Чупин Владимир Викторович

Личная информация

Работа по профессии

1980-1985: ассистент, Московский институт тонкой химической технологии им. М.В. Ломоносова;

1985-1986: стажировка в Университете г. Утрехт, Нидерланды;

1986-1992: доцент кафедры химии и технологии тонких органических соединений МИТХТ им. М.В. Ломоносова;

1992-1995: научный сотрудник, отдел биохимии биомембран, Университет г. Утрехт, Нидерланды;

1995-1998: доцент кафедры химии и технологии тонких органических соединений МГАТХТ им. М.В. Ломоносова;

1998-2003: научный сотрудник, отдел биохимии биомембран, Университет г. Утрехт, Нидерланды;

2003-2004: сотрудник кафедры физической и органической химии, Институт Стратинфа, Университет г. Грёнинген, Нидерланды

2004-2009: страший научный сотрудник лаборатории биомолекулярной ЯМР спектроскопии, Институт биоорганической химии им. академиков М.М. Шемякина и Ю.А. Овчинникова РАН

2009-н. вр.: ведущий научный сотрудник лаборатории биомолекулярной ЯМР спектроскопии, Институт биоорганической химии им. академиков М.М. Шемякина и Ю.А. Овчинникова РАН


Преподавательская деятельность

2005—н. вр.: курс лекций  «Современные физико-химические методы исследований» для студентов МГАТХТ им. М.В. Ломоносова (бывш. МИТХТ), специализирующихся по химической технологии и биотехнологии.

Руководитель 2 кандидатских диссертаций.


Организационная деятельность

Руководитель с российской стороны международной программы NOW (Нидерланды) - Россия между Утрехтским университетом, МИТХТ им. М.В. Ломоносова, Институтом биоорганической химии им. акад. М.М. Шемякина и Ю.А. Овчинникова РАН и МГУ им. Ломоносова.


Период обученияСтрана, городУчебное заведениеДополнительная информация
1971–1977 Россия, Москва Московский институт тонкой химической технологии им. М.В. Ломоносова (МИТХТ) диплом химика
1977–1980 Россия, Москва Московский институт тонкой химической технологии им. М.В. Ломоносова (МИТХТ) Диплом кандидата химических наук за диссертацию «Синтез фосфолипидов с простой эфирной связью и изучение их поведения в составе модельных мембран»
1985–1986 Утрехт, Нидерланды Стажировка в Утрехтском университете, отдел биохимии биомембран Научный сотрудник
1987 Россия, Москва Московский институт тонкой химической технологии им. М.В. Ломоносова (МИТХТ) Присвоено ученое звание доцента
1997 Россия, Москва Московская государственная академия тонкой химической технологии им. М.В. Ломоносова (МГАХТ - бывш. МИТХТ) Диплом доктора химических наук за диссертацию «Роль липидов в структурной организации мембран и взаимодействии с белками»

Научные интересы


Биоорганическая химия, биофизика, ЯМР-спектроскопия, химия липидов, самоорганизующиеся структуры, биологические мембраны, мембранные белки, липид-белковые взаимодействия, нанобиотехнология, G-белок сопряжённые рецепторы, ионные каналы.

Избранные публикации

  1. Chupin V.V., Boldyrev I.A. (2017). 3-{4-[(E)-{4-[(E)-Phenyldiazenyl]phenyl}diazenyl]phenoxy}propane-1,2-diol. Molbank 2017 (1), M932 [+]

    Title compound was designed to be a black quencher of pyrene fluorescence. It was made amphiphilic to serve as a membrane-bound probe. The synthesis is a two-step procedure. The first step is a Mitsunobu reaction of [{(phenyldiazenyl)phenyl}diazenyl]phenol with 1,2-O-isopropylideneglycerol. The second step is the cleavage of the isopropylidene protecting group. The title compound has the extinction coefficient 59,000 at λmax = 380 nm. The Forster distance between the title compound and the pyrene was found to be 37.8 Å.

  2. Gushchin I., Chervakov P., Kuzmichev P., Popov A.N., Round E., Borshchevskiy V., Ishchenko A., Petrovskaya L., Chupin V., Dolgikh D.A., Arseniev A.S., Kirpichnikov M., Gordeliy V. (2013). Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria. Proc. Natl. Acad. Sci. U.S.A. 110 (31), 12631–6 [+]

    Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features. First, ESR's proton donor is a lysine side chain that is situated very close to the bulk solvent. Second, the α-helical structure in the middle of the helix F is replaced by 3(10)- and π-helix-like elements that are stabilized by the Trp-154 and Asn-224 side chains. This feature is characteristic for the proteorhodopsin family of proteins. Third, the proton release region is connected to the bulk solvent by a chain of water molecules already in the ground state. Despite these peculiarities, the positions of water molecule and amino acid side chains in the immediate Schiff base vicinity are very well conserved. These features make ESR a very unusual proton pump. The presented structure sheds light on the large family of proteorhodopsins, for which structural information was not available previously.

