GFP-like proteins: identification, analysis and applications
Publications

1. Markvicheva KN, Bogdanova EA, Staroverov DB, Lukyanov S, Belousov VV.
   Imaging of intracellular hydrogen peroxide production with HyPer upon stimulation of HeLa cells with EGF.
   In: Redox-Mediated Signal Transduction Methods and Protocols Series: Methods in Molecular Biology, Vol. 476 Hancock, John T. (Ed.) Hardcover, 2009 ISBN: 978-1-58829-842-3
   
   
2. Pletnev S, Shcherbo D, Chudakov DM, Pletneva N, Merzlyak EM, Wlodawer A, Dauter Z, Pletnev V.
   A crystallographic study of bright far-red fluorescent protein mKate reveals pH-induced cis-trans isomerization of the chromophore.
   J Biol Chem. 2008 Oct 24;283(43):28980-7
   PMID: 18682399
   
   
3. Subach OM, Gundorov IS, Yoshimura M, Subach FV, Zhang J, Gruenwald D, Souslova EA, Chudakov DM, Verkhusha VV.
   Conversion of Red Fluorescent Protein into a Bright Blue Probe.
   Chem Biol. 2008 Oct 20;15(10):1116-24
   PMID: 18940671
   
   
4. Yampolsky IV, Kislukhin AA, Amatov TT, Shcherbo D, Potapov VK, Lukyanov S, Lukyanov KA.
   Synthesis and properties of the red chromophore of the green-to-red photoconvertible fluorescent protein Kaede and its analogs.
   Bioorg Chem. 2008 Apr;36(2):96-104
   PMID: 18262585
   
   
5. Mishin AS, Subach FV, Yampolsky IV, King W, Lukyanov KA, Verkhusha VV.
   The First Mutant of the Aequorea victoria Green Fluorescent Protein That Forms a Red Chromophore.
   Biochemistry, 2008
   PMID: 18366185
   
   
6. Cox LJ, Hengst U, Gurskaya NG, Lukyanov KA, Jaffrey SR.
   Intra-axonal translation and retrograde trafficking of CREB promotes neuronal survival.
   Nat Cell Biol. 2008 Feb;10(2):149-59
   PMID: 18193038
   
   
7. Chudakov DM, Lukyanov S, Lukyanov KA.
   Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2.
   Nat Protoc. 2007;2(8):2024-32
   PMID: 17703215
   
   
8. Tereshina MB, Belousov VV, Zaraisky AG.
   Study of the mechanism of Ras-dva small GTPase intracellular localization.
   Bioorg Khim. 2007 Sep-Oct;33(5):574-6 (in Russian)
   PMID: 18050665
   
   
9. Shcherbo D, Merzlyak EM, Chepurnykh TV, Fradkov AF, Ermakova GV, Solovieva EA, Lukyanov KA, Bogdanova EA, Zaraisky AG, Lukyanov S, Chudakov DM.
   Bright far-red fluorescent protein for whole-body imaging.
   Nat Methods. 2007 Sep;4(9):741-6
   PMID: 17721542
   
   
10. Pletneva NV, Pletnev SV, Chudakov DM, Tikhonova TV, Popov VO, Martynov VI, Wlodawer A, Dauter Z, Pletnev VZ.
    Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom.
    Bioorg Khim. 2007 Jul-Aug;33(4):421-30 (in Russian)
    PMID: 17886433
    
    
11. Souslova EA, Chudakov DM.
    Genetically encoded intracellular sensors based on fluorescent proteins.
    Biochemistry (Mosc). 2007 Jul;72(7):683-97
    PMID: 17680759
    
    
12. Merzlyak EM, Goedhart J, Shcherbo D, Bulina ME, Shcheglov AS, Fradkov AF, Gaintzeva A, Lukyanov KA, Lukyanov S, Gadella TW, Chudakov DM.
    Bright monomeric red fluorescent protein with an extended fluorescence lifetime.
    Nat Methods. 2007 Jul;4(7):555-7
    PMID: 17572680
    
