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The most cited biological Institute in Russia *

Department of physical methods of researches

The department was established in 1965 under direction of Prof. Victor Ja. Chernyak (previously it was called “department of sedimentation analisys”). From 1993 to 2008 it was headed by Dr. Vladimir A. Drachev, since 2008 the department header is Dr. Victor N. Orlov.

Research areas

The department is dedicated to technical and methodological work on physical and physicochemical methods of investigation of biomacromolecules:

Besides that, staff scientists of the department lead its-own researches on the following trends:

  • Study of structure features of spiral plant viruses
  • Investigation of polyelectrolytes influence on protein aggregation
  • Investigation of characteristics, structure and action mechanism of virus chaperonines (in collaboration with laboratory of molecular bioengineering, Institute of bioorganic chemistry)

Most important achievements

The structure of potato virus X coat protein has been investigated in free form and composed of the virion. It has been found that free subunit has a fixed but non-stable tertiary structure that undergoes denaturation on 33 °C. The stability of potato virus X coat protein subunit composed of virion is much higher because of protein-protein and protein-RNA contacts, both electrostatic and hydrophobic. The model of coat protein structure composed of the vition was suggested. This model explains a height lability of the tertiary structure of free coat protein and structural conformations occurring in the vition [Nemykh et al., 2008, Virology; Dobrov et al., 2007, Mol. Biol. (Mosk)].

An influence of surfactants on the amorphous aggregation of tobacco mosaic virus coat protein was examined. It has been shown that cationic (CTAB) and neutral (Triton X-100) surfactants induce tobacco mosaic virus coat protein aggregation, and in the first case native molecules seems to undergo aggregation but in the second case particulary denaturated ones. Anionic surfactant SDS, in contrary, has been shown to no induce an aggregation at any tested conditions [Panyukov et al., 2006, Int. J. Biochem. Cell. Biol.; Panyukov et al., 2008, Macromol. Biosci.].

A new kinetic approach was proposed for analysis of irreversibly denaturating objects thermogramms obtained by differential scanning calorimetry. The effect of temperature on the heat absorption was examined for rabbit skeletal muscle creatine kinase. The mechanism of denaturation has been suggested, and kinetic parameters of each stage have been determined [Kurganov et al. 2000, Biochemistry; Lyubarev et al. 1999, Biophys. Chem.; Lyubarev et al. 1998, Biophys. Chem.].

Effects of cofactors and the specific ligands on enzymes thermal denaturation were investigated. These effects were demonstrated to result in considerable conformational changes, leading, in their part, to alterations in these macromolecules thermal denaturation pattern. Conformational changes in the isolated myosin head (myosin S1 subfragment 1) were studied using simulation of the myosin ATPase reaction intermediate states. New test for analysis of myosin heads conformational changes during ATPase reaction is proposed [Levashov et al., 1999, BBA; Kaspieva et al. 2001, FEBS Lett.; Golitsina et al. 1996, J. Muscle Res. Cell Motil.; Levitsky et al. 1995, Biophys J.; Nikolaeva et al. 2002, Eur. J. Biochem.].

Using muscle proteins (myosin subfragment 1, tropomyosin, actin) as a model system, the DSC-technique is proved to be an effective tool to detect structural changes in protein-protein interaction. The role of protein-protein and RNA-protein interactions was revealed in the stabilization of tobacco mosaic virus particles architecture [Levitsky et al. 2000, Eur. J. Biochem.; Levitsky et al. 1998, Biochemistry (Moscow); Orlov et al. 1998, FEBS Lett.].

The interrelation between thermal protein denaturation and protein macroscopic aggregation for tobacco mosaic virus coat protein was investigated. The aggregation kinetics has been shown to be dependent on protein concentration [Orlov et al. 2001, Biochemistry (Moscow); Kurganov et al. 2002, Biochemistry (Moscow); Arutyunyan et al. 2001, Biochemistry (Moscow); Rafikova et al. 2003, Int. J. Biochem. Cell. Biol.].

