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Protein tag

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Protein tags are peptide sequences genetically grafted onto a recombinant protein. Tags are attached to proteins for various purposes. They can be added to either end of the target protein, so they are either C-terminus or N-terminus specific or are both C-terminus and N-terminus specific. Some tags are also inserted at sites within the protein of interest; they are known as internal tags.[1]

Affinity tags are appended to proteins so that they can be purified from their crude biological source using an affinity technique. Affinity tags include chitin binding protein (CBP), maltose binding protein (MBP), Strep-tag[2] and glutathione-S-transferase (GST). The poly(His) tag is a widely used protein tag, which binds to matrices bearing immobilized metal ions.

Solubilization tags are used, especially for recombinant proteins expressed in species such as E. coli, to assist in the proper folding in proteins and keep them from aggregating in inclusion bodies. These tags include thioredoxin (TRX) and poly(NANP). Some affinity tags have a dual role as a solubilization agent, such as MBP and GST.

Chromatography tags are used to alter chromatographic properties of the protein to afford different resolution across a particular separation technique. Often, these consist of polyanionic amino acids, such as FLAG-tag or polyglutamate tag.[3]

Epitope tags are short peptide sequences which are chosen because high-affinity antibodies can be reliably produced in many different species. These are usually derived from viral genes, which explain their high immunoreactivity. Epitope tags include ALFA-tag, V5-tag, Myc-tag, HA-tag, Spot-tag, T7-tag and NE-tag. These tags are particularly useful for western blotting, immunofluorescence and immunoprecipitation experiments, although they also find use in antibody purification.

Fluorescence tags are used to give visual readout on a protein. Green fluorescent protein (GFP) and its variants are the most commonly used fluorescence tags.[4] More advanced applications of GFP include using it as a folding reporter (fluorescent if folded, colorless if not).

Protein tags may allow specific enzymatic modification (such as biotinylation by biotin ligase) or chemical modification (such as coupling to other proteins through SpyCatcher or reaction with FlAsH-EDT2 for fluorescence imaging). Often tags are combined, in order to connect proteins to multiple other components. However, with the addition of each tag comes the risk that the native function of the protein may be compromised by interactions with the tag. Therefore, after purification, tags are sometimes removed by specific proteolysis (e.g. by TEV protease, Thrombin, Factor Xa or Enteropeptidase) or intein splicing.

List of protein tags

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(See Proteinogenic amino acid#Chemical properties for the A-Z amino-acid codes)