  3. Semenova A.A., Chugunov A.O., Dubovskii P.V., Chupin V.V., Volynsky P.E., Boldyrev I.A. (2011). The role of chain rigidity in lipid self-association: Comparative study of dihexanoyl- and disorbyl-phosphatidylcholines. Chem. Phys. Lipids 165, 382–386 [+]

    In the course of structure-function investigations of lipids a phosphatidylcholine molecule with short and rigid tails, di-2,4-hexadienoylphosphatidylcholine (DiSorbPC), was synthesized and studied in comparison with its saturated analog, dihexanoylphosphatidylcholine (DHPC). Conjugated double bonds in the acyl chains in DiSorbPC reduce considerably the number of possible conformers of the lipid within an aggregate. This leads to impaired packing of unsaturated acyl chains and thus, to a surprisingly high (115Å(2)) area per molecule for DiSorbPC at the air-water interface and failure to form micelles of regular size and shape. Details on DiSorbPC aggregation and packing provided by a set of experimental techniques combined with molecular dynamics simulations are presented.

  4. Petrovskaya L.E., Lukashev E.P., Chupin V.V., Sychev S.V., Lyukmanova E.N., Kryukova E.A., Ziganshin R.H., Spirina E.V., Rivkina E.M., Khatypov R.A., Erokhina L.G., Gilichinsky D.A., Shuvalov V.A., Kirpichnikov M.P. (2010). Predicted bacteriorhodopsin from Exiguobacterium sibiricum is a functional proton pump. FEBS Lett. 584 (19), 4193–6 [+]

    The predicted Exigobacterium sibiricum bacterirhodopsin gene was amplified from an ancient Siberian permafrost sample. The protein bacteriorhodopsin from Exiguobacterium sibiricum (ESR) encoded by this gene was expressed in Escherichia coli membrane. ESR bound all-trans-retinal and displayed an absorbance maximum at 534nm without dark adaptation. The ESR photocycle is characterized by fast formation of an M intermediate and the presence of a significant amount of an O intermediate. Proteoliposomes with ESR incorporated transport protons in an outward direction leading to medium acidification. Proton uptake at the cytoplasmic surface of these organelles precedes proton release and coincides with M decay/O rise of the ESR.

  5. Mineev K.S., Bocharov E.V., Pustovalova Y.E., Bocharova O.V., Chupin V.V., Arseniev A.S. (2010). Spatial Structure of the Transmembrane Domain Heterodimer of ErbB1 and ErbB2 Receptor Tyrosine Kinases. J. Mol. Biol. 400 (2), 231–243 [+]

    Growth factor receptor tyrosine kinases of the ErbB family play a significant role in vital cellular processes and various cancers. During signal transduction across plasma membrane, ErbB receptors are involved in lateral homodimerization and heterodimerization with proper assembly of their extracellular single-span transmembrane (TM) and cytoplasmic domains. The ErbB1/ErbB2 heterodimer appears to be the strongest and most potent inducer of cellular transformation and mitogenic signaling compared to other ErbB homodimers and heterodimers. Spatial structure of the heterodimeric complex formed by TM domains of ErbB1 and ErbB2 receptors embedded into lipid bicelles was obtained by solution NMR. The ErbB1 and ErbB2 TM domains associate in a right-handed alpha-helical bundle through their N-terminal double GG4-like motif T(648)G(649)X(2)G(652)A(653) and glycine zipper motif T(652)X(3)S(656)X(3)G(660), respectively. The described heterodimer conformation is believed to support the juxtamembrane and kinase domain configuration corresponding to the receptor active state. The capability for multiple polar interactions, along with hydrogen bonding between TM segments, correlates with the observed highest affinity of the ErbB1/ErbB2 heterodimer, implying an important contribution of the TM helix-helix interaction to signal transduction.

  6. Shenkarev Z.O., Paramonov A.S., Lyukmanova E.N., Shingarova L.N., Yakimov S.A., Dubinnyi M.A., Chupin V.V., Kirpichnikov M.P., Blommers M.J., Arseniev A.S. (2010). NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating. J. Am. Chem. Soc. 132 (16), 5630–7 [+]

    The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.