We pioneered in suggestion and implementation of optical train laser fine adjustment in analytical ultracentrifuge «Spinco E» (Beckman, U.S.A.). The maximal permissible rotation speed was determined when employing the most sensitive interference registration system. We have also developed and keep in operation the novel "all-speed" technique of sedimentation balance [Drachev et al. 1979, Nauchnye Dokl. Vyss. Shkoly Biol. Nauki; Chernyak et al. 1975, BBRC; Chernyak et al. 1982, Anal. Biochem.].

A new spectrophotometric cell was developed for enzymatic reactions monitoring at high hydrostatic pressure. Using this cell, the kinetics of lactate dehydrogenase reaction was investigated at 1 kbar pressure [Chernyak et al. 1984, FEBS Lett.].

More than 150 papers were published by department's staff members.

Grants and projects

Department participates in numerous Russian foundation for basic research projects:

  • 12-04-01472-a (Physico-chemical characteristics of gordeiviruses and their isolated coat proteins)

  • 11-04-01350-a (Role of interactions between amyloidogenic proteins in the development of neurodegenerative diseases)

  • 12-04-91330-NNIO_a (Comparative analysis of the role of sulfation and phosphorylation in the regulation of protein-protein interactions using bioinformatics and experimental approaches)

  • 11-04-00935-a (Virus chaperonins: structure, properties and mechanism of functioning).

Educational activities

Graduate and PhD students on 2012:

  • Pavel Semenyuk, PhD student of Faculty of Bioengineering and Bioinformatics, 2010 – 2013

  • Dmitry Abashkin, student of Faculty of Bioengineering and Bioinformatics

The department holds a practice for the Virology subdepartment of Biologycal Faculty graduate students. On 2011, the practice for participants of «RECESS-System Biology» program financed by RFBR and DFG (Germany) was held.

The methodological guidance written on the department is available for the differential scanning calorimetry and isothermal titrating calorimetry.

During the department existing 6 PhD and one doctoral dissertations were performed and successfully defended.

Recent papers
  1. Nesterenko A.M., Orlov E.E., Ermakova G.V., Ivanov I.A., Semenyuk P.I., Orlov V.N., Martynova N.Y., Zaraisky A.G. (2015) Affinity of the heparin binding motif of Noggin1 to heparan sulfate and its visualization in the embryonic tissues. Biochem. Biophys. Res. Commun., 468 (1): 331-336. >>

  2. Anashkin V.A., Salminen A., Tuominen H.K., Orlov V.N., Lahti R., Baykov A.A. (2015) Cystathionine beta-Synthase (CBS) Domain-containing Pyrophosphatase as a Target for Diadenosine Polyphosphates in Bacteria. J. Biol. Chem., 290 (46): 27594-27603. >>

  3. Love A.J., Makarov V.V., Sinitsyna O.V., Shaw J., Yaminsky I.V., Kalinina N.O., Taliansky M.E. (2015) A Genetically Modified Tobacco Mosaic Virus that can Produce Gold Nanoparticles from a Metal Salt Precursor. Front. Plant Sci., 6: . >>

  4. Clare D.K., Pechnikova E.V., Skurat E.V., Makarov V.V., Sokolova O.S., Solovyev A.G., Orlova E.V. (2015) Novel Inter-Subunit Contacts in Barley Stripe Mosaic Virus Revealed by Cryo-Electron Microscopy. Structure, 23 (10): 1815-1826. >>

  5. Makarov V.V., Makarova S.S., Makhotenko A.V., Obraztsova E.A., Kalinina N.O. (2015) In vitro properties of hordeivirus TGB1 protein forming ribonucleoprotein complexes. J. Gen. Virol., 96: 3422-3431. >>

  6. Makshakova O.N., Semenyuk P.I., Kuravsky M.L., Ermakova E.A., Zuev Y.F., Muronetz V.I. (2015) Structural basis for regulation of stability and activity in glyceraldehyde-3-phosphate dehydrogenases. Differential scanning calorimetry and molecular dynamics. J. Struct. Biol., 190 (2): 224-235. >>

