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Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag.

Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K
Biochemistry 60 2560-2575 (2021)
Related entries: 6y7a, 6y7b, 6zcc

Cited: 29 times
EuropePMC logo PMID: 34339177

Abstract

The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.

Articles - 6y8p mentioned but not cited (4)

  1. Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag. Wilhelm J, Kühn S, Tarnawski M, Gotthard G, Tünnermann J, Tänzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K. Biochemistry 60 2560-2575 (2021)
  2. Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA). Graham TGW, Ferrie JJ, Dailey GM, Tjian R, Darzacq X. Elife 11 e76870 (2022)
  3. Sulfonated red and far-red rhodamines to visualize SNAP- and Halo-tagged cell surface proteins. Birke R, Ast J, Roosen DA, Lee J, Roßmann K, Huhn C, Mathes B, Lisurek M, Bushiri D, Sun H, Jones B, Lehmann M, Levitz J, Haucke V, Hodson DJ, Broichhagen J. Org Biomol Chem 20 5967-5980 (2022)
  4. research-article Design rules for efficient endosomal escape. Zoltek M, Vázquez A, Zhang X, Dadina N, Lesiak L, Schepartz A. bioRxiv 2023.11.03.565388 (2023)


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  1. Choosing the Probe for Single-Molecule Fluorescence Microscopy. Schirripa Spagnolo C, Luin S. Int J Mol Sci 23 14949 (2022)
  2. Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. Pecori F, Torres-Padilla ME. Dev Cell 58 435-449 (2023)
  3. Fluorescence microscopy imaging of a neurotransmitter receptor and its cell membrane lipid milieu. Barrantes FJ. Front Mol Biosci 9 1014659 (2022)
  4. Imagining the future of optical microscopy: everything, everywhere, all at once. Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Commun Biol 6 1096 (2023)
  5. Organic fluorescent probes for live-cell super-resolution imaging. Duan X, Zhang M, Zhang YH. Front Optoelectron 16 34 (2023)
  6. Targeted therapy using engineered extracellular vesicles: principles and strategies for membrane modification. Liu Q, Li D, Pan X, Liang Y. J Nanobiotechnology 21 334 (2023)

Articles citing this publication (19)

