Maxim A. Dubinnyi

Education

PeriodCountry, cityEducation institutionAdditional info
1994–2000 Moscow, Russia Moscow Institute of Physics and Technology

Selected publications

  1. Dubovskii P.V., Dubinnyi M.A., Volynsky P.E., Pustovalova Y.E., Konshina A.G., Utkin Y.N., Arseniev A.S., Efremov R.G. (2017). Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin. J. Biomol. Struct. Dyn. , 1–16 [+]

    Cobra cytotoxins (CTs) belong to the three-fingered protein family. They are classified into S- and P-types, the latter exhibiting higher membrane-perturbing capacity. In this work, we investigated the interaction of CTs with phospholipid bilayers, using coarse-grained (CG) and full-atom (FA) molecular dynamics (MD). The object of this work is a CT of an S-type, cytotoxin I (CT1) from N.oxiana venom. Its spatial structure in aqueous solution and in the micelles of dodecylphosphocholine (DPC) were determined by (1)H-NMR spectroscopy. Then, via CG- and FA MD-computations, we evaluated partitioning of CT1 molecule into palmitoyloleoylphosphatidylcholine (POPC) membrane, using the toxin spatial models, obtained either in aqueous solution, or detergent micelle. The latter model exhibits minimal structural changes upon partitioning into the membrane, while the former deviates from the starting conformation, loosing the tightly bound water molecule in the loop-2. These data show that the structural changes elicited by CT1 molecule upon incorporation into DPC micelle take place likely in the lipid membrane, although the mode of the interaction of this toxin with DPC micelle (with the tips of the all three loops) is different from its mode in POPC membrane (primarily with the tip of the loop-1 and both the tips of the loop-1 and loop-2).

    ID:1943
  2. Dubovskii P.V., Dubinnyi M.A., Konshina A.G., Kazakova E.D., Sorokoumova G.M., Ilyasova T.M., Shulepko M.A., Chertkova R.V., Lyukmanova E.N., Dolgikh D.A., Arseniev A.S., Efremov R.G. (2017). Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They? Biochemistry 56 (34), 4468–4477 [+]

    Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana venom, were characterized using nuclear magnetic resonance (NMR) spectroscopy and atomistic molecular dynamics (MD) simulations in water. Compared to the natural protein, it contains an additional Met residue at the N-terminus. In this work, the NMR-derived spatial structure of uniformly (13)C- and (15)N-labeled CTI and its dynamic behavior were investigated and subjected to comparative analysis with the corresponding data for the native toxin. The differences were found in dihedral angles of only a single residue, adjacent to the N-terminal methionine. Microsecond-long MD traces of the toxins reveal an increased flexibility in the residues spatially close to the N-Met. As the detected structural and dynamic changes of the two CTI models do not result in substantial differences in their cytotoxicities, we assume that the recombinant protein can be used for many purposes as a reasonable surrogate of the native one. In addition, we discuss general features of the spatial organization of cytotoxins, implied by the results of the current combined NMR and MD study.

    ID:1923
  3. Dubinnyi M.A., Kaskova Z.M., Rodionova N.S., Baranov M.S., Gorokhovatsky A.Y., Kotlobay A., Solntsev K.M., Tsarkova A.S., Petushkov V.N., Yampolsky I.V. (2015). Novel Mechanism of Bioluminescence: Oxidative Decarboxylation of a Moiety Adjacent to the Light Emitter of Fridericia Luciferin. Angew. Chem. Int. Ed. Engl. 54 (24), 7065–7067 [+]

    A novel luciferin from a bioluminescent Siberian earthworm Fridericia heliota was recently described. In this study, the Fridericia oxyluciferin was isolated and its structure elucidated. The results provide insight into a novel bioluminescence mechanism in nature. Oxidative decarboxylation of a lysine fragment of the luciferin supplies energy for light generation, while a fluorescent CompX moiety remains intact and serves as the light emitter.

    ID:1265
  4. Dubinnyi M.A., Tsarkova A.S., Petushkov V.N., Kaskova Z.M., Rodionova N.S., Kovalchuk S.I., Ziganshin R.H., Baranov M.S., Mineev K.S., Yampolsky I.V. (2015). Novel Peptide Chemistry in Terrestrial Animals: Natural Luciferin Analogues from the Bioluminescent Earthworm Fridericia heliota. Chem. Eur. J. 21 (10), 3942–3947 [+]

    We report isolation and structure elucidation of AsLn5, AsLn7, AsLn11 and AsLn12: novel luciferin analogs from the bioluminescent earthworm Fridericia heliota. They were found to be highly unusual modified peptides, comprising either of the two tyrosine-derived chromophores, CompX or CompY and a set of amino acids, including threonine, gamma-aminobutyric acid, homoarginine, and unsymmetrical N,N-dimethylarginine. These natural compounds represent a unique peptide chemistry found in terrestrial animals and rise novel questions concerning their biosynthetic origin.

