Shemyakin & Ovchinikov Institute of Bioorganic Chemistry
Laboratory of Molecular Technologies
| Home | People | Research | Publications | Protocols | Collaborations |

General information
Professional appointments
Scientific background

Dmitry M. Chudakov

Born: September 13, 1978, Moscow, Russia
Citizenship: Russia
Business address:
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Micklukho-Maklaya 16/10, 117871, Moscow, Russia;
tel: 7(495) 429-80-20
fax: 7(495) 330-70-56

Research scientist, Laboratory of Molecular Technologies (prev. Laboratory of Genes for Regeneration), Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.

B.S., Moscow State University, Moscow, Russia (1998) Molecular biology
M.Sc., Moscow State University, Moscow, Russia (2000) Molecular biology
Ph.D., Institute of Bioorganic Chemistry, Moscow, Russia (2003) Molecular biology

2000-2003 postgraduate student, Laboratory of Genes for Regeneration, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
Ph.D. thesis: "Photo-conversion of Anthozoa chromoproteins"- 2003. Supervisor -K.A.Lukyanov.
2003 - present Research scientist, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. Laboratory of Molecular Technologies (prev. Laboratory of Genes for Regeneration) headed by S.A.Lukyanov.

Area of expertise: GFP-like proteins.

  1. 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

  2. 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

  3. Zakharova MY, Dubiley SA, Chudakov DM, Gabibov AG, Shemyakin IG, Kolesnikov AV.
    Substrate specificity of the anthrax lethal factor.
    Dokl Biochem Biophys. 2008 Jan-Feb;418:14-7 (in Russian)
    PMID: 18429598

  4. 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

  5. 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

  6. 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

  7. Souslova EA, Chudakov DM.
    Genetically encoded intracellular sensors based on fluorescent proteins.
    Biochemistry (Mosc). 2007 Jul;72(7):683-97
    PMID: 17680759

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Souslova EA, Chudakov DM.
    Photoswitchable cyan fluorescent protein as a FRET donor.
    Microsc Res Tech. 2006 Mar;69(3):207-9
    PMID: 16538627

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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