  1. Engineered HaloTag variants for fluorescence lifetime multiplexing. Frei MS, Tarnawski M, Roberti MJ, Koch B, Hiblot J, Johnsson K. Nat Methods 19 65-70 (2022)
  2. Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy. Kompa J, Bruins J, Glogger M, Wilhelm J, Frei MS, Tarnawski M, D'Este E, Heilemann M, Hiblot J, Johnsson K. J Am Chem Soc 145 3075-3083 (2023)
  3. Photoactivatable Fluorescent Dyes with Hydrophilic Caging Groups and Their Use in Multicolor Nanoscopy. Butkevich AN, Weber M, Cereceda Delgado AR, Ostersehlt LM, D'Este E, Hell SW. J Am Chem Soc 143 18388-18393 (2021)
  4. Fluorescent and Bioluminescent Calcium Indicators with Tuneable Colors and Affinities. Mertes N, Busch M, Huppertz MC, Hacker CN, Wilhelm J, Gürth CM, Kühn S, Hiblot J, Koch B, Johnsson K. J Am Chem Soc 144 6928-6935 (2022)
  5. Photobleaching step analysis for robust determination of protein complex stoichiometries. Hummert J, Yserentant K, Fink T, Euchner J, Ho YX, Tashev SA, Herten DP. Mol Biol Cell 32 ar35 (2021)
  6. A general method for the development of multicolor biosensors with large dynamic ranges. Hellweg L, Edenhofer A, Barck L, Huppertz MC, Frei MS, Tarnawski M, Bergner A, Koch B, Johnsson K, Hiblot J. Nat Chem Biol 19 1147-1157 (2023)
  7. Synergizing Exchangeable Fluorophore Labels for Multitarget STED Microscopy. Glogger M, Wang D, Kompa J, Balakrishnan A, Hiblot J, Barth HD, Johnsson K, Heilemann M. ACS Nano 16 17991-17997 (2022)
  8. A chemical tool for blue light-inducible proximity photo-crosslinking in live cells. Mishra PK, Kang MG, Lee H, Kim S, Choi S, Sharma N, Park CM, Ko J, Lee C, Seo JK, Rhee HW. Chem Sci 13 955-966 (2022)
  9. A Fluorescence-based Approach Utilizing Self-labeling Enzyme Tags to Determine Protein Orientation in Large Unilamellar Vesicles. Paweletz LC, Veit S, Pomorski TG. Bio Protoc 12 e4542 (2022)
  10. First thermostable CLIP-tag by rational design applied to an archaeal O6 -alkyl-guanine-DNA-alkyl-transferase. Merlo R, Mattossovich R, Genta M, Valenti A, Di Mauro G, Minassi A, Miggiano R, Perugino G. Comput Struct Biotechnol J 20 5275-5286 (2022)
  11. N-Cyanorhodamines: cell-permeant, photostable and bathochromically shifted analogues of fluoresceins. Heynck L, Matthias J, Bossi ML, Butkevich AN, Hell SW. Chem Sci 13 8297-8306 (2022)
  12. A general highly efficient synthesis of biocompatible rhodamine dyes and probes for live-cell multicolor nanoscopy. Bucevičius J, Gerasimaitė R, Kiszka KA, Pradhan S, Kostiuk G, Koenen T, Lukinavičius G. Nat Commun 14 1306 (2023)
  13. Revealing the tissue-level complexity of endogenous glucagon-like peptide-1 receptor expression and signaling. Ast J, Nasteska D, Fine NHF, Nieves DJ, Koszegi Z, Lanoiselée Y, Cuozzo F, Viloria K, Bacon A, Luu NT, Newsome PN, Calebiro D, Owen DM, Broichhagen J, Hodson DJ. Nat Commun 14 301 (2023)
  14. Silicon functionalization expands the repertoire of Si-rhodamine fluorescent probes. Rao DN, Ji X, Miller SC. Chem Sci 13 6081-6088 (2022)
  15. A Semisynthetic Bioluminescence Sensor for Ratiometric Imaging of Metal Ions In Vivo Using DNAzymes Conjugated to An Engineered Nano-Luciferase. Xiong M, Wu Y, Kong G, Lewis W, Yang Z, Zhang H, Xu L, Liu Y, Liu Q, Zhao X, Zhang XB, Lu Y. Angew Chem Int Ed Engl 62 e202308086 (2023)
  16. Editorial A primer on harnessing non-enzymatic post-translational modifications for drug design. Long MJC, Ly P, Aye Y. RSC Med Chem 12 1797-1807 (2021)
  17. Enzyme self-label-bound ATTO700 in single-molecule and super-resolution microscopy. Trumpp M, Oliveras A, Gonschior H, Ast J, Hodson DJ, Knaus P, Lehmann M, Birol M, Broichhagen J. Chem Commun (Camb) 58 13724-13727 (2022)
  18. HaloTag-based reporters for sparse labeling and cell tracking. Couturier L, Luna J, Mazouni K, Mestdagh C, Phan MS, Corson F, Schweisguth F. Fly (Austin) 16 360-366 (2022)
  19. Quantitative determination of fluorescence labeling implemented in cell cultures. Schirripa Spagnolo C, Moscardini A, Amodeo R, Beltram F, Luin S. BMC Biol 21 190 (2023)


Related citations provided by authors (1)

  1. Kinetic and structural characterization of the self-labeling protein tags HaloTag7, SNAP-tag and CLIP-tag. Wilhelm J, Kuhn S, Tarnawski M, Gotthard G, Tunnermann J, Tanzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K Biorxiv - (2021)

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