Education

Selected publications

1. Panteleev P.V., Balandin S.V., Ivanov V.T., Ovchinnikova T.V. (2017). A Therapeutic Potential of Animal β-hairpin Antimicrobial Peptides. Curr. Med. Chem. 24 (17), 1724–1746 [+]

   Endogenous antimicrobial peptides (AMPs) are evolutionary ancient molecular factors of innate immunity that play the key role in host defense. Because of the low resistance rate, AMPs have caught extensive attention as possible alternatives to conventional antibiotics. Over the last years, it has become evident that biological functions of AMPs are beyond direct killing of microbial cells. This review focuses on a relatively small family of animal host defense peptides with the β-hairpin structure stabilized by disulfide bridges. Their small size, rigid structure, stability to proteases, and plethora of biological functions, including antibacterial, antifungal, antiviral, anticancer, endotoxin-binding, metabolism- and immune- modulating activities, make natural β-hairpin AMPs an attractive molecular basis for drug design.

   ID:1997
2. Ziganshin R.H., Ivanova O.M., Lomakin Y.A., Belogurov A.A. Jr, Kovalchuk S.I., Azarkin I.V., Arapidi G.P., Anikanov N.A., Shender V.O., Piradov M.A., Suponeva N.A., Vorobyeva A.A., Gabibov A.G., Ivanov V.T., Govorun V.M. (2016). The pathogenesis of demyelinating form of Guillain-Barre syndrome: proteo-peptidomic and immunological profiling of physiological fluids. Mol. Cell Proteomics , [+]

   Acute inflammatory demyelinating polyneuropathy (AIDP) - the main form of Guillain-Barre syndrome (GBS) - is a rare and severe disorder of the peripheral nervous system (PNS) with an unknown etiology. One of the hallmarks of the AIDP pathogenesis is a significantly elevated cerebrospinal fluid (CSF) protein level. In this paper CSF peptidome and proteome in AIDP were analyzed and compared with multiple sclerosis (MS) and control patients. A total protein concentration increase was shown to be due to even changes in all proteins rather than some specific response, supporting the hypothesis of protein leakage from blood through the blood-nerve barrier. The elevated CSF protein level in AIDP was complemented by activization of protein degradation and much higher peptidome diversity. Due to the studies of the acute motor axonal form, GBS as a whole is thought to be associated with autoimmune response against neurospecific molecules. Thus, in AIDP, autoantibodies against cell adhesion (CAM) proteins localized at Ranvier's nodes were suggested as possible targets in AIDP. Indeed, AIDP CSF peptidome analysis revealed CAM proteins degradation, however no reliable dependence on the corresponding autoantibodies levels was found. Proteome analysis revealed overrepresentation of Gene Ontology groups related to responses to bacteria and virus infections, which were earlier suggested as possible AIDP triggers. Immunoglobulin blood serum analysis against most common neuronal viruses did not reveal any specific pathogen; however AIDP patients were more immunopositive in average and often had polyinfections. Cytokine analysis of both AIDP CSF and blood did not show a systemic adaptive immune response or general inflammation, while innate immunity cytokines were upregulated. To supplement the widely-accepted though still unproven autoimmunity-based AIDP mechanism we propose a hypothesis of the primary PNS damaging initiated as an innate immunity-associated local inflammation following neurotropic viruses egress, while the autoantibody production might be an optional complementary secondary process.

   ID:1523
3. Fesenko I., Seredina A., Arapidi G., Ptushenko V., Urban A., Butenko I., Kovalchuk S., Babalyan K., Knyazev A., Khazigaleeva R., Pushkova E., Anikanov N., Ivanov V., Govorun V.M. (2016). The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation. Front Plant Sci 7, 1661 [+]

