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Photoswitching of E222Q GFP mutants: “concerted” mechanism of chromophore isomerization and protonation

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Abstract

Photochromic (i.e. reversibly photoswitchable) fluorescent proteins increasingly find applications as biomarkers for advanced bioimaging applications. From a mechanistic point of view, photochromicity usually stems from the reversible cis-trans photoisomerization of the chromophore. We demonstrated experimentally that cis-trans photoisomerization constitutes a very efficient deactivation pathway of isolated chromophores upon visible light excitation. Nonetheless, this intrinsic property is seldom displayed by chromophores in the folded protein structure. We found that the E222Q amino acid replacement restores efficient photochromicity in otherwise poorly switchable green fluorescent protein variants of different optical properties. Glutamic acid 222 is known to play a pivotal role in the inner proton wires that involve the GFP chromophore and the surrounding residues. Hence its substitution with an isosteric but non-ionizable residue presumably leads to a extensive rewiring of proton pathways around the chromophore, which has a deep effect also on the photochromic properties. In this work, we review and discuss the main photophysical properties of photochromic E222Q GFP mutants. Additionally we show, by means of flash-photolysis experiments, that chromophore cis to trans photoswitching involves a molecular mechanism where stereochemical isomerization and chromophore protonation occur in a coordinated way. Such a “concerted” mechanism is, in our opinion, at the basis of efficient photochromic behavior and might be activated by the E222Q mutation.

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Notes and references

  1. R. M. Wachter, Chromogenic cross-link formation in green fluorescent protein, Acc. Chem. Res., 2007, 40, 120–127.

    Article  CAS  PubMed  Google Scholar 

  2. D. M. Chudakov, S. Lukyanov, K. A. Lukyanov, Fluorescent proteins as a toolkit for in vivo imaging, Trends Biotechnol., 2005, 23, 605–613.

    Article  CAS  PubMed  Google Scholar 

  3. S. Habuchi, P. Dedecker, J. Hotta, C. Flors, R. Ando, H. Mizuno, A. Miyawaki, J. Hofkens, Photo-induced protonation/deprotonation in the GFP-like fluorescent protein Dronpa: mechanism responsible for the reversible photoswitching, Photochem. Photobiol. Sci., 2006, 5, 567–576.

    Article  CAS  PubMed  Google Scholar 

  4. K. A. Lukyanov, D. M. Chudakov, S. Lukyanov, V. V. Verkhusha, Innovation: Photoactivatable fluorescent proteins, Nat. Rev. Mol. Cell Biol., 2005, 6, 885–891.

    Article  CAS  PubMed  Google Scholar 

  5. J. Lippincott-Schwartz, G. H. Patterson, Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging, Trends Cell Biol., 2009, 19, 555–565.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. M. Fernandez-Suarez, A. Y. Ting, Fluorescent probes for super-resolution imaging in living cells, Nat. Rev. Mol. Cell Biol., 2008, 9, 929–943.

    Article  CAS  PubMed  Google Scholar 

  7. R. Ando, H. Mizuno, A. Miyawaki, Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting, Science, 2004, 306, 1370–1373.

    Article  CAS  PubMed  Google Scholar 

  8. R. Bizzarri, M. Serresi, F. Cardarelli, S. Abbruzzetti, B. Campanini, C. Viappiani, F. Beltram, Single amino acid replacement makes Aequorea victoria fluorescent proteins reversibly photoswitchable, J. Am. Chem. Soc., 2010, 132, 85–95.

    Article  CAS  PubMed  Google Scholar 

  9. E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, H. F. Hess, Imaging intracellular fluorescent proteins at nanometer resolution, Science, 2006, 313, 1642–1645.

    Article  CAS  PubMed  Google Scholar 

  10. S. T. Hess, T. P. Girirajan, M. D. Mason, Ultra-high resolution imaging by fluorescence photoactivation localization microscopy, Biophys. J., 2006, 91, 4258–4272.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. M. Andresen, A. C. Stiel, J. Folling, D. Wenzel, A. Schonle, A. Egner, C. Eggeling, S. W. Hell, S. Jakobs, Photoswitchable fluorescent proteins enable monochromatic multilabel imaging and dual color fluorescence nanoscopy, Nat. Biotechnol., 2008, 26, 1035–1040.