    
13. Souslova EA, Belousov VV, Lock J, Stromblad S, Kasparov S, Bolshakov AP, Pinelis VG, Labas YA, Lukyanov S, Mayr LM, Chudakov DM.
    Single fluorescent protein-based Ca2+ sensors with increased dynamic range.
    BMC Biotechnol. 2007 Jun 29;7(1):37
    PMID: 17603870
    
    
14. Chudakov DM, Lukyanov S, Lukyanov KA.
    Using photoactivatable fluorescent protein Dendra2 to track protein movement.
    Biotechniques. 2007 May;42(5):553, 555, 557 passim
    PMID: 17515192
    
    
15. Zhang L, Gurskaya NG, Merzlyak EM, Staroverov DB, Mudrik NN, Samarkina ON, Vinokurov LM, Lukyanov S, Lukyanov KA.
    Method for real-time monitoring of protein degradation at the single cell level.
    Biotechniques. 2007 Apr;42(4):446, 448, 450
    PMID: 17489230
    
    
16. Oswald F, Schmitt F, Leutenegger A, Ivanchenko S, D'Angelo C, Salih A, Maslakova S, Bulina M, Schirmbeck R, Nienhaus GU, Matz MV, Wiedenmann J.
    Contributions of host and symbiont pigments to the coloration of reef corals.
    FEBS J. 2007 Feb;274(4):1102-9
    PMID: 17244197
    
    
17. Schuttrigkeit TA, Feilitzsch T, Kompa C, Lukyanov KA, Savitsky A, Rosch N, Voityuk AA, Michel-Beyerle ME.
    Femtosecond study of superlinear light induced fluorescence increase of the coral protein asFP595.
    Chem Phys. 2006;323:149-60
    
    
18. Lukyanov KA, Chudakov DM, Fradkov AF, Labas YA, Matz MV, Lukyanov S.
    Discovery and properties of GFP-like proteins from nonbioluminescent anthozoa.
    Methods Biochem Anal. 2006;47:121-38
    PMID: 16335712
    
    
19. Bulina ME, Lukyanov KA, Britanova OV, Onichtchouk D, Lukyanov S, Chudakov DM.
    Chromophore-assisted light inactivation (CALI) using the phototoxic fluorescent protein KillerRed.
    Nat Protoc. 2006;1(2):947-53
    PMID: 17406328
    
    
20. Evdokimov AG, Pokross ME, Egorov NS, Zaraisky AG, Yampolsky IV, Merzlyak EM, Shkoporov AN, Sander I, Lukyanov KA, Chudakov DM.
    Structural basis for the fast maturation of Arthropoda green fluorescent protein.
    EMBO Rep. 2006 Oct;7(10):1006-12
    PMID: 16936637
    
    
21. Chudakov DM, Chepurnykh TV, Belousov VV, Lukyanov S, Lukyanov KA.
    Fast and precise protein tracking using repeated reversible photoactivation.
    Traffic. 2006 Oct;7(10):1304-10
    PMID: 16889652
    
    
22. Gurskaya NG, Verkhusha VV, Shcheglov AS, Staroverov DB, Chepurnykh TV, Fradkov AF, Lukyanov S, Lukyanov KA.
    Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light.
    Nat Biotechnol. 2006 Apr;24(4):461-5
    PMID: 16550175
    
    
23. Belousov VV, Fradkov AF, Lukyanov KA, Staroverov DB, Shakhbazov KS, Terskikh AV, Lukyanov S.
    Genetically encoded fluorescent indicator for intracellular hydrogen peroxide.
    Nat Methods. 2006 Apr;3(4):281-6
    PMID: 16554833
    
    
24. Field SF, Bulina MY, Kelmanson IV, Bielawski JP, Matz MV.
    Adaptive evolution of multicolored fluorescent proteins in reef-building corals.
    J Mol Evol. 2006 Mar;62(3):332-9
    PMID: 16474984
    
    
25. Souslova EA, Chudakov DM.
    Photoswitchable cyan fluorescent protein as a FRET donor.
    Microsc Res Tech. 2006 Mar;69(3):207-9
    PMID: 16538627
    