   Plant protoplasts are widely used for genetic manipulation and functional studies in transient expression systems. However, little is known about the molecular pathways involved in a cell response to the combined stress factors resulted from protoplast generation. Plants often face more than one type of stress at a time, and how plants respond to combined stress factors is therefore of great interest. Here, we used protoplasts of the moss Physcomitrella patens as a model to study the effects of short-term stress on the chloroplast proteome. Using label-free comparative quantitative proteomic analysis (SWATH-MS), we quantified 479 chloroplast proteins, 219 of which showed a more than 1.4-fold change in abundance in protoplasts. We additionally quantified 1451 chloroplast proteins using emPAI. We observed degradation of a significant portion of the chloroplast proteome following the first hour of stress imposed by the protoplast isolation process. Electron-transport chain (ETC) components underwent the heaviest degradation, resulting in the decline of photosynthetic activity. We also compared the proteome changes to those in the transcriptional level of nuclear-encoded chloroplast genes. Globally, the levels of the quantified proteins and their corresponding mRNAs showed limited correlation. Genes involved in the biosynthesis of chlorophyll and components of the outer chloroplast membrane showed decreases in both transcript and protein abundance. However, proteins like dehydroascorbate reductase 1 and 2-cys peroxiredoxin B responsible for ROS detoxification increased in abundance. Further, genes such as thylakoid ascorbate peroxidase were induced at the transcriptional level but down-regulated at the proteomic level. Together, our results demonstrate that the initial chloroplast reaction to stress is due changes at the proteomic level.

   ID:1991
4. Fesenko I.A., Arapidi G.P., Skripnikov A.Y., Alexeev D.G., Kostryukova E.S., Manolov A.I., Altukhov I.A., Khazigaleeva R.A., Seredina A.V., Kovalchuk S.I., Ziganshin R.H., Zgoda V.G., Novikova S.E., Semashko T.A., Slizhikova D.K., Ptushenko V.V., Gorbachev A.Y., Govorun V.M., Ivanov V.T. (2014). Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens. BMC Plant Biol. 15 (1), 87 [+]

   Protein degradation is a basic cell process that operates in general protein turnover or to produce bioactive peptides. However, very little is known about the qualitative and quantitative composition of a plant cell peptidome, the actual result of this degradation. In this study we comprehensively analyzed a plant cell peptidome and systematically analyzed the peptide generation process.

   ID:1261
5. Яцкин О.Н., Карелин А.А., Иванов В.Т. (2009). Пептидомы мозга, сердца, легких и селезенки крысы: сходство и различия. Биоорг. хим. 35 (4), 471–482 ID:233
6. Stoilova T.B., Kovalchuk S.I., Egorova N.S., Surovoy A.Y., Ivanov V.T. (2008). Gramicidin A-based peptide vector for intracellular protein delivery. Biochim. Biophys. Acta 1778 (10), 2026–31 [+]

   The development of the peptide-based vectors for the intracellular delivery of biologically active macromolecules has opened new prospects of their application in research and therapy. Earlier the amphipathic cell-penetrating peptide (CPP) Pep-1 was reported to mediate cellular uptake of proteins without covalent binding to them. In this work we studied the ability of a series of membrane-active amphipathic peptides, based on the gramicidin A sequence, to transport a model protein across the eukaryotic cell membrane. Among them the positively charged Cys-containing peptide P10C demonstrated the most effective beta-galactosidase intracellular delivery. Besides, this peptide was shown to form noncovalent associates with beta-galactosidase as judged from electrophoresis and enzymatic activity assays. In addition, a series of new gramicidin analogues were prepared and the effect of N-terminus modification of gramicidin on the protein transduction efficiency was studied.

   ID:232
7. Ziganshin R.K.h., Alekseev D.G., Arapidi G.P., Ivanov V.T., Moshkovskiĭ S.A., Govorun V.M. (2008). [Serum proteome profiling for ovarion cancer diagnosis using ClinProt magnetic bead technique and MALDI-TOF-mass-spectrometry]. Biomed Khim 54 (4), 408–19 [+]