    ID:1243
  5. Tsarkova A.S., Dubinnyi M.A., Baranov M.S., Petushkov N., Rodionova S., Zagudaylova B., Yampolsky I.V. (2015). Total synthesis of AsLn2 – a luciferin analogue from the Siberian bioluminescent earthworm Fridericia heliota. Mendeleev Communications 25 (2), 99–100 [+]

    Total synthesis of AsLn2, a luciferin analogue isolated from the Siberian bioluminescent earthworm F. heliota, was performed from (Z)-5-(2,3-dimethoxy-3-oxoprop-1-en-1-yl)-2-hydroxybenzoic acid in six steps.

    ID:1264
  6. Malakhov M.V., Dubinnyi M.A., Vlasova N.V., Zgoda V.G., Efremov R.G., Boldyrev I.A. (2014). End-group differentiating ozonolysis of furocoumarins. RSC Advances 4 (106), 61277–61280 [+]

    Ozonolysis of furocoumarins followed by reductive work-up yields not only common symmetrical dialdehydes, but also o-formylumbelliferones with moderate-to-high yields. Simultaneous formation of both products accounts for the transformation of carbonyl oxides – products of primary ozonide ring opening.

    ID:1097
  7. Petushkov V.N., Dubinnyi M.A., Tsarkova A.S., Rodionova N.S., Baranov M.S., Kublitski V.S., Shimomura O., Yampolsky I.V. (2014). A Novel Type of Luciferin from the Siberian Luminous Earthworm Fridericia heliota: Structure Elucidation by Spectral Studies and Total Synthesis. Angew. Chem. Int. Ed. Engl. 53 (22), 5566–5568 [+]

    Press-release on this article: "Novel luciferin from Siberian bioluminescent worm".

    ID:1016
  8. Petushkov V.N., Dubinnyi M.A., Rodionova N.S., Nadezhdin K.D., Marques S.M., EstevesdaSilva J.C.G., Shimomura O., Yampolsky I.V. (2014). AsLn2, a luciferin-related modified tripeptide from the bioluminescent earthworm Fridericia heliota. Tetrahedron Lett. 55 (2), 463–465 ID:1039
  9. Petushkov V.N., Tsarkova A.S., Dubinnyi M.A., Rodionova N.S., Marques S.M., EstevesdaSilva J.C.G., Shimomura O., Yampolsky I.V. (2014). CompX, a luciferin-related tyrosine derivative from the bioluminescent earthworm Fridericia heliota. Tetrahedron Lett. 55 (2), 460–462 ID:1040
  10. Dubinnyi M.A., Osmakov D.I., Koshelev S.G., Kozlov S.A., Andreev Y.A., Zakaryan N.A., Dyachenko I.A., Bondarenko D.A., Arseniev A.S., Grishin E.V. (2012). Lignan from thyme possessing inhibitory effect on ASIC3 current. J. Biol. Chem. , [+]

    Novel compound was identified in acidic extract of Thymus armeniacus collected in the Lake Sevan region of Armenia. This compound, named sevanol, to our knowledge is the first low molecular weight natural molecule that has a reversible inhibition effect both on transient and sustained current of human ASIC3 channels expressed in Xenopus laevis oocytes. Sevanol completely blocked the transient component (IC50 353+/-23 μM) and partially (~45%) inhibited the amplitude of sustained component (IC50 of 234+/-53 μM). Other types of ASICs channels were intact to sevanol application except ASIC1a that showed more than 6 times less affinity to it as compared with inhibitory action on ASIC3 channel. To elucidate sevanol structure the set of NMR spectra in two solvents: d6-DMSO and D2O was collected and the complete chemical structure was confirmed by LC-ESI+-MS fragmentation. This compound is a new lignan built up of epiphyllic acid and two isocytril esters in positions 9, 10. In vivo administration of sevanol (1-10 mg/kg) significantly reversed of thermal hyperalgesia induced by complete Freund adjuvant (CFA) injection and reduced response to acid in writhing test. Thus we assume the probable considerable role of sevanol in known analgesic and anti-inflammatory properties of thyme.

    ID:725
  11. 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.

    ID:350
  12. 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.

    ID:274
  13. Dubovskii P.V., Lesovoy D.M., Dubinnyi M.A., Konshina A.G., Utkin Y.N., Efremov R.G., Arseniev A.S. (2005). Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins. Biochem. J. 387 (Pt 3), 807–15 [+]

