Laboratory of molecular theranostics

NamePositionContacts
Vladimir Martynov, D.Scdepart. dir.vimart@list.ru+7(495)336-51-11
Alexey Pakhomov, Ph.D.s. r. f.alpah@mail.ru+7(495)336-51-11
Alexey Garkovenkoj. r. f.garkovenko@gmail.com+7(495)330-63-47

Selected publications

  1. Martynov VI, Pakhomov AA, Deyev IE, Petrenko AG (2018). Genetically encoded fluorescent indicators for live cell pH imaging. BIOCHIM BIOPHYS ACTA 1862 (12), 2924–2939
  2. Garkovenko AV, Radchenko VV, Ilnitskaya EV, Koshchaev AG, Shchukina IV, Bakharev AA, Sukhanova SF (2018). Polymorphism of cattle microsatellite complexes. Journal of Pharmaceutical Sciences and Research 10 (6), 1545–1551
  3. Koshchaev AG, Shchukina IV, Garkovenko AV, Ilnitskaya EV, Radchenko VV, Bakharev AA, Khrabrova LA (2018). Allelic variation of marker genes of hereditary diseases and economically important traits in dairy breeding cattle population. Journal of Pharmaceutical Sciences and Research 10 (6), 1566–1572
  4. Pakhomov AA, Martynov VI, Orsa AN, Bondarenko AA, Chertkova RV, Lukyanov KA, Petrenko AG, Deyev IE (2017). Fluorescent protein Dendra2 as a ratiometric genetically encoded pH-sensor. Biochem Biophys Res Commun 493 (4), 1518–1521
  5. Blagodatskikh KA, Kramarov VM, Barsova EV, Garkovenko AV, Shcherbo DS, Shelenkov AA, Ustinova VV, Tokarenko MR, Baker SC, Kramarova TV, Ignatov KB (2017). Improved DOP-PCR (iDOP-PCR): A robust and simple WGA method for efficient amplification of low copy number genomic DNA. PLoS One 12 (9), e0184507
  6. Pakhomov AA, Mironiuk VB, Kononevich YN, Korlyukov AA, Volodin AD, Pryakhina TA, Martynov VI, Muzafarov AM (2017). Synthesis and crystal structure of a meso-decene-BODIPY dye as a functional bright fluorophore for silicone matrices. MENDELEEV COMMUN 27 (4), 363–365
  7. Pakhomov AA, Chertkova RV, Deyev IE, Petrenko AG, Martynov VI (2017). Generation of photoactivatable fluorescent protein from photoconvertible ancestor. Russ. J. Bioorganic Chem. 43 (3), 340–343
  8. Pakhomov AA, Deyev IE, Ratnikova NM, Chumakov SP, Mironiuk VB, Kononevich YN, Muzafarov AM, Martynov VI (2017). BODIPY-based dye for no-wash live-cell staining and imaging. Biotechniques 63 (2), 77–79
  9. Pakhomov AA, Kononevich YN, Korlyukov AA, Martynov VI, Muzafarov AM (2016). Synthesis, crystal structure and optical properties of a new meso-acrylate BODIPY dye. MENDELEEV COMMUN 26 (3), 196–198
  10. Pakhomov AA, Kononevich YN, Stukalova MV, Svidchenko EA, Surin NM, Cherkaev GV, Shchegolikhina OI, Martynov VI, Muzafarov AM (2016). Synthesis and photophysical properties of a new BODIPY-based siloxane dye. Tetrahedron Lett 57 (9), 979–982
  11. Martynov VI, Pakhomov AA, Popova NV, Deyev IE, Petrenko AG (2016). Synthetic Fluorophores for Visualizing Biomolecules in Living Systems. Acta Naturae 8 (4), 33–46
  12. Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ (2016). Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallogr D Struct Biol 72 (8), 922–932
  13. Pakhomov AA, Chertkova RV, Martynov VI (2015). PH-sensor properties of a fluorescent protein from Dendronephthya sp. Russ. J. Bioorganic Chem. 41 (6), 602–606
  14. Ilnitskaya EV, Kononevich YN, Muzafarov AM, Rzhevskiy SA, Shadrin IA, Babaev EV, Martynov VI, Pakhomov AA (2015). Preparation and application of a BODIPY-labeled probe for a real-time polymerase chain reaction. Russ. J. Bioorganic Chem. 41 (4), 451–453
  15. Pletneva NV, Pletnev VZ, Souslova E, Chudakov DM, Lukyanov S, Martynov VI, Arhipova S, Artemyev I, Wlodawer A, Dauter Z, Pletnev S (2013). Yellow fluorescent protein phiYFPv (Phialidium): Structure and structure-based mutagenesis. Acta Crystallogr D Biol Crystallogr 69 (6), 1005–1012