    Article  CAS  PubMed  Google Scholar 

  12. S. Habuchi, R. Ando, P. Dedecker, W. Verheijen, H. Mizuno, A. Miyawaki, J. Hofkens, Reversible single-molecule photoswitching in the GFP-like fluorescent protein Dronpa, Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 9511–9516.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. M. Andresen, A. C. Stiel, S. Trowitzsch, G. Weber, C. Eggeling, M. C. Wahl, S. W. Hell, S. Jakobs, Structural basis for reversible photoswitching in Dronpa, Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 13005–13009.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. H. Mizuno, T. K. Mal, M. Walchli, A. Kikuchi, T. Fukano, R. Ando, J. Jeyakanthan, J. Taka, Y. Shiro, M. Ikura, A. Miyawaki, Light-dependent regulation of structural flexibility in a photochromic fluorescent protein, Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 9227–9232.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. J. N. Henderson, H. W. Ai, R. E. Campbell, S. J. Remington, Structural basis for reversible photobleaching of a green fluorescent protein homologue, Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 6672–6677.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. M. Andresen, M. C. Wahl, A. C. Stiel, F. Grater, L. V. Schafer, S. Trowitzsch, G. Weber, C. Eggeling, H. Grubmuller, S. W. Hell, S. Jakobs, Structure and mechanism of the reversible photoswitch of a fluorescent protein, Proc. Natl. Acad. Sci. U. S. A., 2005, 102, 13070–13074.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. R. A. G. Cinelli, V. Pellegrini, A. Ferrari, P. Faraci, R. Nifosi, M. Tyagi, M. Giacca, F. Beltram, Green fluorescent proteins as optically controllable elements in bioelectronics, Appl. Phys. Lett., 2001, 79, 3353–3355.

    Article  CAS  Google Scholar 

  18. R. Nifosi, A. Ferrari, C. Arcangeli, V. Tozzini, V. Pellegrini, F. Beltram, Photoreversible dark state in a tristable green fluorescent protein variant, J. Phys. Chem. B, 2003, 107, 1679–1684.

    Article  CAS  Google Scholar 

  19. S. Luin, V. Voliani, G. Lanza, R. Bizzarri, P. Amat, V. Tozzini, M. Serresi, F. Beltram, Raman study of chromophore states in photochromic fluorescent proteins, J. Am. Chem. Soc., 2009, 131, 96–103.

    Article  CAS  PubMed  Google Scholar 

  20. N. C. Shaner, P. A. Steinbach, R. Y. Tsien, A guide to choosing fluorescent proteins, Nat. Methods, 2005, 2, 905–909.

    Article  CAS  PubMed  Google Scholar 

  21. A. Miyawaki, Innovations in the imaging of brain functions using fluorescent proteins, Neuron, 2005, 48, 189–199.

    Article  CAS  PubMed  Google Scholar 

  22. W. Cheng, F. Yang, C. L. Takanishi, J. Zheng, Thermosensitive TRPV channel subunits coassemble into heteromeric channels with intermediate conductance and gating properties, J. Gen. Physiol., 2007, 129, 191–207.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. S. Abbruzzetti, S. Sottini, C. Viappiani, J. E. Corrie, Kinetics of proton release after flash photolysis of 1-(2-nitrophenyl)ethyl sulfate (caged sulfate) in aqueous solution, J. Am. Chem. Soc., 2005, 127, 9865–9874.

    Article  CAS  PubMed  Google Scholar 

  24. S. Abbruzzetti, S. Bruno, S. Faggiano, E. Grandi, A. Mozzarelli, C. Viappiani, Time-resolved methods in Biophysics. 2. Monitoring haem proteins at work with nanosecond laser flash photolysis, Photochem. Photobiol. Sci., 2006, 5, 1109–1120.