Peptide tags

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  • ALFA-tag, a de novo designed helical peptide tag (SRLEEELRRRLTE) for biochemical and microscopy applications. The tag is recognized by a repertoire of single-domain antibodies [5]
  • AviTag, a peptide allowing biotinylation by the enzyme BirA and so the protein can be isolated by streptavidin (GLNDIFEAQKIEWHE)
  • C-tag, a peptide that binds to a single-domain camelid antibody developed through phage display (EPEA)[6][7]
  • Calmodulin-tag, a peptide bound by the protein calmodulin (KRRWKKNFIAVSAANRFKKISSSGAL)
  • iCapTag™ (intein Capture Tag), a self-removing peptide-based tag (MIKIATRKYLGKQNVYGIGVERDHNFALKNGFIAHN). The iCapTag™ is controlled by pH change (typically pH 8.5 to pH 6.2). Therefore, this technology can be adapted to a wide range of buffers adjusted to the target pH values of 8.5 and 6.2. The expected purity of target proteins or peptides is between 95-99%. The iCapTag™ contains patented component derived from Nostoc punctiforme (Npu) intein. This tag is used for protein purification of recombinant proteins and its fragments. It can be used in research labs and it is intended for large-scale purification during downstream manufacturing process as well. The iCapTag™-target protein complex can be expressed in a wide range of expression hosts (e.g. CHO and E.coli cells). It is not intended for fully expressed mAbs[8][9][10]
  • polyglutamate tag, a peptide binding efficiently to anion-exchange resin such as Mono-Q (EEEEEE) [3]
  • polyarginine tag, a peptide binding efficiently to cation-exchange resin (from 5 to 9 consecutive R)
  • E-tag, a peptide recognized by an antibody (GAPVPYPDPLEPR)
  • FLAG-tag, a peptide recognized by an antibody (DYKDDDDK)[11]
  • HA-tag, a peptide from hemagglutinin recognized by an antibody (YPYDVPDYA)[12]
  • His-tag, 5-10 histidines bound by a nickel or cobalt chelate (HHHHHH)
    • Gly-His-tags are N-terminal His-Tag variants (e.g. GHHHH, or GHHHHHH, or GSSHHHHHH) that still bind to immobilised metal cations but can also be activated via azidogluconoylation to enable click-chemistry applications[13]
  • Myc-tag, a peptide derived from c-myc recognized by an antibody (EQKLISEEDL)
  • NE-tag, an 18-amino-acid synthetic peptide (TKENPRSNQEESYDDNES) recognized by a monoclonal IgG1 antibody, which is useful in a wide spectrum of applications including Western blotting, ELISA, flow cytometry, immunocytochemistry, immunoprecipitation, and affinity purification of recombinant proteins [14]
  • Rho1D4-tag, refers to the last 9 amino acids of the intracellular C-terminus of bovine rhodopsin (TETSQVAPA). It is a very specific tag that can be used for purification of membrane proteins.
  • S-tag, a peptide derived from Ribonuclease A (KETAAAKFERQHMDS)
  • SBP-tag, a peptide which binds to streptavidin (MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREP)[15]
  • Softag 1, for mammalian expression (SLAELLNAGLGGS)
  • Softag 3, for prokaryotic expression (TQDPSRVG)
  • Spot-tag, a peptide recognized by a nanobody (PDRVRAVSHWSS) for immunoprecipitation, affinity purification, immunofluorescence and super resolution microscopy
  • Strep-tag, a peptide which binds to streptavidin or the modified streptavidin called streptactin (Strep-tag II: WSHPQFEK)[2]
  • T7-tag, an epitope tag derived from the T7 major capsid protein of the T7 gene (MASMTGGQQMG). Used in different immunoassays as well as affinity purification Mainly used [16]
  • TC tag, a tetracysteine tag that is recognized by FlAsH and ReAsH biarsenical compounds (CCPGCC)
  • Ty tag (EVHTNQDPLD)
  • V5 tag, a peptide recognized by an antibody (GKPIPNPLLGLDST)[17]
  • VSV-tag, a peptide recognized by an antibody (YTDIEMNRLGK)
  • Xpress tag (DLYDDDDK), a peptide recognized by an antibody

Covalent peptide tags

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  • Isopeptag, a peptide which binds covalently to pilin-C protein (TDKDMTITFTNKKDAE)[18]
  • SpyTag, a peptide which binds covalently to SpyCatcher protein (AHIVMVDAYKPTK)[19]
  • SnoopTag, a peptide which binds covalently to SnoopCatcher protein (KLGDIEFIKVNK).[20] A second generation, SnoopTagJr, was also developed to bind to either SnoopCatcher or DogTag (mediated by SnoopLigase) (KLGSIEFIKVNK)[21]
  • DogTag, a peptide which covalently binds to DogCatcher (DIPATYEFTDGKHYITNEPIPPK),[22] and can also covalently bind to SnoopTagJr, mediated by SnoopLigase [21]
  • SdyTag, a peptide which binds covalently to SdyCatcher protein (DPIVMIDNDKPIT).[23] SdyTag/SdyCatcher has a kinetic-dependent cross-reactivity with SpyTag/SpyCatcher.