  7. Shenkarev Z.O., Lyukmanova E.N., Paramonov A.S., Shingarova L.N., Chupin V.V., Kirpichnikov M.P., Blommers M.J., Arseniev A.S. (2010). Lipid-protein nanodiscs as reference medium in detergent screening for high-resolution NMR studies of integral membrane proteins. J. Am. Chem. Soc. 132 (16), 5628–9 [+]

    The choice of a suitable detergent-based membrane mimetic is of crucial importance for high-resolution NMR studies of membrane proteins. The present report describes a new approach of detergent screening. It is based on the comparison of 2D (1)H,(15)N-correlation spectra of a protein in a membrane-bilayer "reference" medium and in "trial" detergent-based environments. The proposed "reference" medium is the lipid-protein nanodisc (LPN) representing nanoscale phospholipid bilayers wrapped around by apolipoprotein A-1. The set of zwitterionic (DPC, DMPC/DHPC), anionic (SDS, LMPG, LPPG), and weakly cationic (LDAO) detergent-based media was screened for their ability to represent the native structure of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP. The VSD/LPN complexes composed of saturated zwitterionic (DMPC), anionic (DMPG), or a mixture of unsaturated differently charged (POPC/DOPG, 3:1) lipids were used as reference. All assayed detergent media demonstrate similar CD spectra of the domain with a high level (approximately 60%) of overall helicity but different 2D NMR spectra. Using the reference spectrum of the VSD in LPN, we were able to choose the detergent composition in which the membrane-like structure of the VSD is preserved.

  8. Goncharuk S.A., Shulga A.A., Ermolyuk Y.S., Kuzmichev P.K., Sobol V.A., Bocharov E.V., Chupin V.V., Arseniev A.S., Kirpichnikov M.P. (2009). Bacterial synthesis, purification, and solubilization of membrane protein KCNE3, a regulator of voltage-gated potassium channels. Biochemistry Mosc. 74 (12), 1344–9 [+]

    Описан эффективный способ получения мембранного белка KCNE3, а также его изотопно-меченых производных (15N-, 13C-), в количествах, достаточных для проведения структурно-функциональных исследований. Очищенный белковый препарат в составе мицелл различных детергентов охарактеризован методами динамического светорассеяния, КД-спектроскопии и ЯМР-спектроскопии. Показано, что в мицеллах DPC/LDAO белок находится в мономерной форме и принимает преимущественно альфа-спиральную конформацию. Наличие кросс-пиков от всех глицинов в 15N-HSQC–спектре ЯМР, а также относительно небольшая ширина линий (~20 Гц) подтверждают высокое качество полученного образца и возможность получения структурно-динамической информации о KCNE3 методом гетероядерной спектроскопии ЯМР высокого разрешения.

  9. Shenkarev Z.O., Lyukmanova E.N., Solozhenkin O.I., Gagnidze I.E., Nekrasova O.V., Chupin V.V., Tagaev A.A., Yakimenko Z.A., Ovchinnikova T.V., Kirpichnikov M.P., Arseniev A.S. (2009). Lipid-protein nanodiscs: possible application in high-resolution NMR investigations of membrane proteins and membrane-active peptides. Biochemistry Mosc. 74 (7), 756–65 [+]

    High-resolution NMR is shown to be applicable for investigation of membrane proteins and membrane-active peptides embedded into lipid-protein nanodiscs (LPNs). (15)N-Labeled K+-channel from Streptomyces lividans (KcsA) and the antibiotic antiamoebin I from Emericellopsis minima (Aam-I) were embedded in LPNs of different lipid composition. Formation of stable complexes undergoing isotropic motion in solution was confirmed by size-exclusion chromatography and (31)P-NMR spectroscopy. The 2D 1H-(15)N-correlation spectra were recorded for KcsA in the complex with LPN containing DMPC and for Aam-I in LPNs based on DOPG, DLPC, DMPC, and POPC. The spectra recorded were compared with those in detergent-containing micelles and small bicelles commonly used in high-resolution NMR spectroscopy of membrane proteins. The spectra recorded in LPN environments demonstrated similar signal dispersion but significantly increased (1)H(N) line width. The spectra of Aam-I embedded in LPNs containing phosphatidylcholine showed significant selective line broadening, thus suggesting exchange process(es) between several membrane-bound states of the peptide. (15)N relaxation rates were measured to obtain the effective rotational correlation time of the Aam-I molecule. The obtained value (approximately 40 nsec at 45 degrees C) is indicative of additional peptide motions within the Aam-I/LPN complex.

