Плетнёв Владимир Захарович

Основные научные результаты

Лаборатория занимается исследованиями пространственной структуры и структурно-функциональной взаимосвязи соединений пептидно-белковой природы методами рентгеноструктурного анализа высокого разрешения, методами молекулярной механики, динамики, графики и биоинформатики. .

Лаборатория исследует белки различной функциональной природы с акцентом на структурно-функциональные аспекты специфичности узнавания и связывания лигандов/субстратов.

В последнее время большое внимание уделяется структурным исследованиям флуоресцентных белков (ФБ), используемых в клеточной биологии, биотехнологии и биомедицине в качестве молекулярных бионаномаркеров для визуализации внутренних биологических процессов в клетках или целом организме. Сотрудники установили пространственную структуру большой серии ФБ с эмиссией в зеленой, желтой, красной и дальне-красной спектральных областях при помощи метода рентгеноструктурного анализа высокого разрешения. Анализ структурно-функциональной взаимосвязи исследуемых объектов позволил объяснить многие экспериментально наблюдаемые свойства и сконструировать новые мутантные флуоресцентные варианты с улучшенными фотофизическими характеристиками. Полученные результаты существенно расширяют структурную базу для рационального дизайна более совершенных биомаркеров для практического применения.

Избранные публикации

  1. Baloban M., Shcherbakova D.M., Pletnev S.V., Pletnev V.Z., Lagarias J.C., Verkhusha V.V. (2017). Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Chem. Sci. 8, 4546–4557 [+]
    ID:1833
  2. Pletneva N.V., Pletnev S.V., Efremov R.G., Goryacheva E.A., Artemyev I.V., Arkhipova S.F., Pletnev V.Z. (2017). Crystal structure of the pH-dependent green fluorescent protein WasCFP with the tryptophan based chromophore at extremely low value pH 2.0. Crystallography Reports , in press [+]
    ID:1834
  3. Vajravijayan S., Pletnev S., Pletnev V.Z., Nandhagopal N., Gunasekaran K. (2016). Structural analysis of β-prism lectin from Colocasia esculenta (L.) S chott. Int. J. Biol. Macromol. 91, 518–23 [+]
    ID:1829
  4. Pletneva N.V., Pletnev S., Pakhomov A.A., Chertkova R.V., Martynov V.I., Muslinkina L., Dauter Z., Pletnev V.Z. (2016). Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallogr D Struct Biol 72 (Pt 8), 922–32 [+]

    The fluorescent protein from Dendronephthya sp. (DendFP) is a member of the Kaede-like group of photoconvertible fluorescent proteins with a His62-Tyr63-Gly64 chromophore-forming sequence. Upon irradiation with UV and blue light, the fluorescence of DendFP irreversibly changes from green (506 nm) to red (578 nm). The photoconversion is accompanied by cleavage of the peptide backbone at the C(α)-N bond of His62 and the formation of a terminal carboxamide group at the preceding Leu61. The resulting double C(α)=C(β) bond in His62 extends the conjugation of the chromophore π system to include imidazole, providing the red fluorescence. Here, the three-dimensional structures of native green and photoconverted red forms of DendFP determined at 1.81 and 2.14 Å resolution, respectively, are reported. This is the first structure of photoconverted red DendFP to be reported to date. The structure-based mutagenesis of DendFP revealed an important role of positions 142 and 193: replacement of the original Ser142 and His193 caused a moderate red shift in the fluorescence and a considerable increase in the photoconversion rate. It was demonstrated that hydrogen bonding of the chromophore to the Gln116 and Ser105 cluster is crucial for variation of the photoconversion rate. The single replacement Gln116Asn disrupts the hydrogen bonding of Gln116 to the chromophore, resulting in a 30-fold decrease in the photoconversion rate, which was partially restored by a further Ser105Asn replacement.