Protein tags

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  • BCCP (Biotin Carboxyl Carrier Protein), a protein domain biotinylated by BirA enabling recognition by streptavidin
  • BromoTag, a "bump-and-hole" mutated version of the second bromodomain of Brd4, Brd4-BD2 L387A, that can be highly selectively bound by tag-specific PROTAC degrader AGB1 to form a ternary complex between the "BromoTagged" protein and the E3 ligase VHL, leading to ubiquitination of the tagged protein and its subsequent rapid and effective proteasomal degradation in cells.[24]
  • FAST (Fluorescence-Activating and absorption-Shifting Tag), a mutated photoactive yellow protein (PYP) that reversibly binds cognate fluorogenic ligands
  • CL7-tag, an engineered variant of Colicin E7 that has a strong binding affinity and specificity for immobilized Immunity Protein 7 (Im7). [25]
  • Glutathione-S-transferase-tag, a protein which binds to immobilized glutathione
  • Green fluorescent protein-tag,[4] a protein which is spontaneously fluorescent and can be bound by nanobodies
  • HaloTag, a mutated bacterial haloalkane dehalogenase that covalently attaches to haloalkane substrates
  • SNAP-tag, a mutated eukaryotic DNA methyltransferase that covalently attaches to benzylguanine derivatives
  • CLIP-tag, a mutated eukaryotic DNA methyltransferase that covalently attaches to benzylcytosine derivatives
  • HUH-tag, a sequence-specific single-stranded DNA binding protein that covalently binds to its target sequence
  • Maltose binding protein-tag, a protein which binds to amylose agarose[26]
  • Nus-tag
  • Thioredoxin-tag
  • Fc-tag, derived from immunoglobulin Fc domain, allow dimerization and solubilization. Can be used for purification on Protein-A Sepharose
  • Designed Intrinsically Disordered tags containing disorder promoting amino acids (P,E,S,T,A,Q,G,..)[27]
  • Carbohydrate Recognition Domain or CRDSAT-tag, a protein which binds to lactose agarose or Sepharose[28]

Others

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HiBiT-tag was developed by Scientists at Promega. It is an 11-amino-acid peptide tag, and it can be fused to the N- or C-terminus or internal locations of proteins.[29] Its small size leads to a rapid knock-in of this tag with other proteins through CRISPR/Cas9 technology.[29]

