels of intracellular cAMP. Previous studies have demonstrated that this enhancement of AC responsiveness is observed both in vitro and in vivo following the chronic activation of several types of G&#945;i/o-linked receptors including D2 dopamine and &#956; opioid receptors. Although heterologous sensitization of AC was first reported four decades ago, the mechanism(s) that underlie this phenomenon remain largely unknown. The lack of mechanistic data presumably reflects the complexity involved with this adaptive response, suggesting that nonbiased approaches could aid in identifying the molecular pathways involved in heterologous sensitization of AC. Previous studies have implicated kinase and Gb&#947; signaling as overlapping components that regulate the heterologous sensitization of AC. To identify unique and additional overlapping targets associated with sensitization of AC, the development and validation of a scalable cAMP sensitization assay is required for greater throughput. Previous approaches to study sensitization are generally cumbersome involving continuous cell culture maintenance as well as a complex methodology for measuring cAMP accumulation that involves multiple wash steps. Thus, the development of a robust cell-based assay that can be used for high throughput screening (HTS) in a 384&#160;well format would facilitate future studies. Using two D2 dopamine receptor cellular models (i.e.&#160;CHO-D2L and HEK-AC6/D2L), we have converted our 48-well sensitization assay (&#62;20 steps 4-5 days) to a five-step, single day assay in 384-well format. This new format is amenable to small molecule screening, and we demonstrate that this assay design can also be readily used for reverse transfection of siRNA in anticipation of targeted siRNA library screening.

Persistent activation of inhibitory G protein-coupled receptors results in sensitization of adenylyl cyclase signaling. To identify the essential molecular pathways, nonbiased approaches are necessary; however, this strategy requires the development of a scalable cell-based cAMP sensitization assay. Herein, we describe a sensitization assay for small molecule and siRNA screening.

Farmaco-indotta Sensibilizzazione della ciclasi: L&#39;ottimizzazione del dosaggio e miniaturizzazione per piccole molecole di siRNA e applicazioni di screening

Sensitization of adenylyl cyclase (AC) signaling has been implicated in a variety of neuropsychiatric and neurologic disorders including substance abuse ...

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

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

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

Luminescence Resonance Energy Transfer allo Studio conformazionale Cambiamenti nella membrana proteine ​​espresse in cellule di mammifero

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

Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay

T-cells are remarkably specific and effective when recognizing antigens in the form of peptides embedded in MHC molecules (pMHC) on the surface of Antigen Presenting Cells (APCs). This is despite T-cell antigen receptors (TCRs) exerting usually a moderate affinity (&#181;M range) to antigen when binding is measured in vitro1. In view of the molecular and cellular parameters contributing to T-cell antigen sensitivity, a microscopy-based methodology has been developed as a means to monitor TCR-pMHC binding in situ, as it occurs within the synapse of a live T-cell and an artificial and functionalized glass-supported planar lipid bilayer (SLB), which mimics the cell membrane of an Antigen presenting Cell (APC) 2. Measurements are based on F&#246;rster Resonance Energy Transfer (FRET) between a blue- and red-shifted fluorescent dye attached to the TCR and the pMHC. Because the efficiency of FRET is inversely proportional to the sixth power of the inter-dye distance, one can employ FRET signals to visualize synaptic TCR-pMHC binding. The sensitive of the microscopy approach supports detection of single molecule FRET events. This allows to determine the affinity and off-rate of synaptic TCR-pMHC interactions and in turn to interpolate the on-rate of binding. Analogous assays could be applied to measure other receptor-ligand interactions in their native environment.

Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay

This manuscript describes how to conduct (single molecule) F&#246;rster Resonance Energy Transfer (FRET)- based assays to measure the binding dynamics between T-cell antigen receptor (TCR) and antigenic peptide-loaded MHC molecules as they occur within the immunological synapse of a T-cell in contact with a functionalized planar supported lipid bilayer.

Misurazione TCR-pMHC Binding<em&gt; In Situ</em&gt; Utilizzando un microscopio saggio basato FRET-

T-cells are remarkably specific and effective when recognizing antigens in the form of peptides embedded in MHC molecules (pMHC) on the surface of Antigen ...

Sensitive Detection of Proteopathic Seeding Activity with FRET Flow Cytometry

Increasing evidence supports transcellular propagation of toxic protein aggregates, or proteopathic seeds, as a mechanism for the initiation and progression of pathology in several neurodegenerative diseases, including Alzheimer's disease and the related tauopathies. The potentially critical role of tau seeds in disease progression strongly supports the need for a sensitive assay that readily detects seeding activity in biological samples. 
By combining the specificity of fluorescence resonance energy transfer (FRET), the sensitivity of flow cytometry, and the stability of a monoclonal cell line, an ultra-sensitive seeding assay has been engineered and is compatible with seed detection from recombinant or biological samples, including human and mouse brain homogenates. The assay employs monoclonal HEK 293T cells that stably express the aggregation-prone repeat domain (RD) of tau harboring the disease-associated P301S mutation fused to either CFP or YFP, which produce a FRET signal upon protein aggregation. The uptake of proteopathic tau seeds (but not other proteins) into the biosensor cells stimulates aggregation of RD-CFP and RD-YFP, and flow cytometry sensitively and quantitatively monitors this aggregation-induced FRET. The assay detects femtomolar concentrations (monomer equivalent) of recombinant tau seeds, has a dynamic range spanning three orders of magnitude, and is compatible with brain homogenates from tauopathy transgenic mice and human tauopathy subjects. With slight modifications, the assay can also detect seeding activity of other proteopathic seeds, such as &#945;-synuclein, and is also compatible with primary neuronal cultures. The ease, sensitivity, and broad applicability of FRET flow cytometry makes it useful to study a wide range of protein aggregation disorders.