  7. Lazarev V.F., Benken K.A., Semenyuk P.I., Sarantseva S.V., Bolshakova O.I., Mikhaylova E.R., Muronetz V.I., Guzhova I.V., Margulis B.A. (2015) GAPDH binders as potential drugs for the therapy of polyglutamine diseases: Design of a new screening assay. FEBS Lett., 589 (5): 581-587. >>

  8. Semenyuk P.I., Orlov V.N., Kurochkina L.P. (2015) Effect of chaperonin encoded by gene 146 on thermal aggregation of lytic proteins of bacteriophage EL Pseudomonas aeruginosa. Biochem.-Moscow, 80 (2): 172-179. >>

  9. Semenyuk P.I., Moiseeva E.V., Stroylova Y.Y., Lotti M., Izumrudov V.A., Muronetz V.I. (2015) Sulfated and sulfonated polymers are able to solubilize efficiently the protein aggregates of different nature. Arch. Biochem. Biophys., 567: 22-29. >>

  10. Chalova A.S., Sudnitsyna M.V., Semenyuk P.I., Orlov V.N., Gusev N.B. (2014) Effect of disulfide crosslinking on thermal transitions and chaperone-like activity of human small heat shock protein HspB1. Cell Stress Chaperones, 19 (6): 963-972. >>

  11. Stroylova Y.Y., Semenyuk P.I., Asriyantz R.A., Gaillard C., Haertle T., Muronetz V.I. (2014) Creation of Catalytically Active Particles From Enzymes Crosslinked with a Natural Bifunctional Agent-Homocysteine Thiolactone. Biopolymers, 101 (9): 975-984. >>

  12. Makarov V.V., Makarova S.S., Love A.J., Sinitsyna O.V., Dudnik A.O., Yaminsky I.V., Taliansky M.E., Kalinina N.O. (2014) Biosynthesis of Stable Iron Oxide Nanoparticles in Aqueous Extracts of Hordeum vulgare and Rumex acetosa Plants. Langmuir, 30 (20): 5982-5988. >>

  13. Dobrov E.N., Nikitin N.A., Trifonova E.A., Parshina E.Y., Makarov V.V., Maksimov G.V., Karpova O.V., Atabekov J.G. (2014) beta-structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation. J. Biomol. Struct. Dyn., 32 (5): 701-708. >>

  14. Semenyuk P.I., Muronetz V.I., Haertle T., Izumrudov V.A. (2013) Effect of poly(phosphate) anions on glyceraldehyde-3-phosphate dehydrogenase structure and thermal aggregation: comparison with influence of poly(sulfoanions). Biochim. Biophys. Acta-Gen. Subj., 1830 (10): 4800-4805. >>

  15. Ksenofontov A.L., Paalme V., Arutyunyan A.M., Semenyuk P.I., Fedorova N.V., Rumvolt R., Baratova L.A., Jarvekulg L., Dobrov E.N. (2013) Partially Disordered Structure in Intravirus Coat Protein of Potyvirus Potato Virus A. PLoS One, 8 (7): . >>

  16. Makarov V.V., Skurat E.V., Semenyuk P.I., Abashkin D.A., Kalinina N.O., Arutyunyan A.M., Solovyev A.G., Dobrov E.N. (2013) Structural Lability of Barley Stripe Mosaic Virus Virions. PLoS One, 8 (4): . >>

  17. Volkov D.S., Semenyuk P.I., Korobov M.V., Proskurnin M.A. (2012) Quantification of nanodiamonds in aqueous solutions by spectrophotometry and thermal lens spectrometry. J. Anal. Chem., 67 (10): 842-850. >>

  18. Kurochkina L.P., Semenyuk P.I., Orlov V.N., Robben J., Sykilinda N.N., Mesyanzhinov V.V. (2012) Expression and Functional Characterization of the First Bacteriophage-Encoded Chaperonin. J. Virol., 86 (18): 10103-10111. >>