Applications

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References

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  1. ^ Mahmoudi Gomari, Mohammad; Saraygord-Afshari, Neda; Farsimadan, Marziye; Rostami, Neda; Aghamiri, Shahin; Farajollahi, Mohammad M. (December 2020). "Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry". Biotechnology Advances. 45: 107653. doi:10.1016/j.biotechadv.2020.107653. ISSN 0734-9750. PMID 33157154. S2CID 226276355.
  2. ^ a b Schmidt, Thomas G.M.; Koepke, Jürgen; Frank, Ronald; Skerra, Arne (1996). "Molecular Interaction Between the Strep-tag Affinity Peptide and its Cognate Target, Streptavidin". Journal of Molecular Biology. 255 (5): 753–66. doi:10.1006/jmbi.1996.0061. PMID 8636976.
  3. ^ a b Fairhead M, Krndija D, Lowe ED, Howarth M (January 2014). "Plug-and-play pairing via defined divalent streptavidins". Journal of Molecular Biology. 426 (1): 199–214. doi:10.1016/j.jmb.2013.09.016. PMC 4047826. PMID 24056174.
  4. ^ a b Zhang, Jin; Campbell, Robert; Ting, Alice; Tsien, Roger (2002). "Creating new fluorescent probes for cell biology". Nat Rev Mol Cell Biol. 3 (12): 906–918. doi:10.1038/nrm976. PMID 12461557. S2CID 11588100.
  5. ^ Götzke, Hansjörg; Kilisch, Markus; Martínez-Carranza, Markel; Sograte-Idrissi, Shama; Rajavel, Abirami; Schlichthaerle, Thomas; Engels, Niklas; Jungmann, Ralf; Stenmark, Pål; Opazo, Felipe; Frey, Steffen (2019). "The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications". Nature Communications. 10 (1): 4403. Bibcode:2019NatCo..10.4403G. doi:10.1038/s41467-019-12301-7. PMC 6764986. PMID 31562305.
  6. ^ De Genst, Erwin J.; Guilliams, Tim; Wellens, Joke; O'Day, Elizabeth M.; Waudby, Christopher A.; Meehan, Sarah; Dumoulin, Mireille; Hsu, Shang-Te Danny; Cremades, Nunilo; Verschueren, Koen H.G.; Pardon, Els; Wyns, Lode; Steyaert, Jan; Christodoulou, John; Dobson, Christopher M. (September 2010). "Structure and Properties of a Complex of α-Synuclein and a Single-Domain Camelid Antibody" (PDF). Journal of Molecular Biology. 402 (2): 326–343. doi:10.1016/j.jmb.2010.07.001. PMID 20620148.
  7. ^ "CaptureSelect C-tag Affinity Matrix - Thermo Fisher Scientific". www.thermofisher.com.
  8. ^ Cooper, Merideth A.; Taris, Joseph E.; Shi, Changhua; Wood, David W. (2018). "A Convenient Split-Intein Tag Method for the Purification of Tagless Target Proteins". Current Protocols in Protein Science. 91 (1): 5.29.1–5.29.23. doi:10.1002/cpps.46. ISSN 1934-3655. PMID 29516483. S2CID 3749506.
  9. ^ Prabhala, Sai Vivek; Gierach, Izabela; Wood, David W. (2022). "The Evolution of Intein-Based Affinity Methods as Reflected in 30 years of Patent History". Frontiers in Molecular Biosciences. 9: 857566. doi:10.3389/fmolb.2022.857566. ISSN 2296-889X. PMC 9033041. PMID 35463948.
  10. ^ "iCapTag™ Technology - Protein Capture Science". www.proteincapturescience.com.
  11. ^ Einhauer, A.; Jungbauer, A. (2001). "The FLAG™ peptide, a versatile fusion tag for the purification of recombinant proteins". Journal of Biochemical and Biophysical Methods. 49 (1–3): 455–65. doi:10.1016/S0165-022X(01)00213-5. PMID 11694294.
  12. ^ Prakriya, Murali; Feske, Stefan; Gwack, Yousang; Srikanth, Sonal; Rao, Anjana; Hogan, Patrick G. (2006). "Orai1 is an essential pore subunit of the CRAC channel". Nature. 443 (7108): 230–3. Bibcode:2006Natur.443..230P. doi:10.1038/nature05122. PMID 16921383. S2CID 4310221.
  13. ^ Brune, Karl D.; Liekniņa, Ilva; Sutov, Grigorij; Morris, Alexander R.; Jovicevic, Dejana; Kalniņš, Gints; Kazāks, Andris; Kluga, Rihards; Kastaljana, Sabine; Zajakina, Anna; Jansons, Juris; Skrastiņa, Dace; Spunde, Karīna; Cohen, Alexander A.; Bjorkman, Pamela J.; Morris, Howard R.; Suna, Edgars; Tārs, Kaspars (2021-11-16). "N-Terminal Modification of Gly-His-Tagged Proteins with Azidogluconolactone". ChemBioChem. 22 (22): 3199–3207. doi:10.1002/cbic.202100381. ISSN 1439-7633. PMID 34520613. S2CID 237515136.
  14. ^ Ho, Philip WL.; Tse, Zero HM.; Liu, HF.; Lu, S.; Ho, Jessica WM.; Kung, Michelle HW.; Ramsden, David B.; Ho, SL. (2013). "Assessment of cellular estrogenic activity based on estrogen receptor-mediated reduction of soluble-form catechol-O-methyltransferase (COMT) expression in an ELISA-based system". PLOS ONE. 8 (9): e74065. Bibcode:2013PLoSO...874065H. doi:10.1371/journal.pone.0074065. PMC 3765251. PMID 24040167.
