Generic placeholder image

Protein & Peptide Letters

Editor-in-Chief

ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

General Research Article

Assessment of Proteolysis by Pyrylium and Other Fluorogenic Reagents

Author(s): Mohamed K. Al-Essa*, Ebaa Alzayadneh and Kamal Al-Hadidi

Volume 28, Issue 7, 2021

Published on: 31 December, 2020

Page: [809 - 816] Pages: 8

DOI: 10.2174/0929866528999201231214954

open access plus

Abstract

Aims: We aim to evaluate the potential application of amine reactive fluorogenic reagents for estimating enzymatic proteolysis.

Background: Proteolytic enzymes play important roles in regulating many physiological processes in living organisms.

Objectives: Assessment of protein degradation by using reagents for protein assay techniques.

Methods: We have assayed samples at the start and after 30-60 minutes incubation with trypsin by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents and NanoOrange as non-amine reactive dye.

Results: All BSA prepared samples with trypsin have shown significantly higher fluorescence intensity (FI) versus controls (which reflects proteolysis) when assayed by Chromeo P503 (Py 1 pyrylium compound) and CBQCA (3-(4-carboxybenzoyl) quinoline-2-carboxaldehyde) as amine reactive reagents. However, same samples assayed with NanoOrange as non-amine reactive reagent did not show any significant variation between samples containing trypsin and controls.

Conclusion: These results are confirming reliability of highly sensitive protein assays utilizing amine reactive fluorogenic reagents for general estimation of proteolysis.

Keywords: Proteolysis, spectrofluorometry, pyrylium, CBQCA, chromeo P503, nanoOrange.