    ID:1587
  5. Плетнёв В.З., Плетнева Н.В., Ефремов Р.Г., Горячева Е.А., Артемьев И.В., Архипова С.Ф., Саркисян К.С., Мишин А.С., Лукьянов К.А., Плетнев С.В. (2016). Пространственная структура рН-зависимого зеленого флуоресцентного белка WASCFP с депротонированным хромофором на основе триптофана. Биоорг. хим. 42 (6), 675–682 ID:1600
  6. Doerr N., Wang Y., Kipp K.R., Liu G., Benza J.J., Pletnev V., Pavlov T.S., Staruschenko A., Mohieldin A.M., Takahashi M., Nauli S.M., Weimbs T. (2016). Regulation of Polycystin-1 Function by Calmodulin Binding. PLoS ONE 11 (8), e0161525 [+]
    ID:1830
  7. Pletnev V.Z., Pletneva N.V., Efremov R.G., Goryacheva E.A., Artemyev I.V., Arkhipova S.F., Sarkisyan K.S., Mishin A.S., Lukyanov K.A., Pletnev S.V. (2016). Three-dimensional structure of pH-dependent fluorescent protein WasCFP with the tryptophan based deprotonated chromophore. Rus. J. Bioorg. Chem. 42 (6), 612–618 ID:1832
  8. Pletnev V.Z., Pletneva N.V., Sarkisyan K.S., Mishin A.S., Lukyanov K.A., Goryacheva E.A., Ziganshin R.H., Dauter Z., Pletnev S. (2015). Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore. Acta Crystallogr. D Biol. Crystallogr. 71 (Pt 8), 1699–707 [+]
    ID:1323
  9. Luker K.E., Pata P., Shemiakina I.I., Pereverzeva A., Stacer A.C., Shcherbo D.S., Pletnev V.Z., Skolnaja M., Lukyanov K.A., Luker G.D., Pata I., Chudakov D.M. (2015). Comparative study reveals better far-red fluorescent protein for whole body imaging. Sci Rep 5, 10332 [+]
    ID:1324
  10. Pletneva N.V., Pletnev V.Z., Sarkisyan K.S., Gorbachev D.A., Egorov E.S., Mishin A.S., Lukyanov K.A., Dauter Z., Pletnev S. (2015). Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore. PLoS ONE 10 (12), e0145740 [+]

    Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins (FPs), KillerRed and its monomeric variant SuperNova, were described up to date. Here, we present a crystallographic study of their two orange successors, dimeric KillerOrange and monomeric mKillerOrange, at 1.81 and 1.57 Å resolution, respectively. They are the first orange-emitting protein photosensitizers with a tryptophan-based chromophore (Gln65-Trp66-Gly67). Same as their red progenitors, both orange photosensitizers have a water-filled channel connecting the chromophore to the β-barrel exterior and enabling transport of ROS. In both proteins, Trp66 of the chromophore adopts an unusual trans-cis conformation stabilized by H-bond with the nearby Gln159. This trans-cis conformation along with the water channel was shown to be a key structural feature providing bright orange emission and phototoxicity of both examined orange photosensitizers.

    ID:1391
  11. Pletneva N.V., Pletnev S.V., Bogdanov A.M., Goriacheva E.A., Artemev I.V., Suslova E.A., Arkhipova S.F., Pletnev V.Z. (2014). Three dimensional structure of the dimeric gene-engineered variant of green fluorescent protein EGFP-K162Q in P6(1) crystal space group. Bioorg. Khim. 40 (4), 414–20 [+]
    ID:1326
  12. Pletnev V.Z., Pletneva N.V., Lukyanov K.A., Souslova E.A., Fradkov A.F., Chudakov D.M., Chepurnykh T., Yampolsky I.V., Wlodawer A., Dauter Z., Pletnev S. (2013). Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Acta Crystallogr. D Biol. Crystallogr. 69 (Pt 9), 1850–60 [+]
    ID:1017
  13. Pletneva N.V., Pletnev V.Z., Souslova E., Chudakov D.M., Lukyanov S., Martynov V.I., 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 (Pt 6), 1005–12 [+]

    The yellow fluorescent protein phiYFPv (λem(max) ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow-orange range (535-555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The `yellow' chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.

    ID:850
  14. Pletnev S., Pletneva N.V., Souslova E.A., Chudakov D.M., Lukyanov S., Wlodawer A., Dauter Z., Pletnev V. (2012). Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670. Acta Crystallogr. D Biol. Crystallogr. 68 (Pt 9), 1088–97 [+]

    The crystal structures of the far-red fluorescent proteins (FPs) eqFP650 (λ(ex)(max)/λ(em)(max) 592/650 nm) and eqFP670 (λ(ex)(max)/λ(em)(max) 605/670 nm), the successors of the far-red FP Katushka (λ(ex)(max)/λ(em)(max) 588/635 nm), have been determined at 1.8 and 1.6 Å resolution, respectively. An examination of the structures demonstrated that there are two groups of changes responsible for the bathochromic shift of excitation/emission bands of these proteins relative to their predecessor. The first group of changes resulted in an increase of hydrophilicity at the acylimine site of the chromophore due to the presence of one and three water molecules in eqFP650 and eqFP670, respectively. These water molecules provide connection of the chromophore with the protein scaffold via hydrogen bonds causing an ∼15 nm bathochromic shift of the eqFP650 and eqFP670 emission bands. The second group of changes observed in eqFP670 arises from substitution of both Ser143 and Ser158 by asparagines. Asn143 and Asn158 of eqFP670 are hydrogen bonded with each other, as well as with the protein scaffold and with the p-hydroxyphenyl group of the chromophore, resulting in an additional ∼20 nm bathochromic shift of the eqFP670 emission band as compared to eqFP650. The role of the observed structural changes was verified by mutagenesis.