    The CTs (cytotoxins) I and II are positively charged three-finger folded proteins from venom of Naja oxiana (the Central Asian cobra). They belong to S- and P-type respectively based on Ser-28 and Pro-30 residues within a putative phospholipid bilayer binding site. Previously, we investigated the interaction of CTII with multilamellar liposomes of dipalmitoylphosphatidylglycerol by wide-line (31)P-NMR spectroscopy. To compare interactions of these proteins with phospholipids, we investigated the interaction of CTI with the multilamellar liposomes of dipalmitoylphosphatidylglycerol analogously. The effect of CTI on the chemical shielding anisotropy and deformation of the liposomes in the magnetic field was determined at different temperatures and lipid/protein ratios. It was found that both the proteins do not affect lipid organization in the gel state. In the liquid crystalline state of the bilayer they disturb lipid packing. To get insight into the interactions of the toxins with membranes, Monte Carlo simulations of CTI and CTII in the presence of the bilayer membrane were performed. It was found that both the toxins penetrate into the bilayer with the tips of all the three loops. However, the free-energy gain on membrane insertion of CTI is smaller (by approximately 7 kcal/mol; 1 kcal identical with 4.184 kJ) when compared with CTII, because of the lower hydrophobicity of the membrane-binding site of CTI. These results clearly demonstrate that the P-type cytotoxins interact with membranes stronger than those of the S-type, although the mode of the membrane insertion is similar for both the types.

    ID:970
  14. Feofanov A.V., Sharonov G.V., Dubinnyi M.A., Astapova M.V., Kudelina I.A., Dubovskii P.V., Rodionov D.I., Utkin Y.N., Arseniev A.S. (2004). Comparative study of structure and activity of cytotoxins from venom of the cobras Naja oxiana, Naja kaouthia, and Naja haje. Biochemistry Mosc. 69 (10), 1148–57 [+]

    Cytotoxins are positively charged polypeptides that constitute about 60% of all proteins in cobra venom; they have a wide spectrum of biological activities. By CD spectroscopy, cytotoxins CT1 and CT2 Naja oxiana, CT3 Naja kaouthia, and CT1 and CT2 Naja haje were shown to have similar secondary structure in an aqueous environment, with dominating beta-sheet structure, and to vary in the twisting angle of the beta-sheet and the conformation of disulfide groups. Using dodecylphosphocholine micelles and liposomes, CT1 and CT2 Naja oxiana were shown to incorporate into lipid structures without changes in the secondary structure of the peptides. The binding of CT1 and CT2 Naja oxiana with liposomes was associated with an increase in the beta-sheet twisting and a sign change of the dihedral angle of one disulfide group. The cytotoxins were considerably different in cytotoxicity and cooperativity of the effect on human promyelocytic leukemia cells HL60, mouse myelomonocytic cells WEHI-3, and human erythroleukemic cells K562. The most toxic CT2 Naja oxiana and CT3 Naja kaouthia possessed low cooperativity of interaction (Hill coefficient h = 0.6-0.8), unlike 10-20-fold less toxic CT1 and CT2 Naja haje (h = 1.2-1.7). CT1 Naja oxiana has an intermediate position on the cytotoxicity scale and is characterized by h = 0.5-0.8. The cytotoxins under study induced necrosis of HL60 cells and failed to activate apoptosis. The differences in cytotoxicity are supposed to be related not with features of the secondary structure of the peptides, but with interactions of side chains of variable amino acid residues with lipids and/or membrane proteins.

    ID:341
  15. Dubovskii P.V., Lesovoy D.M., Dubinnyi M.A., Utkin Y.N., Arseniev A.S. (2003). Interaction of the P-type cardiotoxin with phospholipid membranes. Eur. J. Biochem. 270 (9), 2038–46 [+]

    The cardiotoxin (cytotoxin II, or CTII) isolated from cobra snake (Naja oxiana) venom is a 60-residue basic membrane-active protein featuring three-finger beta sheet fold. To assess possible modes of CTII/membrane interaction 31P- and 1H-NMR spectroscopy was used to study binding of the toxin and its effect onto multilamellar vesicles (MLV) composed of either zwitterionic or anionic phospholipid, dipalmitoylglycerophosphocholine (Pam2Gro-PCho) or dipalmitoylglycerophosphoglycerol (Pam2Gro-PGro), respectively. The analysis of 1H-NMR linewidths of the toxin and 31P-NMR spectral lineshapes of the phospholipid as a function of temperature, lipid-to-protein ratios, and pH values showed that at least three distinct modes of CTII interaction with membranes exist: (a) nonpenetrating mode; in the gel state of the negatively charged MLV the toxin is bound to the surface electrostatically; the binding to Pam2Gro-PCho membranes was not observed; (b) penetrating mode; hydrophobic interactions develop due to penetration of the toxin into Pam2Gro-PGro membranes in the liquid-crystalline state; it is presumed that in this mode CTII is located at the membrane/water interface deepening the side-chains of hydrophobic residues at the tips of the loops 1-3 down to the boundary between the glycerol and acyl regions of the bilayer; (c) the penetrating mode gives way to isotropic phase, stoichiometrically well-defined CTII/phospholipid complexes at CTII/lipid ratio exceeding a threshold value which was found to depend at physiological pH values upon ionization of the imidazole ring of His31. Biological implications of the observed modes of the toxin-membrane interactions are discussed.

    ID:275