Graphical Abstract

[1]
Varshavsky, A. Regulated protein degradation. Trends Biochem. Sci., 2005, 30(6), 283-286.
[http://dx.doi.org/10.1016/j.tibs.2005.04.005]
[2]
Glickman, M.H.; Ciechanover, A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev., 2002, 82(2), 373-428.
[http://dx.doi.org/10.1152/physrev.00027.2001]
[3]
Sánchez, A.; Vázquez, A. Bioactive peptides: a review. Food Quality and Safety, 2017, 1(1), 29-46.
[http://dx.doi.org/10.1093/fqs/fyx006]
[4]
Verhamme, I.M.; Leonard, S.E.; Perkins, R.C. Proteases: pivot points in functional proteomics. Methods Mol. Biol., 2019, 1871, 313-392.
[http://dx.doi.org/10.1007/978-1-4939-8814-3_20]
[5]
Kasche, V. Proteases in Peptide Synthesis. In: Proteolytic Enzymes: A Practical Approach; Beynon, R.J.; Bond, J.S., Eds.; Oxford University Press: New York, NY, 2001; pp. 265-292.
[6]
Blobel, C.P. Remarkable roles of proteolysis on and beyond the cell surface. Curr. Opin. Cell Biol., 2000, 12(5), 606-612.
[http://dx.doi.org/10.1016/S0955-0674(00)00139-3]
[7]
Kaminskyy, V.; Zhivotovsky, B. Proteases in autophagy. Biochim. Biophys. Acta, 2012, 1824, 44-50.
[http://dx.doi.org/10.1016/j.bbapap.2011.05.013]
[8]
Craik, C.S.; Page, M.J.; Madison, E.L. Proteases as therapeutics. Biochem. J., 2011, 435(1), 1-16.
[http://dx.doi.org/10.1042/BJ20100965]
[9]
Overall, C.M.; Kleifeld, O. Tumour microenvironment - opinion: validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy. Nat. Rev. Cancer, 2006, 6(3), 227-239.
[http://dx.doi.org/10.1038/nrc1821]
[10]
Mótyán, J.A.; Tóth, F.; Tőzsér, J. Research applications of proteolytic enzymes in molecular biology. Biomolecules, 2013, 3(4), 923-942.
[http://dx.doi.org/10.3390%2Fbiom3040923] [PMID: 24970197]
[11]
Manning, M.C.; Chou, D.K.; Murphy, B.M.; Payne, R.W.; Katayama, D.S. Stability of protein pharmaceuticals: an update. Pharm. Res., 2010, 27(4), 544-575.
[http://dx.doi.org/10.1007/s11095-009-0045-6] [PMID: 20143256]
[12]
Rawlings, N.D.; Barrett, A.J. Evolutionary families of peptidases. Biochem. J., 1993, 290(1), 205-218.
[http://dx.doi.org/10.1042/bj2900205]
[13]
Barrett, A.J. Proteolytic enzymes: nomenclature and classification. In: Proteolytic Enzymes: A Practical Approach; Beynon, R.J.; Bond, J.S., Eds.; Oxford University Press: New York, NY, 2001; pp. 1-21.
[14]
Rawlings, N.D.; Barrett, A.J. Families of serine peptidases. Methods Enzymol., 1994, 244, 19-61.
[http://dx.doi.org/10.1016/0076-6879(94)44004-2]
[15]
Zhou, X.; Wang, T.; Wang, A.; Li, R. Optima of trypsin-catalyzed hydrolysis and its inhibition determined by SDS-PAGE. Adv. Enzyme Res., 2016, 4(1), 1-6.
[http://dx.doi.org/10.4236/aer.2016.41001]
[16]
Ryan, B.J.; Henehan, G.T. Overview of approaches to preventing and avoiding proteolysis during expression and purification of proteins. Curr Protoc Protein Sci., 2013, 71(1), 5.25.1-5.25.7.
[http://dx.doi.org/10.1002/0471140864.ps0525s71]
[17]
Church, F.C.; Swaisgood, H.E.; Porter, D.H.; Catignani, G.L. Spectrophotometric assay using o-phthaldialdehyde for determination of proteolysis in milk and isolated milk proteins. J. Dairy Sci., 1983, 66(6), 1219-1227.
[http://dx.doi.org/10.3168/jds.S0022-0302(83)81926-2]
[18]
Church, F.C.; Porter, D.H.; Catignani, G.L.; Swaisgood, H.E. An o-phthalaldehyde spectrophotometric assay for proteinases. Anal. Biochem., 1985, 146(2), 343-348.
[http://dx.doi.org/10.1016/0003-2697(85)90549-4]
[19]
Bouton, Y.; Grappin, R. Measurement of proteolysis in cheese: relationship between phosphotungstic acid-soluble N fraction by Kjeldahl and 2,4,6- trinitrobenzenesulphonic acid-reactive groups in water-soluble N. J. Dairy Res., 1994, 61(3), 437-440.
[http://dx.doi.org/10.1017/S0022029900030880]
[20]
Erlanger, B.F.; Kokowsky, N.; Cohen, W. The preparation and properties of two new chromogenic substrates of trypsin. Arch. Biochem. Biophys., 1961, 95, 271-278.