  10. Dubovskii P.V., Volynsky P.E., Polyansky A.A., Karpunin D.V., Chupin V.V., Efremov R.G., Arseniev A.S. (2008). Three-dimensional structure/hydrophobicity of latarcins specifies their mode of membrane activity. Biochemistry 47 (11), 3525–33 [+]

    Latarcins, linear peptides from the Lachesana tarabaevi spider venom, exhibit a broad-spectrum antimicrobial activity, likely acting on the bacterial cytoplasmic membrane. We study their spatial structures and interaction with model membranes by a combination of experimental and theoretical methods to reveal the structure-activity relationship. In this work, a 26 amino acid peptide, Ltc1, was investigated. Its spatial structure in detergent micelles was determined by (1)H nuclear magnetic resonance (NMR) and refined by Monte Carlo simulations in an implicit water-octanol slab. The Ltc1 molecule was found to form a straight uninterrupted amphiphilic helix comprising 8-23 residues. A dye-leakage fluorescent assay and (31)P NMR spectroscopy established that the peptide does not induce the release of fluorescent marker nor deteriorate the bilayer structure of the membranes. The voltage-clamp technique showed that Ltc1 induces the current fluctuations through planar membranes when the sign of the applied potential coincides with the one across the bacterial inner membrane. This implies that Ltc1 acts on the membranes via a specific mechanism, which is different from the carpet mode demonstrated by another latarcin, Ltc2a, featuring a helix-hinge-helix structure with a hydrophobicity gradient along the peptide chain. In contrast, the hydrophobic surface of the Ltc1 helix is narrow-shaped and extends with no gradient along the axis. We have also disclosed a number of peptides, structurally homologous to Ltc1 and exhibiting similar membrane activity. This indicates that the hydrophobic pattern of the Ltc1 helix and related antimicrobial peptides specifies their activity mechanism. The latter assumes the formation of variable-sized lesions, which depend upon the potential across the membrane.

  11. Bocharov E.V., Mineev K.S., Volynsky P.E., Ermolyuk Y.S., Tkach E.N., Sobol A.G., Chupin V.V., Kirpichnikov M.P., Efremov R.G., Arseniev A.S. (2008). Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state. J. Biol. Chem. 283 (11), 6950–6 [+]

    Proper lateral dimerization of the transmembrane domains of receptor tyrosine kinases is required for biochemical signal transduction across the plasma membrane. The spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 embedded into lipid bicelles was obtained by solution NMR, followed by molecular dynamics relaxation in an explicit lipid bilayer. ErbB2 transmembrane segments associate in a right-handed alpha-helical bundle through the N-terminal tandem GG4-like motif Thr652-X3-Ser656-X3-Gly660, providing an explanation for the pathogenic power of some oncogenic mutations.

  12. Lyukmanova E.N., Shenkarev Z.O., Paramonov A.S., Sobol A.G., Ovchinnikova T.V., Chupin V.V., Kirpichnikov M.P., Blommers M.J., Arseniev A.S. (2008). Lipid-protein nanoscale bilayers: a versatile medium for NMR investigations of membrane proteins and membrane-active peptides. J. Am. Chem. Soc. 130 (7), 2140–1 ID:356
  13. Dubinnyi M.A., Lesovoy D.M., Dubovskii P.V., Chupin V.V., Arseniev A.S. (2006). Modeling of 31P-NMR spectra of magnetically oriented phospholipid liposomes: A new analytical solution. Solid State Nucl Magn Reson 29 (4), 305–11 [+]

    31P-NMR spectroscopy is widely used for studies of phospholipid liposomes, a commonly used model of a biological membrane. For the correct analysis of 31P-NMR spectra of the liposomes it is necessary to take into account that they are deformed by the magnetic field of the spectrometer. The liposomes become ellipsoidal and this affects the lineshape of the spectrum. In the present communication we suggest a new analytical formula for modeling of 31P-NMR spectra of the prolate phospholipid liposomes. The formula assumes a Lorentzian broadening function and exactly ellipsoidal shape of the liposomes. Based on the formula a program called P-FIT is designed for the practical analysis of the experimental multicomponent spectra of the prolate liposomes. The versatility of the program developed in a Mathematica environment is demonstrated by simulations of a number of 31P-NMR spectra with different complexity.