   Using reverse-phase (MB-HIC 8 and HB-HIC 18) weak cation exchange (MB-WCX) and metal affinity ClinProt magnetoc beads peptides and protein factions were obtained from human sera for their profiling by MALDI-TOF mass spectrometry. Proteome profiling of sera from I-IV stage ovarian cancer patients (47 women, average age 51) and from healthy women (47 subjects, average age 49) using MB-WCX beads allowed calculation of the best diagnostic models based on the Genetic Algorithm and Supervised Neural Network classifiers; these model generated 100% sensitivity and specificity when the test set of subjects was analyzed. Introduction of additional sera from patients with colorectal cancer (19) and ulcerous colitis (5) to the statistical model confirmed 100% ovarian cancer recognition. Statistical mass-spectrometry analysis of mass-spectrometry peak areas included to the diagnostic classifiers showed 3 peaks distinctive for ovarian cancer and 4 peaks distinctive for ovarian and colorectal cancer.

   ID:921
8. Sazonova O.V., Blishchenko E.Y., Tolmazova A.G., Khachin D.P., Leontiev K.V., Karelin A.A., Ivanov V.T. (2007). Stimulation of fibroblast proliferation by neokyotorphin requires Ca influx and activation of PKA, CaMK II and MAPK/ERK. FEBS J. 274 (2), 474–84 [+]

   Neokyotorphin [TSKYR, hemoglobin alpha-chain fragment (137-141)] has previously been shown to enhance fibroblast proliferation, its effect depending on cell density and serum level. Here we show the dependence of the effect of neokyotorphin on cell type and its correlation with the effect of protein kinase A (PKA) activator 8-Br-cAMP, but not the PKC activator 4beta-phorbol 12-myristate, 13-acetate (PMA). In L929 fibroblasts, the proliferative effect of neokyotorphin was suppressed by the Ca2+ L-type channel inhibitors verapamil or nifedipine, the intracellular Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid acetoxymethyl ester, kinase inhibitors H-89 (PKA), KN-62 (Ca2+/calmodulin-dependent kinase II) and PD98059 (mitogen-activated protein kinase). The proliferative effect of 8-Br-cAMP was also suppressed by KN-62 and PD98059. PKC suppression (downregulation with PMA or inhibition with bisindolylmaleimide XI) did not affect neokyotorphin action. The results obtained point to a cAMP-like action for neokyotorphin.

   ID:230
9. Volpina O.M., Volkova T.D., Koroev D.O., Ivanov V.T., Ozherelkov S.V., Khoretonenko M.V., Vorovitch M.F., Stephenson J.R., Timofeev A.V. (2005). A synthetic peptide based on the NS1 non-structural protein of tick-borne encephalitis virus induces a protective immune response against fatal encephalitis in an experimental animal model. Virus Res. 112 (1-2), 95–9 [+]

   Synthetic peptide corresponds to amino acids 37—55 of NS1 non-structural protein from tick-borne encephalitis virus (strain Sophyin) was able to protect 60% of animals against lethal challenge with the homologous highly pathogenic tick-borne encephalitis virus strain, and adoptive transfer experiments indicated the involvement of the antibodies induced by this peptide in its protective activity in mice.

   ID:113
10. Ivanov V.T., Yatskin O.N. (2005). Peptidomics: a logical sequel to proteomics. Expert review of proteomics 2 (4), 463–73 [+]

    Rapid progress of separation techniques as well as methods of structural analysis provided conditions in the past decade for total screening of complex biologic mixtures for any given class of biomolecules. The present review updates the reader with the modern state of peptidomics, a chapter of chemical biology that deals with structure and biologic properties of sets of peptides present in biologic tissues, cells or fluids. Scope and limitations of currently employed experimental techniques are considered and the main results are outlined. Considerable attention will be afforded to the biologic role of peptides formed in vivo by proteolysis of nonspecialized precursor proteins with other well-defined functions. In conclusion, the connection is discussed between peptidomics and the much more mature and still closely related field of proteomics.