    Article  CAS  PubMed  Google Scholar 

  25. A. Banderini, S. Sottini, C. Viappiani, Method for acquiring extended real-time kinetic signals in nanosecond laser flash photolysis experiments, Rev. Sci. Instrum., 2004, 75, 2257–2261.

    Article  CAS  Google Scholar 

  26. V. Voliani, R. Bizzarri, R. Nifosi, S. Abbruzzetti, E. Grandi, C. Viappiani, F. Beltram, Cis-trans photoisomerization of fluorescent-protein chromophores, J. Phys. Chem. B, 2008, 112, 10714–10722.

    Article  CAS  PubMed  Google Scholar 

  27. X. He, A. F. Bell, P. J. Tonge, Ground state isomerization of a model green fluorescent protein chromophore, FEBS Lett., 2003, 549, 35–38.

    Article  CAS  PubMed  Google Scholar 

  28. A. A. Voityuk, M. E. Michel-Beyerle, N. Rosch, Structure and rotation barriers for ground and excited states of the isolated chromophore of the green fluorescent protein, Chem. Phys. Lett., 1998, 296, 269–276.

    Article  CAS  Google Scholar 

  29. N. Reuter, H. Lin, W. Thiel, Green fluorescent proteins: Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamics simulation’s of the wild type and S65T mutant, J. Phys. Chem. B, 2002, 106, 6310–6321.

    Article  CAS  Google Scholar 

  30. J. Dong, F. Abulwerdi, A. Baldridge, J. Kowalik, K. M. Solntsev, L. M. Tolbert, Isomerization in fluorescent protein chromophores involves addition/elimination, J. Am. Chem. Soc., 2008, 130, 14096–14098.

    Article  CAS  PubMed  Google Scholar 

  31. J. S. Yang, G. J. Huang, Y. H. Liu, S. M. Peng, Photoisomerization of the green fluorescence protein chromophore and the meta- and para-amino analogues, Chem. Commun., 2008, 1344–1346.

    Google Scholar 

  32. W. Weber, V. Helms, J. A. McCammon, P. W. Langhoff, Shedding light on the dark and weakly fluorescent states of green fluorescent proteins, Proc. Natl. Acad. Sci. U. S. A., 1999, 96, 6177–6182.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. A. C. Stiel, S. Trowitzsch, G. Weber, M. Andresen, C. Eggeling, S. W. Hell, S. Jakobs, M. C. Wahl, 1.8 A bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants, Biochem. J., 2007, 402, 35–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. R. Ando, C. Flors, H. Mizuno, J. Hofkens, A. Miyawaki, Highlighted generation of fluorescence signals using simultaneous two-color irradiation on Dronpa mutants, Biophys. J., 2007, 92, L97–L99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. V. Adam, M. Lelimousin, S. Boehme, G. Desfonds, K. Nienhaus, M. J. Field, J. Wiedenmann, S. McSweeney, G. U. Nienhaus, D. Bourgeois, Structural characterization of IrisFP, an optical highlighter undergoing multiple photo-induced transformations, Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 18343–18348.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. M. Lelimousin, M. Noirclerc-Savoye, C. Lazareno-Saez, B. Paetzold, S. Le Vot, R. Chazal, P. Macheboeuf, M. J. Field, D. Bourgeois, A. Royant, Intrinsic dynamics in ECFP and Cerulean control fluorescence quantum yield, Biochemistry, 2009, 48, 10038–10046.

    Article  CAS  PubMed  Google Scholar 

  37. R. M. Dickson, A. B. Cubitt, R. Y. Tsien, W. E. Moerner, On/off blinking and switching behaviour of single molecules of green fluorescent protein, Nature, 1997, 388, 355–358.

    Article  CAS  PubMed  Google Scholar 

  38. T. B. McAnaney, W. Zeng, C. F. Doe, N. Bhanji, S. Wakelin, D. S. Pearson, P. Abbyad, X. Shi, S. G. Boxer, C. R. Bagshaw, Protonation, Photobleaching, and Photoactivation of Yellow Fluorescent Protein (YFP 10C): A Unifying Mechanism, Biochemistry, 2005, 44, 5510–5524.