  16. Pakhomov AA, Tretyakova SA, Martynov VI (2012). The influence of chromophore-protein interactions on spectroscopic properties of the yellow fluorescent protein. Dokl Biochem Biophys 445 (1), 207–209
  17. Pakhomov AA, Martynov VI (2011). A method for the determination of the three-dimensional structure of fluorescent proteins based on homology modeling and mass spectrometry. Russ. J. Bioorganic Chem. 37 (3), 383–386
  18. Pakhomov AA, Martynov VI (2011). [3D-structure determination of fluorescent proteins by homology modeling combined with mass spectrometry]. Bioorg Khim 37 (3), 429–432
  19. Pakhomov AA, Martynov VI (2011). Probing the structural determinants of yellow fluorescence of a protein from Phialidium sp. Biochem Biophys Res Commun 407 (1), 230–235
  20. Pletneva NV, Pletnev VZ, Lukyanov KA, Gurskaya NG, Goryacheva EA, Martynov VI, Wlodawer A, Dauter Z, Pletnev S (2010). Structural evidence for a dehydrated intermediate in green fluorescent protein chromophore biosynthesis. J Biol Chem 285 (21), 15978–15984
  21. Pakhomov AA, Tretyakova YA, Martynov VI (2010). Posttranslational reactions that shift spectra of asFP595, a Protein from Anemonia sulcata, towards the long-wavelength region. Russ. J. Bioorganic Chem. 36 (1), 109–113
  22. Pakhomov AA, Tretiakova IA, Martynov VI (2010). Posttranslational reactions resulting in a long-wavelength shift in the spectra of asFP595 protein from Anemonia sulcata. Bioorg Khim 36 (1), 117–121
  23. Pletnev S, Gurskaya NG, Pletneva NV, Lukyanov KA, Chudakov DM, Martynov VI, Popov VO, Kovalchuk MV, Wlodawer A, Dauter Z, Pletnev V (2009). Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed. J Biol Chem 284 (46), 32028–32039
  24. Pakhomov AA, Martynov VI (2009). Posttranslational chemistry of proteins of the GFP family. Biochemistry (Mosc) 74 (3), 250–259
  25. Pakhomov AA, Martynov VI (2008). GFP Family: Structural Insights into Spectral Tuning. Cell Chem Biol 15 (8), 755–764
  26. Vonarshenko AV, Radchenko VV, Gapon MV, Rodionov IL, Babichenko II, Kakuev DL, Artamonov ID, Garkovenko AV, Dyachkova LG, Lipkin VM, Kostanyan IA (2007). Identification and expression of haponin, a new protein from HL-60 cells. Russ. J. Bioorganic Chem. 33 (6), 607–609
  27. Pakhomov AA, Martynov VI (2007). Chromophore aspartate oxidation-decarboxylation in the green-to-red conversion of a fluorescent protein from Zoanthus sp. 2. Biochemistry 46 (41), 11528–11535
  28. Pletneva N, Pletnev V, Tikhonova T, Pakhomov AA, Popov V, Martynov VI, Wlodawer A, Dauter Z, Pletnev S (2007). Refined crystal structures of red and green fluorescent proteins from the button polyp Zoanthus. Acta Crystallogr D Biol Crystallogr 63 (10), 1082–1093
  29. Pletneva NV, Pletnev SV, Chudakov DM, Tikhonova TV, Popov VO, Martynov VI, Wlodawer A, Dauter Z, Pletnev VZ (2007). Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 Å. Russ. J. Bioorganic Chem. 33 (4), 390–398
  30. Pletneva NV, Pletnev SV, Chudakov DM, Tikhonova TV, Popov VO, Martynov VI, Wlodawer A, Dauter Z, Pletnev VZ (2007). Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom. Bioorg Khim 33 (4), 421–430
  31. Tretyakova YA, Pakhomov AA, Martynov VI (2007). Chromophore structure of the kindling fluorescent protein asFP595 from Anemonia sulcata. J Am Chem Soc 129 (25), 7748–7749
  32. Pakhomov AA, Pletneva NV, Balashova TA, Martynov VI (2006). Structure and reactivity of the chromophore of a GFP-like chromoprotein from Condylactis gigantea. Biochemistry 45 (23), 7256–7264