    ID:226
11. Ivanov V.T., Karelin A.A., Yatskin O.N. (2005). Generation of peptides by human erythrocytes: facts and artifacts. Biopolymers 80 (2-3), 332–46 [+]

    Previously reported data on peptide composition of human erythrocyte lysate were obtained under conditions that did not exclude proteolytic degradation of hemoglobin in the process of peptide isolation. Comparative chromatographic analysis of the diluted erythrocyte lysate incubated in acidic conditions with or without proteolytic enzyme inhibitors showed that several peptides earlier identified as intraerythrocyte ones in fact result from hemoglobin degradation by erythrocyte acidic protease(s) during incubation of the lysate. A rational scheme excluding postlysis proteolysis was developed for isolation of peptide fraction. Further analysis resulted in determination of structure and content of about 50 endogenous intraerythrocyte hemoglobin fragments. A primary endopeptidase splitting of alpha- and beta-globin chains followed by consecutive exopeptidase trimming of primary fragments is suggested as a degradation mechanism. The intraerythrocyte peptides were shown to differ from peptides excreted by the erythrocytes to the extracellular medium in the primary culture. It was also found that intraerythrocyte peptides cannot play the role of precursors of hemoglobin fragments present in tissue extracts.

    ID:227
12. Blishchenko E.Y., Sazonova O.V., Kalinina O.A., Moiseeva E.V., Vass A.A., Karelin A.A., Ivanov V.T. (2005). Antitumor effect of valorphin in vitro and in vivo: combined action with cytostatic drugs. Cancer Biol. Ther. 4 (1), 118–24 [+]

    The action of the cytostatic drugs (epirubicin and vincristine) in combination with the endogenous antiproliferative beta-hemoglobin fragment (33-39), valorphin, was studied in tumor (L929 and A549) cell cultures, primary culture of murine bone marrow cells and in murine model of breast carcinoma in vivo. Simultaneous application of 1 microM valorphin and 1 microM epirubicin, in vitro, did not result in an additive suppressive effect on cell culture growth. Additive effects were achieved with alternating applications of the peptide and the drugs, namely, 0.5 microM (but not 1 microM) epirubicin added 24 h prior to 1 microM valorphin; 1 microM valorphin added 48 h prior to 0.1 microM epirubicin, or 0.1 microM vincristine, or 0.05 microM vincristine, which resulted in 100% cell death in the both series with vincristine and up to 78% cell biomass reduction in the experiments with epirubicin. In the in vivo model (female BLRB mice with subcutaneously inoculated syngeneic mammary carcinoma), simultaneous treatment with 25 mg/m(2) epirubicin and 1 mg/kg valorphin resulted in 42% of tumor growth inhibition, as compared with the negative control group and 22% inhibition as compared with the epirubcin-treated group (at 20th day of treatment). Survival was significantly improved (69% compared to 39% in the group treated with epirubicin only) at day 26 after the treatment beginning.

    ID:228
13. Afonin P.V., Fokin A.V., Tsygannik I.N., Mikhailova I.Y., Onoprienko L.V., Mikhaleva I.I., Ivanov V.T., Mareeva T.Y., Nesmeyanov V.A., Li N., Pangborn W.A., Duax W.L., Pletnev V.Z. (2001). Crystal structure of an anti-interleukin-2 monoclonal antibody Fab complexed with an antigenic nonapeptide. Protein Sci. 10 (8), 1514–21 [+]

    The three-dimensional structure of the Fab fragment of a monoclonal antibody (LNKB-2) to human interleukin-2 (IL-2) complexed with a synthetic antigenic nonapeptide, Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-OMe, has been determined at 3.0 A resolution. In the structure, four out of the six hypervariable loops of the Fab (complementarity determining regions [CDRs] L1, H1, H2, and H3) are involved in peptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. The Tyr residues in the Fab antigen binding site play a major role in antigen-antibody recognition. The structures of the complexed and uncomplexed Fab were compared. In the antigen binding site the CDR-L1 loop of the antibody shows the largest structural changes upon peptide binding. The peptide adopts a mostly alpha-helical conformation similar to that in the epitope fragment 64-72 of the IL-2 antigen. The side chains of residues Leu 66, Val 69, and Leu 70, which are shielded internally in the IL-2 structure, are involved in interactions with the Fab in the complex studied. This indicates that antibody-antigen complexation involves a significant rearrangement of the epitope-containing region of the IL-2 with retention of the alpha-helical character of the epitope fragment.