[http://dx.doi.org/10.1016/0003-9861(61)90145-X]
[21]
Zimmerman, M.; Yurewicz, E.; Patel, G. A new fluorogenic substrate for chymotrypsin. Anal. Biochem., 1976, 70, 258-262.
[http://dx.doi.org/10.1016/S0003-2697(76)80066-8]
[22]
Zimmerman, M.; Ashe, B.; Yurewicz, E.C.; Patel, G. Sensitive assays for trypsin, elastase, and chymotrypsin using new fluorogenic substrates. Anal. Biochem., 1977, 78, 47-51.
[http://dx.doi.org/10.1016/0003-2697(77)90006-9]
[23]
Doucet, A.; Kleifeld, O.; Kizhakkedathu, J.N.; Overall, C.M. Identification of proteolytic products and natural protein N-termini by Terminal Amine Isotopic Labeling of Substrates (TAILS). Methods Mol. Biol., 2011, 753, 273-287.
[http://dx.doi.org/10.1007/978-1-61779-148-2_18] [PMID: 21604129]
[24]
Kleifeld, O.; Doucet, A.; auf dem Keller, U.; Prudova, A.; Schilling, O.; Kainthan, R.K; Starr, A.E.; Foster, L.J.; Kizhakkedathu, J.N.; Overall, C.M. Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol., 2010, 28(3), 281-288.
[http://dx.doi.org/10.1038/nbt.1611]
[25]
Sarath, G.; Zeece, M.G.; Penheiter, A.R. Protease Assay Methods. In: Proteolytic Enzymes: A Practical Approach; Beynon, R.J.; Bond, J.S., Eds.; Oxford University Press: New York, NY, 2001; pp. 45-76.
[26]
Chavira, R. Assaying proteinases with azocoll. Anal. Biochem., 1984, 136(2), 446-450.
[http://dx.doi.org/10.1016/0003-2697(84)90242-2]
[27]
Coêlho, D.F; Saturnino, T.P.; Fernandes, F.F.; Mazzola, P.G.; Silveira, E.; Tambourgi, E.B. Azocasein substrate for determination of proteolytic activity: reexamining a traditional method using bromelain samples. Biomed. Res. Int., 2016, 2016, 8409183.
[http://dx.doi.org/10.1155/2016/8409183]
[28]
Denadai-Souza, A.; Bonnart, C.; Tapias, N.S.; Marcellin, M.; Gilmore, B.; Alric, L.; Bonnet, D.; Burlet-Schiltz, O.; Hollenberg, M.D.; Vergnolle, N.; Deraison, C. Functional proteomic profiling of secreted serine proteases in health and inflammatory bowel disease. Sci. Rep., 2018, 8(1), 7834.
[http://dx.doi.org/10.1038/s41598-018-26282-y]
[29]
Tooth, D.; Garsed, K.; Singh, G.; Marciani, L.; Lam, C.; Fordham, I.; Fields, A.; Banwait, R.; Lingaya, M.; Layfield, R.; Hastings, M.; Whorwell, P.; Spiller, R. Characterisation of faecal protease activity in irritable bowel syndrome with diarrhoea: origin and effect of gut transit. Gut, 2014, 63(5), 753-760.
[http://dx.doi.org/10.1136/gutjnl-2012-304042]
[30]
Gibson, S.A.; McFarlan, C.; Hay, S.; MacFarlane, G.T. Significance of microflora in proteolysis in the colon. Appl. Environ. Microbiol., 1989, 55(3), 679-683.
[http://dx.doi.org/10.1128/AEM.55.3.679-683.1989] [PMID: 2648991]
[31]
Macfarlane, G.T.; Allison, C.; Gibson, S.A.; Cummings, J.H. Contribution of the microflora to proteolysis in the human large intestine. J. Appl. Bacteriol., 1988, 64(1), 37-46.
[http://dx.doi.org/10.1111/j.1365-2672.1988.tb02427.x]
[32]
Kania, K.; Byrnes, E.A.; Beilby, J.P.; Webb, S.A.; Strong, K.J. Urinary proteases degrade albumin: implications for measurement of albuminuria in stored samples. Ann. Clin. Biochem., 2010, 47(2), 151-157.
[http://dx.doi.org/10.1258/acb.2009.009247]
[33]
Krochmal, M.; Kontostathi, G.; Magalhães, P.; Makridakis, M.; Klein, J.; Husi, H.; Leierer, J.; Mayer, G.; Bascands, J.L.; Denis, C.; Zoidakis, J.; Zürbig, P.; Delles, C.; Schanstra, J.P.; Mischak, H.; Vlahou, A. Urinary peptidomics analysis reveals proteases involved in diabetic nephropathy. Sci. Rep., 2017, 7(1), 15160.
[http://dx.doi.org/10.1038/s41598-017-15359-9]
[34]
Altshuler, A.E.; Penn, A.H.; Yang, J.A.; Kim, G.R.; Schmid-Schönbein, G.W. Protease activity increases in plasma, peritoneal fluid, and vital organs after hemorrhagic shock in rats. PLoS One, 2012, 7(3), e32672.
[http://dx.doi.org/10.1371/journal.pone.0032672]
[35]