    
26. Bulina ME, Chudakov DM, Britanova OV, Yanushevich YG, Staroverov DB, Chepurnykh TV, Merzlyak EM, Shkrob MA, Lukyanov S, Lukyanov KA.
    A genetically encoded photosensitizer.
    Nat Biotechnol. 2006 Jan;24(1):95-9
    PMID: 16369538
    
    
27. Lukyanov KA, Chudakov DM, Fradkov AF, Labas YA, Matz MV and Lukyanov SA.
    Discovery and properties of GFP-like proteins from non-bioluminescent Anthozoa.
    In: Green fluorescent protein: properties and applications. Chalfie, M., Kain, S., (Eds). Willey-Liss, New York, 2005; 121-38
    
    
28. Chudakov DM, and Lukyanov KA.
    Using photoactivatable GFPs to study protein dynamics and function.
    In: Jorde, L.B., Little, P.F.R., Dunn, M.J. and Subramaniam, S. (Eds), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons Ltd: Chichester, 2005; 2129-37
    
    
29. Chudakov DM, Lukyanov S, Lukyanov KA.
    Fluorescent proteins as a toolkit for in vivo imaging.
    Trends Biotechnol. 2005 Dec;23(12):605-13
    PMID: 16269193
    
    
30. Shkrob MA, Yanushevich YG, Chudakov DM, Gurskaya NG, Labas YA, Poponov SY, Mudrik NN, Lukyanov S, Lukyanov KA.
    Far-red fluorescent proteins evolved from a blue chromoprotein from Actinia equina.
    Biochem J. 2005 Dec 15;392(Pt 3):649-54
    PMID: 16164420
    
    
31. Lukyanov KA, Chudakov DM, Lukyanov S, Verkhusha VV.
    Innovation: Photoactivatable fluorescent proteins.
    Nat Rev Mol Cell Biol. 2005 Nov;6(11):885-91
    PMID: 16167053
    
    
32. Yampolsky IV, Remington SJ, Martynov VI, Potapov VK, Lukyanov S, Lukyanov KA.
    Synthesis and properties of the chromophore of the asFP595 chromoprotein from Anemonia sulcata.
    Biochemistry. 2005 Apr 19;44(15):5788-93
    PMID: 15823037
    
    
33. Quillin ML, Anstrom DM, Shu X, O'Leary S, Kallio K, Chudakov DM, Remington SJ.
    Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution.
    Biochemistry. 2005 Apr 19;44(15):5774-87
    PMID: 15823036
    
    
34. Yanushevich YG, Shagin DA, Fradkov AF, Shakhbazov KS, Barsova EV, Gurskaya NG, Labas YA, Matz MV, Lukyanov KA, Lukyanov SA.
    Spectral diversity among the members of the family of Green Fluorescent Protein in hydroid jellyfish (Cnidaria, Hydrozoa).
    Bioorg Khim. 2005 Jan-Feb;31(1):49-53 (in Russian)
    PMID: 15787213
    
    
35. Remington SJ, Wachter RM, Yarbrough DK, Branchaud B, Anderson DC, Kallio K, Lukyanov KA.
    zFP538, a yellow-fluorescent protein from Zoanthus, contains a novel three-ring chromophore.
    Biochemistry. 2005 Jan 11;44(1):202-12
    PMID: 15628861
    
    
36. Verkhusha VV, Chudakov DM, Gurskaya NG, Lukyanov S, Lukyanov KA.
    Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins.
    Chem Biol. 2004;11(6):845-54
    PMID: 15217617
    
    
37. Chudakov DM, Verkhusha VV, Staroverov DB, Souslova EA, Lukyanov S, Lukyanov KA.
    Photoswitchable cyan fluorescent protein for protein tracking.
    Nat Biotechnol. 2004 Nov;22(11):1435-9
    PMID: 15502815
    
    
38. Bulina ME, Lukyanov KA, Yampolsky IV, Chudakov DM, Staroverov DB, Shcheglov AS, Gurskaya NG, Lukyanov S.
    New class of blue animal pigments based on Frizzled and Kringle protein domains.
    J Biol Chem. 2004 Oct 15;279(42):43367-70
    PMID: 15297465
    