    ID:89
14. Volpina O.M., Surovoy A.Y., Zhmak M.N., Kuprianova M.A., Koroev D.O., Chepurkin A.V., Toloknov A.S., Ivanov V.T. (1999). A peptide construct containing B-cell and T-cell epitopes from the foot-and-mouth disease viral VP1 protein induces efficient antiviral protection. Vaccine 17 (6), 577–84 [+]

    A new peptide construct Palm135-158-GGA-170-188(Acm) contains a virus specific T-helper epitope within the 170—188 sequence of VP1, in addition to the main antigenic 135—158 region of the foot-and-mouth disease viral VP1 protein (strain A22). The construct has higher protective, antigenic, immunogenic and T-cell proliferative activity then the previously described shorter peptide Palm(2)135—159.

    ID:112
15. Volpina O.M., Yarov A.V., Zhmak M.N., Kuprianova M.A., Chepurkin A.V., Toloknov A.S., Ivanov V.T. (1996). Synthetic vaccine against foot-and-mouth disease based on a palmitoyl derivative of the VP1 protein 135-159 fragment of the A22 virus strain. Vaccine 14 (14), 1375–80 [+]

    The peptide Palm2 135—159, a dipalmitoyl derivative of the 135—159 fragment of VP1 protein of the foot-and-mouth disease virus strain A22 was synthesized. In the experiments on mice, guinea pigs and sheep Palm2 135—159 possesses antiviral activity. It was shown that the synthetic vaccine provides 1 year protection of sheep against foot-and-mouth disease after a single administration. The peptide vaccine is allowed for veterinary use in Russia.

    ID:111
16. Ovchinnikov Yu.A., Bystrov V.F., Ivanov V.T. (1984). NMR solution conformation of gramicidin A double helix. FEBS Lett. 165 (1), 51–56 [+]

    The conformation of species 3 of Val-gramicidin A in dioxane has been determined by two-dimensional NMR spectroscopy. It is presented by the left handed ππ^5.6_LD double helix, a suitable model of an ion permeable pore across the membrane matrix.

    ID:143
17. Bystrov V.F., Gavrilov Yu.D., Ivanov V.T., Ovchinnikov Yu.A. (1977). Refinement of the solution conformation of valinomycin with the aid of coupling constants from thr 13C-nuclear-magnetic-resonance spectra. Eur. J. Biochem. 78 (1), 63–82 [+]

    he C'= O and C^α signals in the ¹³C nuclear magnetic resonance (NMR) spectra of valinomycin have been assigned and the vicinal ¹H…¹³C coupling constants have been determined by double and triple heteronuclear resonance. In conjunction with the vicinal H-NC^α-H and H-C^αC^β-H proton-proton constants, the results led to unequivocal determination of the torsion angles φ and of the population distribution of the C^α-C^β rotational states. The Φ torsion angles for the hydroxy acid residues were estimated from the vicinal ¹H-C^αC'-¹⁵N constants. The combined data permitted refinement of the conformational states of valinomycin in different solvents. For the K^S+ complex of valinomycin the observed couplings are in complete accord with the conformations we had earlier proposed for solutions and that had also been established by X-ray analysis. In the ¹³C spectra of the valinomycin-Tl⁺ complex ¹³C…^203,205Tl⁺ spin-spin couplings were observed for the l and d-valine carbonyls, unequivocal proof of the donor-acceptor interaction with the cation. In media of weak polarity (cyclohexane, chloroform) the conformation of the valinomycin molecule is similar to that of the K⁺ complex. In such a 'bracelet' structure formed by six fused β-turns of type II and II', the amino acid carbonyls are axial with certain inclination towards the symmetry axis. On formation of a 1:1 complex with a cation the carbonyl orientation changes, now bending towards the center of the molecular cavity. In the 'propeller' conformation, predominant in solvents of medium polarity (for instance CCl₄/(C²H₃)₂SO, 3/1) the three β-turns are of type II. The ¹H and ¹³C chemical shifts are interpreted in terms of conformational changes in the valinomycin molecule, intermolecular and intramolecular hydrogen bonds and interaction with the metal cation.