    ID:734
  15. Pletneva N.V., Pletnev V.Z., Shemiakina I.I., Chudakov D.M., Artemyev I., Wlodawer A., Dauter Z., Pletnev S. (2011). Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore. Protein Sci. 20 (7), 1265–74 [+]

    The wild type red fluorescent protein eqFP578 (from sea anemone Entacmaea quadricolor, λ(ex) = 552 nm, λ(em) = 578 nm) and its bright far-red fluorescent variant Katushka (λ(ex) = 588 nm, λ(em) = 635 nm) are characterized by the pronounced pH dependence of their fluorescence. The crystal structures of eqFP578f (eqFP578 with two point mutations improving the protein folding) and Katushka have been determined at the resolution ranging from 1.15 to 1.85 Å at two pH values, corresponding to low and high level of fluorescence. The observed extinguishing of fluorescence upon reducing pH in eqFP578f and Katushka has been shown to be accompanied by the opposite trans-cis and cis-trans chromophore isomerization, respectively. Asn143, Ser158, His197 and Ser143, Leu174, and Arg197 have been shown to stabilize the respective trans and cis fluorescent states of the chromophores in eqFP578f and Katushka at higher pH. The cis state has been suggested as being primarily responsible for the observed far-red shift of the emission maximum of Katushka relative to that of eqFP578f.

    ID:528
  16. Pletneva N.V., Pletnev V.Z., Lukyanov K.A., Gurskaya N.G., Goryacheva E.A., Martynov V.I., Wlodawer A., Dauter Z., Pletnev S. (2010). Structural evidence for a dehydrated intermediate in green fluorescent protein chromophore biosynthesis. J. Biol. Chem. 285 (21), 15978–84 [+]

    The acGFPL is the first-identified member of a novel, colorless and non-fluorescent group of green fluorescent protein (GFP)-like proteins. Its mutant aceGFP, with Gly replacing the invariant catalytic Glu-222, demonstrates a relatively fast maturation rate and bright green fluorescence (lambda(ex) = 480 nm, lambda(em) = 505 nm). The reverse G222E single mutation in aceGFP results in the immature, colorless variant aceGFP-G222E, which undergoes irreversible photoconversion to a green fluorescent state under UV light exposure. Here we present a high resolution crystallographic study of aceGFP and aceGFP-G222E in the immature and UV-photoconverted states. A unique and striking feature of the colorless aceGFP-G222E structure is the chromophore in the trapped intermediate state, where cyclization of the protein backbone has occurred, but Tyr-66 still stays in the native, non-oxidized form, with C(alpha) and C(beta) atoms in the sp(3) hybridization. This experimentally observed immature aceGFP-G222E structure, characterized by the non-coplanar arrangement of the imidazolone and phenolic rings, has been attributed to one of the intermediate states in the GFP chromophore biosynthesis. The UV irradiation (lambda = 250-300 nm) of aceGFP-G222E drives the chromophore maturation further to a green fluorescent state, characterized by the conventional coplanar bicyclic structure with the oxidized double Tyr-66 C(alpha)=C(beta) bond and the conjugated system of pi-electrons. Structure-based site-directed mutagenesis has revealed a critical role of the proximal Tyr-220 in the observed effects. In particular, an alternative reaction pathway via Tyr-220 rather than conventional wild type Glu-222 has been proposed for aceGFP maturation.