    
39. Pakhomov AA, Martynova NY, Gurskaya NG, Balashova TA, Martynov VI.
    Photoconversion of the chromophore of a fluorescent protein from Dendronephthya sp.
    Biochemistry (Mosc). 2004 Aug;69(8):901-8
    PMID: 15377271
    
    
40. Shagin DA, Barsova EV, Yanushevich YG, Fradkov AF, Lukyanov KA, Labas YA, Semenova TN, Ugalde JA, Meyers A, Nunez JM, Widder EA, Lukyanov SA, Matz MV.
    GFP-like proteins as ubiquitous Metazoan superfamily: evolution of functional features and structural complexity.
    Mol Biol Evol. 2004 May;21(5):841-50
    PMID: 14963095
    
    
41. Verkhusha VV, Lukyanov KA.
    The molecular properties and applications of Anthozoa fluorescent proteins and chromoproteins.
    Nat Biotechnol. 2004 Mar;22(3):289-96
    PMID: 14990950
    
    
42. Verkhusha VV, Matz MV, Sakurai T, Lukyanov KA.
    GFP-like fluorescent proteins and chromoproteins of the class Anthozoa.
    In: Protein structures: kaleidoscope of structural properties and functions. Ed. Uversky V.N., Research Signpost, Kerala, India, 2003; 405-39
    
    
43. Martynov VI, Maksimov BI, Martynova NY, Pakhomov AA, Gurskaya NG, Lukyanov SA.
    A purple-blue chromoprotein from Goniopora tenuidens belongs to the DsRed subfamily of GFP-like proteins.
    J Biol Chem. 2003 Nov 21;278(47):46288-92
    PMID: 12975373
    
    
44. Chudakov DM, Lukyanov KA.
    Use of green fluorescent protein (GFP) and its homologs for in vivo protein motility studies.
    Biochemistry (Mosc). 2003 Sep;68(9):952-7
    PMID: 14606935
    
    
45. Yanushevich YG, Gurskaya NG, Staroverov DB, Lukyanov SA, Lukyanov KA.
    A natural fluorescent protein that changes its fluorescence during maturation.
    Bioorg Khim. 2003 Jul-Aug;29(4):356-60 (in Russian)
    PMID: 12947756
    
    
46. Gurskaya NG, Fradkov AF, Pounkova NI, Staroverov DB, Bulina ME, Yanushevich YG, Labas YA, Lukyanov S, Lukyanov KA.
    A colourless green fluorescent protein homologue from the non-fluorescent hydromedusa Aequorea coerulescens and its fluorescent mutants.
    Biochem J. 2003 Jul 15;373(Pt 2):403-8
    PMID: 12693991
    
    
47. Bulina ME, Verkhusha VV, Staroverov DB, Chudakov DM, Lukyanov KA.
    Hetero-oligomeric tagging diminishes non-specific aggregation of target proteins fused with Anthozoa fluorescent proteins.
    Biochem J. 2003 Apr 1;371(Pt 1):109-14
    PMID: 12472468
    
    
48. Chudakov DM, Belousov VV, Zaraisky AG, Novoselov VV, Staroverov DB, Zorov DB, Lukyanov S, Lukyanov KA.
    Kindling fluorescent proteins for precise in vivo photolabeling.
    Nat Biotechnol. 2003 Feb;21(2):191-4
    PMID: 12524551
    
    
49. Chudakov DM, Feofanov AV, Mudrik NN, Lukyanov S, Lukyanov KA.
    Chromophore environment provides clue to kindling fluorescent protein riddle.
    J Biol Chem. 2003 Feb 28;278(9):7215-9
    PMID: 12496281
    
    
50. Fradkov AF, Verkhusha VV, Staroverov DB, Bulina ME, Yanushevich YG, Martynov VI, Lukyanov S, Lukyanov KA.
    Far-red fluorescent tag for protein labelling.
    Biochem J. 2002 Nov 15;368(Pt 1):17-21
    PMID: 12350221
    
    
51. Matz MV, Lukyanov KA, Lukyanov SA.
    Family of the green fluorescent protein: journey to the end of the rainbow.
    Bioessays. 2002 Oct;24(10):953-9
    PMID: 12325128
    