Cell-to-cell transfer of protein aggregates, or proteopathic seeds, may underlie the progression of pathology in neurodegenerative diseases. Here, a novel FRET flow cytometry assay is described that enables specific and sensitive detection of seeding activity from recombinant or biological samples.

Rilevazione sensibile di Proteopathic Semina attività con FRET Citometria a flusso

Increasing evidence supports transcellular propagation of toxic protein aggregates, or proteopathic seeds, as a mechanism for the initiation and ...

Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers

Fluorescence assays are the most common readouts used in droplet microfluidics due to their bright signals and fast time response. Applications such as multiplex assays, enzyme evolution, and molecular biology enhanced cell sorting require the detection of two or more colors of fluorescence. Standard multicolor detection systems that couple free space lasers to epifluorescence microscopes are bulky, expensive, and difficult to maintain. In this paper, we describe a scheme to perform multicolor detection by exciting discrete regions of a microfluidic channel with lasers coupled to optical fibers. Emitted light is collected by an optical fiber coupled to a single photodetector. Because the excitation occurs at different spatial locations, the identity of emitted light can be encoded as a temporal shift, eliminating the need for more complicated light filtering schemes. The system has been used to detect droplet populations containing four unique combinations of dyes and to detect sub-nanomolar concentrations of fluorescein.

Multicolor fluorescence detection in droplet microfluidics typically involves bulky and complex epifluorescence microscope-based detection systems. Here we describe a compact and modular multicolor detection scheme that utilizes an array of optical fibers to temporally encode multicolor data collected by a single photodetector.

Multicolore fluorescenza Detection per Droplet microfluidica tramite fibre ottiche

Fluorescence assays are the most common readouts used in droplet microfluidics due to their bright signals and fast time response. Applications such as ...

A Protocol for Using F&#246;rster Resonance Energy Transfer (FRET)-force Biosensors to Measure Mechanical Forces across the Nuclear LINC Complex

The LINC complex has been hypothesized to be the critical structure that mediates the transfer of mechanical forces from the cytoskeleton to the nucleus. Nesprin-2G is a key component of the LINC complex that connects the actin cytoskeleton to membrane proteins (SUN domain proteins) in the perinuclear space. These membrane proteins connect to lamins inside the nucleus. Recently, a F&#246;rster Resonance Energy Transfer (FRET)-force probe was cloned into mini-Nesprin-2G (Nesprin-TS (tension sensor)) and used to measure tension across Nesprin-2G in live NIH3T3 fibroblasts. This paper describes the process of using Nesprin-TS to measure LINC complex forces in NIH3T3 fibroblasts. To extract FRET information from Nesprin-TS, an outline of how to spectrally unmix raw spectral images into acceptor and donor fluorescent channels is also presented. Using open-source software (ImageJ), images are pre-processed and transformed into ratiometric images. Finally, FRET data of Nesprin-TS is presented, along with strategies for how to compare data across different experimental groups.

A Protocol for Using F&amp;#246;rster Resonance Energy Transfer (FRET)-force Biosensors to Measure Mechanical Forces across the Nuclear LINC Complex

A number of FRET-based force biosensors have recently been developed, enabling the protein-specific resolution of intracellular force. In this protocol, we demonstrate how one of these sensors, designed for the linker of the nucleoskeleton-cytoskeleton (LINC) complex protein Nesprin-2G can be used to measure actomyosin forces on the nuclear LINC complex.

Un protocollo per l&#39;utilizzo di trasferimento di energia per risonanza (FRET) biosensori -force per misurare le forze meccaniche in tutto il complesso LINC nucleare

The LINC complex has been hypothesized to be the critical structure that mediates the transfer of mechanical forces from the cytoskeleton to the nucleus. ...

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the optical window where biological samples are most transparent. Here, we outline techniques to adsorb amphiphilic polymers and polynucleic acids onto the surface of SWNTs to engineer their corona phases and create novel molecular sensors for small molecules and proteins. These functionalized SWNT sensors are both biocompatible and stable. Polymers are adsorbed onto the nanotube surface either by direct sonication of SWNTs and polymer or by suspending SWNTs using a surfactant followed by dialysis with polymer. The fluorescence emission, stability, and response of these sensors to target analytes are confirmed using absorbance and near-infrared fluorescence spectroscopy. Furthermore, we demonstrate surface immobilization of the sensors onto glass slides to enable single-molecule fluorescence microscopy to characterize polymer adsorption and analyte binding kinetics.

We present a protocol for engineering the corona phase of near infrared fluorescent single walled carbon nanotubes (SWNTs) using amphiphilic polymers and DNA to develop sensors for molecular targets without known recognition elements.

Ingegneria riconoscimento molecolare con polimeri bio-mimetici sui singoli Walled nanotubi di carbonio

Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the ...