    Article  CAS  PubMed  Google Scholar 

  39. G. Chirico, A. Diaspro, F. Cannone, M. Collini, S. Bologna, V. Pellegrini, F. Beltram, Selective Fluorescence Recovery after Bleaching of Single E2GFP Proteins Induced by Two-Photon Excitation, ChemPhysChem, 2005, 6, 328–335.

    Article  CAS  PubMed  Google Scholar 

  40. G. S. Harms, L. Cognet, P. H. Lommerse, G. A. Blab, T. Schmidt, Autofluorescent proteins in single-molecule research: applications to live cell imaging microscopy, Biophys. J., 2001, 80, 2396–2408.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. J. S. Biteen, M. A. Thompson, N. K. Tselentis, G. R. Bowman, L. Shapiro, W. E. Moerner, Super-resolution imaging in live Caulobacter crescentus cells using photoswitchable EYFP, Nat. Methods, 2008, 5, 947–949.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. R. Nifosi, V. Tozzini, Cis-trans photolsomerization of the chromophore in the green fluorescent protein variant E(2)GFP: A molecular dynamics study, Chem. Phys., 2006, 323, 358–368.

    Article  CAS  Google Scholar 

  43. R. Bizzarri, C. Arcangeli, D. Arosio, F. Ricci, P. Faraci, F. Cardarelli, F. Beltram, Development of a novel GFP-based ratiometric excitation and emission pH indicator for intracellular studies, Biophys. J., 2006, 90, 3300–3314.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. R. Bizzarri, R. Nifosi, S. Abbruzzetti, W. Rocchia, S. Guidi, D. Arosio, G. Garau, B. Campanini, E. Grandi, F. Ricci, C. Viappiani, F. Beltram, Green Fluorescent Protein Ground States: The Influence of a Second Protonation Site near the Chromophore(), Biochemistry, 2007, 46, 5494–5504.

    Article  CAS  PubMed  Google Scholar 

  45. M. Serresi, R. Bizzarri, F. Cardarelli, F. Beltram, Real-time measurement of endosomal acidification by a novel genetically encoded biosensor, Anal. Bioanal. Chem., 2009, 393, 1123–1133.

    Article  CAS  PubMed  Google Scholar 

  46. G. Jung, A. Zumbusch, Improving autofluorescent proteins: comparative studies of the effective brightness of Green Fluorescent Protein (GFP) mutants, Microsc. Res. Tech., 2006, 69, 175–185.

    Article  CAS  PubMed  Google Scholar 

  47. G. Jung, C. Brauchle, A. Zumbusch, Two-color fluorescence correlation spectroscopy of one chromophore: Application to the E222Q mutant of the green fluorescent protein, J. Chem. Phys., 2001, 114, 3149–3156.

    Article  CAS  Google Scholar 

  48. C. Bosisio, V. Quercioli, M. Collini, L. D’Alfonso, G. Baldini, S. Bettati, B. Campanini, S. Raboni, G. Chirico, Protonation and conformational dynamics of GFP mutants by two-photon excitation fluorescence correlation spectroscopy, J. Phys. Chem. B, 2008, 112, 8806–8814.

    Article  CAS  PubMed  Google Scholar 

  49. P. Dedecker, J. Hotta, R. Ando, A. Miyawaki, Y. Engelborghs, J. Hofkens, Fast and reversible photoswitching of the fluorescent protein dronpa as evidenced by fluorescence correlation spectroscopy, Biophys. J., 2006, 91, L45–47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. J. J. van Thor, T. Gensch, K. J. Hellingwerf, L. N. Johnson, Phototransformation of green fluorescent protein with UV and visible light leads to decarboxylation of glutamate 222, Nat. Struct. Biol., 2002, 9, 37–41.

    Article  PubMed  CAS  Google Scholar 

  51. G. Jung, J. Wiehler, A. Zumbusch, The photophysics of green fluorescent protein: influence of the key amino acids at positions 65, 203, and 222, Biophys. J., 2005, 88, 1932–1947.