    
52. Yanushevich YG, Bulina ME, Gurskaya NG, Savitskii AP, Lukyanov KA.
    Key amino acid residues responsible for the color of green and yellow fluorescent proteins from the coral polyp Zoanthus.
    Bioorg Khim. 2002 Jul-Aug;28(4):303-7 (in Russian)
    PMID: 12197386
    FULL TEXT
    
    
53. Barinova I, Zhexembekova M, Barsova E, Lukyanov S, Heberle-Bors E, Touraev A.
    Antirrhinum majus microspore maturation and transient transformation in vitro.
    J Exp Bot. 2002 May;53(371):1119-29
    PMID: 11971923
    
    
54. Bulina ME, Chudakov DM, Mudrik NN, Lukyanov KA.
    Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis.
    BMC Biochem. 2002 Apr 24;3:7
    PMID: 11972899
    
    
55. Labas YA, Gurskaya NG, Yanushevich YG, Fradkov AF, Lukyanov KA, Lukyanov SA, Matz MV.
    Diversity and evolution of the green fluorescent protein family.
    Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4256-61
    PMID: 11929996
    
    
56. Terskikh AV, Fradkov AF, Zaraisky AG, Kajava AV, Angres B.
    Analysis of DsRed Mutants. Space around the fluorophore accelerates fluorescence development.
    J Biol Chem. 2002 Mar 8;277(10):7633-6
    PMID: 11773062
    
    
57. Yanushevich YG, Staroverov DB, Savitsky AP, Fradkov AF, Gurskaya NG, Bulina ME, Lukyanov KA, Lukyanov SA.
    A strategy for the generation of non-aggregating mutants of Anthozoa fluorescent proteins.
    FEBS Lett. 2002 Jan 30;511(1-3):11-4
    PMID: 11821040
    
    
58. Gurskaya NG, Savitsky AP, Yanushevich YG, Lukyanov SA, Lukyanov KA.
    Color transitions in coral's fluorescent proteins by site-directed mutagenesis.
    BMC Biochem. 2001;2:6
    PMID: 11459517
    FULL TEXT
    
    
59. Gurskaya NG, Fradkov AF, Terskikh A, Matz MV, Labas YA, Martynov VI, Yanushevich YG, Lukyanov KA, Lukyanov SA.
    GFP-like chromoproteins as a source of far-red fluorescent proteins.
    FEBS Lett. 2001 Oct 19;507(1):16-20
    PMID: 11682051
    
    
60. Martynov VI, Savitsky AP, Martynova NY, Savitsky PA, Lukyanov KA, Lukyanov SA.
    Alternative cyclization in GFP-like proteins family. The formation and structure of the chromophore of a purple chromoprotein from Anemonia sulcata.
    J Biol Chem. 2001 Jun 15;276(24):21012-6
    PMID: 11259412
    
    
61. Yarbrough D, Wachter RM, Kallio K, Matz MV, Remington SJ.
    Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.
    Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):462-7
    PMID: 11209050
    
    
62. Terskikh A, Fradkov A, Ermakova G, Zaraisky A, Tan P, Kajava AV, Zhao X, Lukyanov S, Matz M, Kim S, Weissman I, Siebert P.
    "Fluorescent timer": protein that changes color with time.
    Science. 2000 Nov 24;290(5496):1585-8
    PMID: 11090358
    
    
63. Lukyanov KA, Fradkov AF, Gurskaya NG, Matz MV, Labas YA, Savitsky AP, Markelov ML, Zaraisky AG, Zhao X, Fang Y, Tan W, Lukyanov SA.
    Natural animal coloration can be determined by a nonfluorescent green fluorescent protein homolog.
    J Biol Chem. 2000 Aug 25;275(34):25879-82
    PMID: 10852900
    
    
64. Fradkov AF, Chen Y, Ding L, Barsova EV, Matz MV, Lukyanov SA.
    Novel fluorescent protein from Discosoma coral and its mutants possesses a unique far-red fluorescence.
    FEBS Lett. 2000 Aug 18;479(3):127-30
    PMID: 10981720
    
    
65. Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA.
    Fluorescent proteins from nonbioluminescent Anthozoa species.
    Nat Biotechnol. 1999 Oct;17(10):969-73
    PMID: 10504696