    ID:404
  17. Pletnev S., Gurskaya N.G., Pletneva N.V., Lukyanov K.A., Chudakov D.M., Martynov V.I., Popov V.O., Kovalchuk M.V., Wlodawer A., Dauter Z., Pletnev V. (2009). Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed. J. Biol. Chem. 284 (46), 32028–39 [+]

    KillerRed is the only known fluorescent protein that demonstrates notable phototoxicity, exceeding that of the other green and red fluorescent proteins by at least 1,000-fold. KillerRed could serve as an instrument to inactivate target proteins or to kill cell populations in photodynamic therapy. However, the nature of KillerRed phototoxicity has remained unclear, impeding the development of more phototoxic variants. Here we present the results of a high resolution crystallographic study of KillerRed in the active fluorescent and in the photobleached non-fluorescent states. A unique and striking feature of the structure is a water-filled channel reaching the chromophore area from the end cap of the beta-barrel that is probably one of the key structural features responsible for phototoxicity. A study of the structure-function relationship of KillerRed, supported by structure-based, site-directed mutagenesis, has also revealed the key residues most likely responsible for the phototoxic effect. In particular, Glu(68) and Ser(119), located adjacent to the chromophore, have been assigned as the primary trigger of the reaction chain.

    ID:299
  18. Shcherbo D., Murphy C.S., Ermakova G.V., Solovieva E.A., Chepurnykh T.V., Shcheglov A.S., Verkhusha V.V., Pletnev V.Z., Hazelwood K.L., Roche P.M., Lukyanov S., Zaraisky A.G., Davidson M.W., Chudakov D.M. (2009). Far-red fluorescent tags for protein imaging in living tissues. Biochem. J. 418 (3), 567–74 [+]

    Разработан яркий, мономерный, фотостабильный, pH-стабильный, дальне-красный флуоресцентый белок mKate2. Белок mKate2 хорошо показал себя в качестве метки во фьюзах с рядом белков, как в культуре клеток, так и в трансгенных лягушках Xenopus laevis (совместно с лабораторией Молекулярных основ эмбриогенеза ИБХ РАН).

    ID:31
  19. Pletneva N.V., Pletnev S.V., Chudakov D.M., Tikhonova T.V., Popov V.O., Martynov V.I., Wlodawer A., Dauter Z., Pletnev V.Z. (2009). [Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom]. Bioorg. Khim. 33 (4), 421–30 [+]

    The three-dimensional structure of yellow fluorescent proteins zYFP538 (zFP538) from the button polyp Zoanthus sp. was determined at a resolution of 1.8 angstrom by X-ray analysis. The monomer of zYFP538 adopts a structure characteristic of the green fluorescent protein (GFP) family, a beta-barrel formed from 11 antiparallel beta segments and one internal alpha helix with a chromophore embedded into it. Like the TurboGFP, the beta-barrel of zYFP538 contains a water-filled pore leading to the chromophore Tyr67 residue, which presumably provides access of molecular oxygen necessary for the maturation process. The post-translational modification of the chromophore-forming triad Lys66-Tyr67-Gly68 results in a tricyclic structure consisting of a five-membered imidazolinone ring, a phenol ring of the Tyr67 residue, and an additional six-membered tetrahydropyridine ring. The chromophore formation is completed by cleavage of the protein backbone at the Calpha-N bond of Lys66. It was suggested that the energy conflict between the buried positive charge of the intact Lys66 side chain in the hydrophobic pocket formed by the Ile44, Leu46, Phe65, Leu204 and Leu219 side chains is the most probable trigger that induces the transformation of the bicyclic green form to the tricyclic yellow form. A stereochemical analysis of the contacting surfaces at the intratetramer interfaces helped reveal a group of conserved key residues responsible for the oligomerization. Along with others, these residues should be taken into account in designing monomeric forms suitable for practical application as markers of proteins and cell organelles.

    ID:306
  20. Zavalova L.L., Antipova N.V., Fadeeva Iu.I., Pavliukov M.S., Pletneva N.V., Pletnev V.Z., Baskova I.P. (2009). [Catalytic sites of medicinal leech enzyme destabilase-lysozyme (Mldl). Structure-functional correlation]. Bioorg. Khim. 38 (2), 229–33 [+]

    Based on three-dimensional model of the bifunctional enzyme Destabilase-Lysozyme (mlDL-Ds2) in complex with trimer of N-acetylglucosoamine (NAG)3 the functional role of the stereochemically based group of amino acids (Glu14, Asp26, Ser 29, Ser31, Lys38, His92), in manifestation of glycosidase and isopeptidase activities has been elucidated. By method of site-directed mutagenesis it has been shown that mlDL glycosidase active site includes catalytic Glu14 and Asp26, and isopeptidase site functions as Ser/Lys dyad presented by catalytic residues Lys38 and Ser29. Thus, among the invertebrate lysozymes mlDL presents first example of the bifunctional enzyme with identified position of the isopeptidase active site and localization of the corresponding catalytic residues.

    ID:738