Biology subjects

Egorov, V. V.

Publications and source records attributed to Egorov, V. V..

11 recordsLinked to original sources

bioRxiv2024

Stick of Sticks: Structural Features of the Amyloidogenic Peptide-DNA Complex

The search for peptides that can specifically bind to regulatory regions in DNA is a necessary step for creating drugs that can regulate gene expression. The study is dedicated to the peculiarities of binding of a model peptide, which carries an ionic self-complementary motif and can form amyloid-like fibrils [1], with model double-stranded DNAs. The stoichiometric ratios of the components of the complex were found using the retardation method in agarose gel. Using microscale thermophoresis, it was shown that the peptide in the amyloid-like state is capable of binding to model 45-bp double-stranded DNA, with a micromolar equilibrium dissociation constant. Using cryo-electron, transmission electron, and atomic force microscopy, the morphology of peptide-DNA complexes was studied. Using dynamic light scattering and nanoparticle tracking analysis, as well as small-angle neutron scattering, the spatial parameters of the resulting DNA-peptide complexes were characterized. Molecular dynamics simulations showed that the arginine side chains of the peptide are prone to interact with guanine nitrogenous bases. It was shown that the formation of peptide-dsDNA complexes interferes with the operation of restriction endonucleases that have guanine-cytosine pairs in the recognition center, which is consistent with the results of prediction of interaction sites obtained using computer modeling. The results of the work can be used in the development of peptides capable of interacting with functional regions of DNA, as well as in the development of new carriers for transfection of DNA constructs.

biophysics↗

bioRxiv2024

Spontaneous formation of different forms of alpha-synuclein fibrils from a recombinant protein

Alpha-synuclein is a protein, the conformational changes of which lead to the development of such socially significant diseases as Parkinsons disease and amyotrophic lateral sclerosis. The methods for differential diagnostics of these diseases based on the use of alpha-synuclein in a non-native conformation obtained from patients as a seed for inducing fibrillogenesis and studying the morphology of the resulting amyloid-like fibrils were described in a number of studies. The authors associate such properties of the seed with the presence of post-translational modifications in the protein obtained from patients. At the same time, the production of fibrils differing in morphology from recombinant alpha-synuclein under various conditions of fibrillogenesis is also described. In this work, we show that the formation of morphologically distinct fibril types from recombinant alpha-synuclein lacking post-translational modifications is possible under the same conditions, and that spontaneously arising different fibril types, when used as a seed for fibrillogenesis, lead to the formation of recombinant protein fibrils morphological similar to the parental seed. The results of the work can be used both in studying the fundamental mechanisms of conformation transfer and in developing test systems for synucleinopathies.

molecular biology↗

bioRxiv2024

MANGIFERIN AS A POTENTIAL INHIBITOR OF TRANSTHYRETIN FIBRILOGENESIS

By using in silico molecular docking, we predicted a high potential of mangiferin to inhibit transthyretin amyloidogenesis. Subsequently, we tested this prediction in an in vitro system. The study involved testing effect of mangiferrin in a system that included isolated and purified recombinant transthyretin under fibrillogenesis conditions and a detection assay based on the fluorescent dye thioflavin T, characteristic of amyloid fibrils. The conditions for fibrillogenesis of this protein at neutral pH values were established. Using the developed test system, it was shown that mangiferin is able to inhibit abnormal transthyretin fibrillogenesis.

molecular biology↗

bioRxiv2023

How the immune mousetrap works: structural evidence for the immunomodulatory action of a peptide from influenza NS1 protein

One of the critical stages of the T-cell immune response is the dimerization of the intramembrane domains of T-cell receptors (TCR). Structural similarities between the immunosuppressive domains of viral proteins and the transmembrane domains of TCR have led several authors to hypothesize the mechanism of immune response suppression by highly pathogenic viruses: viral proteins embed themselves in the membrane and act on the intramembrane domain of the TCRalpha subunit, hindering its functional oligomerization. It has also been suggested that this mechanism is used by influenza A virus in NS1-mediated immunosuppression. We have shown that the peptide corresponding to the primary structure of the potential immunosuppressive domain of NS1 protein (G51) can reduce concanavalin A-induced proliferation of PBMC cells, as well as in vitro, G51 can affect the oligomerization of the core peptide corresponding to the intramembrane domain of TCR, using AFM and small-angle neutron scattering. The results obtained using in cellulo and in vitro model systems suggest the presence of functional interaction between the NS1 fragment and the intramembrane domain of the TCR alpha subunit. We have proposed a possible scheme for such interaction obtained by computer modeling. This suggests the existence of another NS1-mediated mechanism of immunosuppression in influenza. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/573289v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@12b4ce4org.highwire.dtl.DTLVardef@1c53557org.highwire.dtl.DTLVardef@30f519org.highwire.dtl.DTLVardef@2b71bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

Inside and outside of virus-like particles HBc and HBc/4M2e: a comprehensive study of the structure

The structure of the core particles of the hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) have been studied using a combination of molecular modeling and cryogenic electron microscopy (cryo-EM). It has also been shown that synthesis of particles occurs inside bacterial cells, but despite the big inner volume of the core shell particle, purified HBc/4M2e do not contain detectable amounts of bacterial proteins. It has been shown that a fragment of the M2e is prone to the formation of amyloid-like fibrils. However, as a part of HBc immunodominant loop M2e domains as repeats, does not exhibit a tendency to aggregation. Full-atom HBc-4M2E model with 3A resolution was obtained by molecular modeling methods based on cryo-EM data.

biophysics↗

bioRxiv2022

Peptide from NSP7 is able to form amyloid-like fibrils: artifact or challenge to drug design?

