Ковальчук Сергей Игоревич

Кандидат химических наук

Младший научный сотрудник (Лаборатория протеомики)

Тел.: +7 (495) 000-00-00

Эл. почта: xerx222@gmail.com

Избранные публикации

  1. Kuzmenkov A.I., Sachkova M.Y., Kovalchuk S.I., Grishin E.V., Vassilevski A.A. (2016). Lachesana tarabaevi, an expert in membrane-active toxins. Biochem. J. 473 (16), 2495–506 [+]

    In the present study, we show that venom of the ant spider Lachesana tarabaevi is unique in terms of molecular composition and toxicity. Whereas venom of most spiders studied is rich in disulfide-containing neurotoxic peptides, L. tarabaevi relies on the production of linear (no disulfide bridges) cytolytic polypeptides. We performed full-scale peptidomic examination of L. tarabaevi venom supported by cDNA library analysis. As a result, we identified several dozen components, and a majority (∼80% of total venom protein) exhibited membrane-active properties. In total, 33 membrane-interacting polypeptides (length of 18-79 amino acid residues) comprise five major groups: repetitive polypeptide elements (Rpe), latarcins (Ltc), met-lysines (MLys), cyto-insectotoxins (CIT) and latartoxins (LtTx). Rpe are short (18 residues) amphiphilic molecules that are encoded by the same genes as antimicrobial peptides Ltc 4a and 4b. Isolation of Rpe confirms the validity of the iPQM (inverted processing quadruplet motif) proposed to mark the cleavage sites in spider toxin precursors that are processed into several mature chains. MLys (51 residues) present 'idealized' amphiphilicity when modelled in a helical wheel projection with sharply demarcated sectors of hydrophobic, cationic and anionic residues. Four families of CIT (61-79 residues) are the primary weapon of the spider, accounting for its venom toxicity. Toxins from the CIT 1 and 2 families have a modular structure consisting of two shorter Ltc-like peptides. We demonstrate that in CIT 1a, these two parts act in synergy when they are covalently linked. This finding supports the assumption that CIT have evolved through the joining of two shorter membrane-active peptides into one larger molecule.

  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.

  3. Shender V.O., Pavlyukov M.S., Ziganshin R.H., Arapidi G.P., Kovalchuk S.I., Anikanov N.A., Altukhov I.A., Alexeev D.G., Butenko I.O., Shavarda A.L., Khomyakova E., Evtushenko E., Ashrafyan L.A., Antonova I.B., Kuznetcov I.N., Gorbachev A.Y., Shakhparonov M.I., Govorun V.M. (2014). Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication. Mol. Cell Proteomics , [+]

    Ovarian cancer ascites is a native medium for cancer cells that allows investigation of their secretome in natural environment. This medium is of interest as a promising source of potential biomarkers and also as a medium for cell-cell communication. The aim of this study was to elucidate specific features of malignant ascites metabolome and proteome. To omit components that belong to systemic response to the ascites formation we compared malignant ascites with cirrhosis one. Metabolome analysis revealed 41 components that differed significantly between malignant and cirrhosis ascites. Most of the identified cancer-specific metabolites are known to be important signaling molecules. Proteomic analysis identified 2096 and 1855 proteins in the ovarian cancer and cirrhosis ascites, respectively, 424 proteins were specific for the malignant ascites. Functional analysis of the proteome demonstrated that the major differences between cirrhosis and malignant ascites were observed for the cluster of spliceosomal proteins. Additionally, we demonstrated that several splicing RNAs were exclusively detected in malignant ascites, where they probably existed within protein complexes. This result was confirmed in vitro using an ovarian cancer cell line. Identification of spliceosomal proteins and RNAs in an extracellular medium is of particular interest, the finding suggests that they may play a role in the communication between cancer cells. Besides, malignant ascites contains a high number of exosomes that are known to play an important role for signal transduction. Thus our study reveals the specific features of malignant ascites that are associated with its function as a medium of intercellular communication.

  4. 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.