Roth, C.; Pantel, K.; Müller, V.; Rack, B.; Kasimir-Bauer, S.; Janni, W.; Schwarzenbach, H. Apoptosis-related deregulation of proteolytic activities and high serum levels of circulating nucleosomes and DNA in blood correlate with breast cancer progression. BMC Cancer, 2011, 11, 4.
[http://dx.doi.org/10.1186/1471-2407-11-4]
[36]
Li, Y.; Li, Y.; Chen, T.; Kuklina, A.S.; Bernard, P.; Esteva, F.J.; Shen, H.; Ferrari, M.; Hu, Y. Circulating proteolytic products of carboxypeptidase N for early detection of breast cancer. Clin. Chem., 2014, 60(1), 233-242.
[http://dx.doi.org/10.1373/clinchem.2013.211953]
[37]
Deng, Z.; Li, Y.; Fan, J.; Wang, G.; Li, Y.; Zhang, Y.; Cai, G.; Shen, H.; Ferrari, M.; Hu, T.Y. Circulating peptidome to indicate the tumor-resident proteolysis. Sci. Rep., 2015, 5, 9327.
[http://dx.doi.org/10.1038/srep09327]
[38]
Wiita, A.P.; Hsu, G.W.; Lu, C.M.; Esensten, J.H.; Wells, J.A. Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling. Proc. Natl. Acad. Sci. USA., 2014, 111(21), 7594-7599.
[http://dx.doi.org/10.1073/pnas.1405987111]
[39]
Root, A.; Allen, P.; Tempst, P.; Yu, K. Protein biomarkers for early detection of pancreatic ductal adenocarcinoma: progress and challenges. Cancers (Basel), 2018, 10(3), 67.
[http://dx.doi.org/10.3390/cancers10030067]
[40]
Schilling, O.; Overall, C.M. Proteomic discovery of protease substrates. Curr. Opin. Chem. Biol., 2007, 11(1), 36-45.
[http://dx.doi.org/10.1016/j.cbpa.2006.11.037]
[41]
Luo, S.Y.; Araya, L.E.; Julien, O. Protease substrate identification using N-terminomics. ACS Chem. Biol., 2019, 14(11), 2361-2371.
[http://dx.doi.org/10.1021/acschembio.9b00398]
[42]
Vizovišek, M.; Vidmar, R.; Fonović, M.; Turk, B. Current trends and challenges in proteomic identification of protease substrates. Biochimie, 2016, 122, 77-87.
[http://dx.doi.org/10.1016/j.biochi.2015.10.017]
[43]
Hu, D.; Ansari, D.; Pawłowski, K.; Zhou, Q.; Sasor, A.; Welinder, C.; Kristl, T.; Bauden, M.; Rezeli, M.; Jiang, Y.; Marko-Varga, G.; Andersson, R. Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma. Oncotarget, 2018, 9(11), 9789-9807.
[http://dx.doi.org/10.18632/oncotarget.23929]
[44]
Ivry, S.L.; Meyer, N.O.; Winter, M.B.; Bohn, M.F.; Knudsen, G.M.; O'Donoghue, A.J.; Craik, C.S. Global substrate specificity profiling of post-translational modifying enzymes. Protein Sci., 2018, 27(3), 584-594.
[http://dx.doi.org/10.1002/pro.3352]
[45]
Borrebaeck, C. Precision diagnostics: moving towards protein biomarker signatures of clinical utility in cancer. Nat. Rev. Cancer, 2017, 17(3), 199-204.
[http://dx.doi.org/10.1038/nrc.2016.153]
[46]
Turner, E.H.; Dickerson, J.A.; Ramsay, L.M.; Swearingen, K.E.; Wojcik, R.; Dovichi, N.J. Reaction of fluorogenic reagents with proteins III. Spectroscopic and electrophoretic behavior of proteins labeled with Chromeo P503. J. Chromatogr. A, 2008, 1194(2), 253-256.
[http://dx.doi.org/10.1016/j.chroma.2008.04.046] [http://dx.doi.org/18482729]
[47]
Hoefelschweiger, B.K.; Duerkop, A.; Wolfbeis, O.S. Novel type of general protein assay using a chromogenic and fluorogenic amine-reactive probe. Anal. Biochem., 2005, 344(1), 122-129.
[http://dx.doi.org/10.1016/j.ab.2005.06.030]
[48]
You, W.W; Haugland, R.P.; Ryan, D.K.; Haugland, R.P. 3-(4-Carboxybenzoyl)quinoline-2-carboxaldehyde, a reagent with broad dynamic range for the assay of proteins and lipoproteins in solution. Anal. Biochem., 1997, 244(2), 277-282.
[http://dx.doi.org/10.1006/abio.1996.9920]
[49]
Jones, L.J.; Haugland, R.P.; Singer, V.L. Development and characterization of the NanoOrange protein quantitation assay: A fluorescence-based assay of proteins in solution. Biotechniques, 2003, 34(4), 850-854. 856, 858 passim.
[http://dx.doi.org/10.2144/03344pt03]
[50]
Saller, C.F. Method for evaluating the breakdown of proteins, polypeptides and peptides. U.S. patent 0028286 A1, 2012.

© 2024 Bentham Science Publishers | Privacy Policy