  19. Makarov V.V., Iconnikova A.Y., Guseinov M.A., Vishnichenko V.K., Kalinina N.O. (2012) In vitro phosphorylation of the N-terminal half of hordeivirus movement protein. Biochem.-Moscow, 77 (9): 1072-1081. >>

  20. Eroshenko L.V., Marakhovskaya A.S., Vangeli I.M., Semenyuk P.I., Orlov V.N., Yaguzhinsky L.S. (2012) Bronsted Acids Bounded to the Mitochondrial Membranes as a Substrate for ATP Synthase. Dokl. Biochem. Biophys., 444 (1): 158-161. >>

  21. Makarova S.S., Minina E.A., Makarov V.V., Semenyuk P.I., Kopertekh L., Schiemann J., Serebryakova M.V., Erokhina T.N., Solovyev A.G., Morozov S.Y. (2011) Orthologues of a plant-specific At-4/1 gene in the genus Nicotiana and the structural properties of bacterially expressed 4/1 protein. Biochimie, 93 (10): 1770-1778.

  22. Moiseeva V.S., Motovilov K.A., Lobysheva N.V., Orlov V.N., Yaguzhinsky L.S. (2011) The formation of metastable bond between protons and mitoplast surface. Doklady Biochemistry and Biophysics, 438 (1): 127-130.

  23. Davydov D.A., Romanyuk A.V., Rakhnyanskaya A.A., Semenyuk P.I., Orlov V.N., Samoshin V.V., Yaroslavov A.A. (2011) Cationic Polymer Adsorption on Bilayer Membrane Containing Anionic and Cationic Lipids. Colloid Journal, 73 (1): 33-38.

  24. Chernorizov K.A., Elkina J.L., Semenyuk P.I., Svedas V.K., Muronetz V.I. (2010) Novel Inhibitors of Glyceraldehyde-3-phosphate Dehydrogenase: Covalent Modification of NAD-Binding Site by Aromatic Thiols. Biochemistry-Moscow, 75 (12): 1444-1449.

  25. Davydov D.A., Rakhnyanskaya A.A., Orlov V.N., Bychkova A.V., Kovarskii A.L., Yaroslavov A.A. (2010) Complexes of Anionic Liposomes and a Cationic Polymer: Composition, Structure, and Characteristics. Polymer Science Series A, 52 (7): 693-703.

  26. Makarov V.V., Obraztsova E.A., Solovyev A.G., Morozov S.Y., Taliansky M.E., Yaminsky I.V., Kalinina N.O. (2010) The internal domain of hordeivirus movement protein TGB1 forms in vitro filamentous structures. Biochemistry-Moscow, 75 (6): 752-758.

  27. Maloletkina O.I., Markossian K.A., Asryants R.A., Semenyuk P.I., Makeeva V.F., Kurganov B.I. (2010) Effect of 2-hydroxypropyl-beta-cyclodextrin on thermal inactivation, denaturation and aggregation of glyceraldehyde-3-phosphate dehydrogenase from rabbit skeletal muscle. International Journal of Biological Macromolecules, 46 (5): 487-492.

  28. Maloletkina O.I., Markossian K.A., Belousova L.V., Kleimenov S.Y., Orlov V.N., Makeeva V.F., Kurganov B.I. (2010) Thermal stability and aggregation of creatine kinase from rabbit skeletal muscle. Effect of 2-hydroxypropyl-beta-cyclodextrin. Biophysical Chemistry, 148 (1): 121-130.

  29. Rakhnyanskaya A.A., Pebalk I.D., Orlov V.N., Gritskova I.A., Prokopov N.I., Yaroslavov A.A. (2010) Controlled Adsorption-Desorption of Cationic Polymers on the Surface of Anionic Latex Particles. Polymer Science Series A, 52 (5): 483-489.

  30. Makarov V.V., Rybakova E.N., Efimov A.V., Dobrov E.N., Serebryakova M.V., Solovyev A.G., Yaminsky I.V., Taliansky M.E., Morozov S.Y., Kalinina N.O. (2009) Domain organization of the N-terminal portion of hordeivirus movement protein TGBpl. Journal of General Virology, 90: 3022-3032.

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