    Article  CAS  PubMed  Google Scholar 

  52. S. Abbruzzetti, E. Grandi, C. Viappiani, S. Bologna, B. Campanini, S. Raboni, S. Bettati, A. Mozzarelli, Kinetics of acid-induced spectral changes in the GFPmut2 chromophore, J. Am. Chem. Soc., 2005, 127, 626–635.

    Article  CAS  PubMed  Google Scholar 

  53. S. Violot, P. Carpentier, L. Blanchoin, D. Bourgeois, Reverse pH-dependence of chromophore protonation explains the large Stokes shift of the red fluorescent protein mKeima, J. Am. Chem. Soc., 2009, 131, 10356–10357.

    Article  CAS  PubMed  Google Scholar 

  54. S. Pletnev, D. Shcherbo, D. M. Chudakov, N. Pletneva, E. M. Merzlyak, A. Wlodawer, Z. Dauter, V. Pletnev, A crystallographic study of bright far-red fluorescent protein mKate reveals pH-induced cis-trans isomerization of the chromophore, J. Biol. Chem., 2008, 283, 28980–28987.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. M. Irie, Diarylethenes for memories and switches, Chem. Rev., 2000, 100, 1685–1716.

    Article  CAS  PubMed  Google Scholar 

  56. G. H. Patterson, S. M. Knobel, W. D. Sharif, S. R. Kain, D. W. Piston, Use of the green fluorescent protein and its mutants in quantitative fluorescence microscopy, Biophys. J., 1997, 73, 2782–2790.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. D. Sinnecker, P. Voigt, N. Hellwig, M. Schaefer, Reversible photobleaching of enhanced green fluorescent proteins, Biochemistry, 2005, 44, 7085–7094.

    Article  CAS  PubMed  Google Scholar 

  58. L. V. Schafer, G. Groenhof, M. Boggio-Pasqua, M. A. Robb, H. Grubmuller, Chromophore protonation state controls photoswitching of the fluoroprotein asFP595, PLoS Comput. Biol., 2008, 4, e1000034.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  59. K. Brejc, T. K. Sixma, P. A. Kitts, S. R. Kain, R. Y. Tsien, M. Ormo, S. J. Remington, Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein, Proc. Natl. Acad. Sci. U. S. A., 1997, 94, 2306–2311.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. T. Brakemann, G. Weber, M. Andresen, G. Groenhof, A. C. Stiel, S. Trowitzsch, C. Eggeling, H. Grubmuller, S. W. Hell, M. C. Wahl, S. Jakobs, Molecular basis of the light-driven switching of the photochromic fluorescent protein Padron, J. Biol. Chem., 2010, 285, 14603–14609.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. S. Olsen, K. Lamothe, T. J. Martinez, Protonic gating of excited-state twisting and charge localization in GFP chromophores: a mechanistic hypothesis for reversible photoswitching, J. Am. Chem. Soc., 2010, 132, 1192–1193.

    Article  CAS  PubMed  Google Scholar 

  62. A. R. Faro, V. Adam, P. Carpentier, C. Darnault, D. Bourgeois, E. de Rosny, Low-temperature switching by photoinduced protonation in photochromic fluorescent proteins, Photochem. Photobiol. Sci., 2010, 9, 254–262.

    Article  CAS  PubMed  Google Scholar 

  63. S. L. C. Moors, S. Michielssens, C. Flors, P. Dedecker, J. Hofkens, A. Ceulemans, How is cis-trans isomerization controlled in Dronpa mutants? A replica exchange molecular dynamics study, J. Chem. Theory Comput., 2008, 4, 1012–1020.

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Ranieri Bizzarri.

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This article is published as part of a themed issue on photofunctional proteins: from understanding to engineering.

‡ Stefania Abbruzzetti and Ranieri Bizzarri contributed equally to this work.

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Abbruzzetti, S., Bizzarri, R., Luin, S. et al. Photoswitching of E222Q GFP mutants: “concerted” mechanism of chromophore isomerization and protonation. Photochem Photobiol Sci 9, 1307–1319 (2010). https://doi.org/10.1039/c0pp00189a

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