    ID:139
18. Ovchinnikov Y.A., Ivanov V.T., Evstratov A.V., Sumskaya L.V., Melnik E.I., Chumburidze T.S., Portnova S.L., Balashova T.A. (1973). Sandwich complexes as a functional form of the enniatin ionophores. FEBS Lett. 36 (1), 65–71 [+]

    The ability of the enniatin cyclodepsipeptides (CDP) (fig. 1) to form complexes with alkali metal ions (M+) and induce ionic permeability in artificial and biological membranes has been described in a number of papers [ 1,2]. The complexes were found to be equimolar in both solutions and in the crystalline state; by analogy with valinomycin and the nactins the role of the M+ carriers across the membrane was ascribed to them [3,49. In the present paper evidence is produced showing that an important part in the functioning of this group of ionophores is played by complexes with 2: 1 and 3:2 macrocycle:cation ratios.
     

    ID:141
19. Bystrov V.F., Ivanov V.T., Portnova S.L., Balashova T.A., Ovchinnikov Yu.A. (1973). Refinement of the angular dependence of the peptide vicinal NH-CaH coupling constant. Tetrahedron 29 (6), 873–877 [+]

    The refined dependence of the peptide NHCαH vicinal coupling constant on the dihedral angle θ have been derived on the basis of the accumulated experimental data. The mean permissible values (in Hz) are approximated by ³J_NHCH = 9·4 cos² θ - 1·1 cos θ + 0·4 An analogous relationship for the sum of two vicinal NH-CαH₂ coupling constants in the glycyl residue have been calculated from the above dependence. Measurements on N-methylacetamide in various solvents and in the presence of an alkali salt showed the vicinal constant NH-CH to vary by not more than ± 3%. Some of the other proposed ³J_NHCH(θ) dependencies give too low values for the cis-oriented NH and CαH bonds. This may be due to the fact that in these correlations the data for compounds with cis-amide bonds have been used for 0° - θ - 90° region of the dependence.

    ID:1044
20. Ivanov V.T., Shemyakin M.M., Ovchinnikov Yu.A. (1969). Topochemische Untersuchungen an Peptidsystemen. Angew. Chemie 14, 523–529 ID:168
21. Ovchinnikov Yu.A., Shemyakin M.M., Ivanov V.T., Antonov V.K., Vinogradova E.I., Shkrob A.M., Malenkov G.G., Evstratov A.V., Laine I.A., Melnik E.I., Ryabova I.D. (1969). Cyclodepsipeptides as chemical tool for studying ionic transport through membranes. J. Membr. Biol. 1, 402–403 [+]

    This paper reports a study of the chemistry of valinomycin, enniatins and related membrane-active depsipeptides that increase alkali metal ion permeability of model and biological membranes. The antimicrobial activity of these compounds and thir effect on membranes has been correlated with their cation-complexing ability. the complexing reaction has been studied by spectropolarimetric studies have revealed coexistence of conformers of the cyclopeptides and conductometric methods.  Nuclear magnetic resonance, optical rotatory dispersion, and infrared spectrophotometric studies have revealed the coexistence ofconformers of the cyclodepsipeptides in solution and have led to elucidation of the spatial structure of valinomycin, enniatin B and their K+ complexes. The effect of the conformational properties of the cyclodepsipeptides on their complexation efficiency and selectivity, surface-active properties and behavior towards phospholipid monolayers, bimolecular phospholipid membranes and a number of biological membrane systems has been ascertained. The studies have clearly shown the feasibility of using cyclodepsipeptides with predetermined structural and conformational parameters as chemical tools for membrane studies. It is suggested that the principle of conformation-dependent cation binding through ion-dipole interactions may possibly lie at the basis of the mode of action of systems governing the natural ion permeability in biological membranes.

    ID:142