Using a set of programs for analyzing the primary structure of amyloidogenic proteins, we analyzed the primary structure of the of the COVID-19 NSP7 protein. Peptides containing potential amyloidogenic determinants in the primary structure have been synthesized and shown to be capable of forming amyloid-like fibrils in vitro. In the future, this peptide can be used as a basis for creating antiviral agents that act directly on the spatial structure of the NSP7 subunit of the COVID-19 polymerase.

molecular biology↗

bioRxiv2020

THE MATRIX IS EVERYWHERE: CACO3 BIOMINERALIZATION BY THE BACILLUS LICHENIFORMIS PLANKTONIC CELLS

To date, the mechanisms of CaCO3 nucleus formation and crystal growth induced by bacterial cells still remain debatable. Here, an insight on the role of planktonic cells of Bacillus licheniformis DSMZ 8782 in the biomineralization is presented. We showed that during 14-days bacterial growth in a liquid urea/Ca2+-containing medium the transformation of CaCO3 polymorphs followed the classical pathway "ACC-vaterite-calcite/aragonite". By microscopic techniques, we detected the formation of extracellular matrix (ECM) around the cells at the stage of exponential growth and appearance of electron-dense inclusions at 24 h after the inoculation. The cells formed filaments and created a network, the nodes of which served as sites for further crystal growth. The ECM formation accompanied with the expression of proteins required for biofilm formation, the aldehyde/alcohol dehydrogenase, stress-associated Clp family proteins, and a porin family protein (ompA ortholog) associated with bacterial extracellular vesicles. We demonstrated that urea and CaCl2 acted as denaturing agents causing matrix formation in addition to their traditional role as a source of carbonate and Ca2+ ions. We showed that CaCO3 nucleation occured inside B. licheniformis cells and further crystal growth and polymorphic transformations took place in the extracellular matrix without attaching to the cell surface. The spatial arrangement of the cells was important for the active crystal growth and dependent on environmental factors. The extracellular matrix played a double role being formed as a stress response and providing a favorable microenvironment for biomineralization (a high concentration of ions necessary for CaCO3 crystal aggregation, fixation and stabilization).

microbiology↗

bioRxiv2019

Time machine: Can a dye from 1928 be re-purposed for modern, fluorescence-based detection of amyloid-like fibrils?

This manuscript describes the chemical synthesis of a compound similar to fluorene and Congo red, including characterization of its spectral properties. It was shown that the dye, during interaction with amyloid-like fibrils of several proteins (lysozyme, insulin, and beta-2-microglobulin), has the ability to change fluorescent spectrum. In contrast, monomeric forms of these proteins did not induce significant spectral changes.

biochemistry↗

bioRxiv2018

Changing Times: Fluorescence-lifetime Analysis of Amyloidogenic SF-IAPP Fusion Protein

The fluorescence lifetime of the superfolder green fluorescent protein (SF) and the SF protein fused with islet amyloid polypeptide (SF-IAPP) were studied in polyacrylamide gel. It was shown that the SF average fluorescence lifetime under these conditions slightly differs from that of the SF-IAPP monomer. SF-IAPP does not lose the ability to form amyloid-like fibrils; meanwhile, the average fluorescence lifetime of the fusion protein in fibrils is reduced. We propose the application of Fluorescent-lifetime Imaging Microscopy (FLIM) to the measurement of average fluorescence lifetimes of fusion proteins (amyloidogenic protein-SF) in the context of studies using cellular models of conformational diseases.

biophysics↗

bioRxiv2018

A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation

Triazavirine (TZV), a small molecule with a broad spectrum of antiviral activity, shows a tendency to induce the aggregation of melittin (MLT), a cationic membrane-disrupting peptide from the poison of the European bee. In MLT:TZV mixtures, high molecular weight precipitates form once a critical MLT:TZV ratio has been exceeded. Molecular dynamics simulation of MLT-TZV interactions, followed by molecular docking, led us to the hypothesis of multicenter binding of TZV supramolecular complexes to MLT.

biophysics↗

bioRxiv2017

The amyloidogenicity of the influenza virus PB1-derived peptide sheds light on its antiviral activity

The influenza virus polymerase complex is a promising target for new antiviral drug development. It is known that, within the influenza virus polymerase complex, the PB1 subunit region from the 1st to the 25th amino acid residues has to be is in an alpha-helical conformation for proper interaction with the PA subunit. We have previously shown that PB1(6-13) peptide at low concentrations is able to interact with the PB1 subunit N-terminal region in a peptide model which shows aggregate formation and antiviral activity in cell cultures.\n\nIn this paper, it was shown that PB1(6-13) peptide is prone to form the amyloid-like fibrillar aggregates. The peptide homo-oligomerization kinetics were examined, and the affinity and characteristic interaction time of PB1(6-13) peptide monomers and the influenza virus polymerase complex PB1 subunit N-terminal region were evaluated by the SPR and TR-SAXS methods. Based on the data obtained, a hypothesis about the PB1(6-13) peptide mechanism of action was proposed: the peptide in its monomeric form is capable of altering the conformation of the PB1 subunit N-terminal region, causing a change from an alpha helix to a beta structure. This conformational change disrupts PB1 and PA subunit interaction and, by that mechanism, the peptide displays antiviral activity.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC=\"FIGDIR/small/211284_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (77K):\norg.highwire.dtl.DTLVardef@185db47org.highwire.dtl.DTLVardef@ff2fd2org.highwire.dtl.DTLVardef@19c8587org.highwire.dtl.DTLVardef@10282b1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