  15. ^ Keefe, Anthony D.; Wilson, David S.; Seelig, Burckhard; Szostak, Jack W. (2001). "One-Step Purification of Recombinant Proteins Using a Nanomolar-Affinity Streptavidin-Binding Peptide, the SBP-Tag". Protein Expression and Purification. 23 (3): 440–6. doi:10.1006/prep.2001.1515. PMID 11722181.
  16. ^ "Epitope Tags & Fusion Proteins – antibodies-online". www.antibodies-online.com.
  17. ^ McNutt, Markey C.; Lagace, Thomas A.; Horton, Jay D. (2007). "Catalytic Activity is Not Required for Secreted PCSK9 to Reduce Low Density Lipoprotein Receptors in HepG2 Cells". Journal of Biological Chemistry. 282 (29): 20799–803. doi:10.1074/jbc.C700095200. PMID 17537735.
  18. ^ Zakeri, Bijan; Howarth, Mark (2010). "Spontaneous Intermolecular Amide Bond Formation between Side Chains for Irreversible Peptide Targeting". Journal of the American Chemical Society. 132 (13): 4526–7. doi:10.1021/ja910795a. PMID 20235501.
  19. ^ Zakeri, Bijan; Fierer, Jacob O.; Celik, Emrah; Chittock, Emily C.; Schwarz-Linek, Ulrich; Moy, Vincent T.; Howarth, Mark (2012). "Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin". Proceedings of the National Academy of Sciences. 109 (12): E690–7. Bibcode:2012PNAS..109E.690Z. doi:10.1073/pnas.1115485109. PMC 3311370. PMID 22366317.
  20. ^ Veggiani, Gianluca; Nakamura, Tomohiko; Brenner, Michael; Gayet, Raphael; Yan, Jun; Robinson, Carol; Howarth, Mark (2016). "Programmable polyproteams built using twin peptide superglues". Proceedings of the National Academy of Sciences. 113 (5): 1202–7. Bibcode:2016PNAS..113.1202V. doi:10.1073/pnas.1519214113. PMC 4747704. PMID 26787909.
  21. ^ a b Buldun, Can M.; Jean, Jisoo X.; Bedford, Michael R.; Howarth, Mark (14 February 2018). "SnoopLigase Catalyzes Peptide–Peptide Locking and Enables Solid-Phase Conjugate Isolation". Journal of the American Chemical Society. 140 (8): 3008–3018. doi:10.1021/jacs.7b13237. PMID 29402082. S2CID 207189163.
  22. ^ Keeble, Anthony H.; Yadav, Vikash K.; Ferla, Matteo P.; Bauer, Claudia C.; Chuntharpursat-Bon, Eulashini; Huang, Jin; Bon, Robin S.; Howarth, Mark (July 2021). "DogCatcher allows loop-friendly protein-protein ligation". Cell Chemical Biology. 29 (2): 339–350.e10. doi:10.1016/j.chembiol.2021.07.005. ISSN 2451-9456. PMC 8878318. PMID 34324879.
  23. ^ Tan, Lee Ling; Hoon, Shawn S.; Wong, Fong T.; Ahmed, S. Ashraf (26 October 2016). "Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly". PLOS ONE. 11 (10): e0165074. Bibcode:2016PLoSO..1165074T. doi:10.1371/journal.pone.0165074. PMC 5082641. PMID 27783674.
  24. ^ Ciulli, Bond; Alessi, Craigon (Oct 2021). "Development of BromoTag: A "Bump-and-Hole"–PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins". J Med Chem. 64 (20): 15477–15502. doi:10.1021/acs.jmedchem.1c01532. PMC 8558867. PMID 34652918.
  25. ^ Chow, Louise T.; Vassylyev, Dmitry G. (2022). "Application of a Novel CL7/Im7 Affinity System in Purification of Complex and Pharmaceutical Proteins". Affinity Chromatography. Methods in Molecular Biology. Vol. 2466. pp. 61–82. doi:10.1007/978-1-0716-2176-9_5. ISBN 978-1-0716-2175-2. PMID 35585311.
  26. ^ Bedouelle, Hugues; Duplay, Pascale (Feb 1988). "Production in Escherichia coli and one-step purification of bifunctional hybrid proteins which bind maltose. Export of the Klenow polymerase into the periplasmic space". Eur J Biochem. 171 (3): 541–549. doi:10.1111/j.1432-1033.1988.tb13823.x. PMID 3278900.
  27. ^ Minde, David P; Halff, Els F; Tans, Sander (2013). "Designing disorder: Tales of the unexpected tails". Intrinsically Disordered Proteins. 1 (1): 5–15. doi:10.4161/idp.26790. PMC 5424805. PMID 28516025.
  28. ^ Kriznik, Alexandre; Yéléhé-Okouma, Mélissa; Lec, Jean-Christophe; Groshenry, Guillaume; Le Cordier, Hélène; Charron, Christophe; Quinternet, Marc; Mazon, Hortense; Talfournier, François; Boschi-Muller, Sandrine; Jouzeau, Jean-Yves; Reboul, Pascal (Oct 2018). "CRDSAT Generated by pCARGHO: A New Efficient Lectin-Based Affinity Tag Method for Safe, Simple, and Low-Cost Protein Purification". Biotechnol J. 14 (4): 1800214. doi:10.1002/biot.201800214. PMID 30298550. S2CID 52942568.
  29. ^ a b Schwinn, Marie K.; Machleidt, Thomas; Zimmerman, Kris; Eggers, Christopher T.; Dixon, Andrew S.; Hurst, Robin; Hall, Mary P.; Encell, Lance P.; Binkowski, Brock F.; Wood, Keith V. (2018-02-16). "CRISPR-Mediated Tagging of Endogenous Proteins with a Luminescent Peptide". ACS Chemical Biology. 13 (2): 467–474. doi:10.1021/acschembio.7b00549. ISSN 1554-8929. PMID 28892606.
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