  33. Pletneva N, Pletnev S, Tikhonova T, Popov V, Martynov V, Pletnev V (2006). Structure of a red fluorescent protein from Zoanthus, zRFP574, reveals a novel chromophore. Acta Crystallogr D Biol Crystallogr 62 (5), 527–532
  34. Yampolsky IV, Remington SJ, Martynov VI, Potapov VK, Lukyanov S, Lukyanov KA (2005). Synthesis and properties of the chromophore of the asFP595 chromoprotein from Anemonia sulcata. Biochemistry 44 (15), 5788–5793
  35. Pakhomov AA, Martynova NY, Gurskaya NG, Balashova TA, Martynov VI (2004). Photoconversion of the chromophore of a fluorescent protein from Dendronephthya sp. coral. Biochemistry (Mosc) 69 (8), 1108–1117
  36. Pakhomov AA, Martynova NY, Gurskaya NG, Balashova TA, Martynov VI (2004). Photoconversion of the chromophore of a fluorescent protein from Dendronephthya sp. Biochemistry (Mosc) 69 (8), 901–908
  37. Smirnova EV, Garkovenko AV, Rakitina TV, Berezhnoǐ SN, Astapova MV, Surina EA, Babichenko II, Kostanian IA, Lipkin VM (2004). Precursors of HLDF differentiation factor and ribosomal protein RPS21 have a common N-terminal sequence. Bioorg Khim 30 (2), 130–140
  38. Smirnova EV, Garkovenko AV, Rakitina TV, Berezhnoi SN, Astapova MV, Surina EA, Babichenko II, Kostanyan IA, Lipkin VM (2004). The precursor of differentiation factor HLDF and ribosomal protein RPS21 have a common N-terminal sequence. Russ. J. Bioorganic Chem. 30 (2), 114–123
  39. Martynov VI, Maksimov BI, Martynova NY, Pakhomov AA, Gurskaya NG, Lukyanov SA (2003). A Purple-blue Chromoprotein from Goniopora tenuidens Belongs to the DsRed Subfamily of GFP-like Proteins. J Biol Chem 278 (47), 46288–46292
  40. Fradkov AF, Verkhusha VV, Staroverov DB, Bulina ME, Yanushevich YG, Martynov VI, Lukyanov S, Lukyanov KA (2002). Far-red fluorescent tag for protein labelling. Biochem J 368 (1), 17–21
  41. Gurskaya NG, Fradkov AF, Terskikh A, Matz MV, Labas YA, Martynov VI, Yanushevich YG, Lukyanov KA, Lukyanov SA (2001). GFP-like chromoproteins as a source of far-red fluorescent proteins. FEBS Lett 507 (1), 16–20
  42. Martynov VI, Savitsky AP, Martynova NY, Savitsky PA, Lukyanov KA, Lukyanov SA (2001). Alternative cyclization in GFP-like proteins family. The formation and structure of the chromophore of a purple chromoprotein from Anemonia sulcata. J Biol Chem 276 (24), 21012–21016
  43. Martynov VI, Kostina MB, Feigina MIu, Miroshnikov AI (1983). Limited proteolysis studies on molecular organization of bovine rhodopsin in the photoreceptor membrane. 9 (0), 734–745

Vladimir Martynov

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 33, office. 633
  • Phone: +7(495)336-51-11
  • E-mail: vimart@list.ru

Fluorogenic marker for instant live-cell membrane staining and imaging (2017-11-24)

A new organic-compound-based fluorogenic marker has been created for live-cell membrane staining. Unlike current commercial cell markers, the obtained fluorogenic marker does not fluoresce in the aquatic environment, but acquires fluorescence immediately after being placed in a nonpolar medium, for example, in the cell membrane. This property allows one to instantly stain cells without further washing out the unbound dye. This marker can be applied in fluorescence microscopy for live-cell imaging and flow cytometry.

Publications

  1. Pakhomov AA, Deyev IE, Ratnikova NM, Chumakov SP, Mironiuk VB, Kononevich YN, Muzafarov AM, Martynov VI (2017). BODIPY-based dye for no-wash live-cell staining and imaging. Biotechniques 63 (2), 77–79