Publications by authors named "Skvortsov V"

Data from a mass spectrometry experiment of a mouse line developed to study the mechanisms of fibromuscular dysplasia and deposited by d'Escamard et al. in ProteomeXchange (PXD051750) have been analyzed. Identification of peptides with post-translational modifications (PTMs) was repeated using more stringent conditions than in the original work.

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A set of linear regression equations predicting the IC50 values for SARS-CoV-2 main protease inhibitors was analyzed. For 180 competitive inhibitors, we have simulated the molecular dynamics of enzyme-inhibitor complexes with known structures or modeled using molecular docking. In the docking procedure, the selection of final poses was restricted by similarity to known structural analogs.

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The antibodies of schizophrenic patients that hydrolyze myelin basic protein (MBP) have been actively studied recently, but the mechanism of the catalytic properties of immunoglobulin molecules remains unknown. Determination of specific immunoglobulin sequences associated with the high activity of MBP proteolysis will help to understand the mechanisms of abzyme catalysis. In the course of comparative mass spectrometric analysis of IgG peptides from the blood serum of patients with acute schizophrenia and healthy people, 12 sequences were identified, which were found only in antibodies that hydrolyze MBP.

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Background: Primary hyperparathyroidism (PHPT) is a common endocrine disorder caused by a parathyroid tumor or hyperplasia, which is often accompanied with quality of life (QoL) impairment. A parathyroidectomy (PTX) is the preferred standard treatment for PHPT patients. In this single center study we aimed to evaluate the impact of PHPT on patient's QoL and identify QoL changes at early and long-term follow-up after surgery.

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The paper analyzes a set of equations that adequately predict the IC50 value for SARS-CoV-2 main protease inhibitors. The training set was obtained using filtering by criteria independent of prediction of target value. It included 76 compounds, and the test set included nine compounds.

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The experimental results available in the ProteomeXchange database (accession code PXD016538) (Simats et al. (2020) Molecular and Cellular Proteomics, 19(12), 1921-1936) obtained using a comprehensive multi-omics approach were analyzed in mouse blood to identify potential biomarkers of ischemic stroke. Acetylation, methylation, and ubiquitination were considered as post-translational modifications.

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The experimental data obtained by Simats A. et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936) was analysed using a bioinformatic approach.

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Several variants of models for predicting the IC values of inhibitors of influenza virus neuraminidase are presented for both individual strains and also for combinations of data for neuraminidases of several strains. They are based on the use of calculated energy contributions to the amount of change in the free energy of enzyme-inhibitor complexes. In contrast to previous works, aimed at the complex modeling, we added a procedure of comparison of the docking variants with one of the neuraminidase inhibitors, for which the structure of the complexes was determined experimentally.

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Several variants of models for predicting the IC50 values of inhibitors of influenza virus neuraminidase are presented for both individual strains and for combinations of data for neuraminidases of several strains. They are based on the use of calculated energy contributions to the amount of change in the free energy of enzyme-inhibitor complexes. In contrast to previous works, aimed at the complex modeling, we added a procedure of comparison of the docking variants with one of the neuraminidase inhibitors, for which the structure of the complexes was determined experimentally.

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Unlabelled: The relevance of the research is determined by the growth of cases of abdominal tuberculosis (AT), which is difficult to diagnose.

Aim: Identify clinical features and possibilities of timely AT diagnosis.

Materials And Methods: Medical reports of 116 AT patients.

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The overall model for prediction of IC50 values for inhibitors of neuraminidase influenza virus A and B has been created. It combines data about IC50 values of complexes of 40 variants of neuraminidases of influenza A (7 serotypes) and B and three known inhibitors (oseltamivir, zanamivir, peramivir). The model also uses only data of enthalpy contributions to the potential energy of inhibitor/protein and substrate (MUNANA)/protein complexes.

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The development of molecular techniques of research in the end of XX century permitted to broaden nomenclature of species forming genus Staphylococcus that nowadays numbers 51 species and 27 sub-species. The pathogenic species of genus have a capacity to coagulate blood plasma of mammals forming group of coagulase-positive staphylococci including 7 species: S. aureus, S.

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Preliminary results of construction of overall model for prediction of IC50 value of ligands of influenza virus neuraminidase of any strain are presented. We used MM-PBSA (MM-GBSA) energy terms calculated for the complexes obtained after modeling of 30 variants of neuraminidase structures, subsequent docking and simulation of molecular dynamics as independent variables in prediction equations. The structures of known neuraminidase-inhibiting drugs (oseltamivir, zanamivir and peramivir) and a neuraminidase substrate (MUNANA) were used as ligands.

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The aim of this study was to evaluate sequence coverage of five model proteins (CYB5A, SMAD4, RAB27B, FECH, and CXXC1) by means of shotgun proteomic data analysis employing different methods of data treatment including database-dependent search engines (MASCOT and X!Tandem) and de novo sequencing software ((PEAKS, Novor, and PepNovo+). In order to achieve maximal results, multiprotease hydrolysis including enzymes trypsin, LYS-C, ASPN and GluC was performed in solution and using the FASP method. High resolution mass spectrometry was carried out with a Q EXACTIVE HF hybrid mass spectrometer in the positive ionization mode; parent ions with the highest intensity and a charge range from +2 to +6 were fragmented in the HCD mode.

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Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) ("Sigma-Aldrich", USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS was performed using pure UPS2 and UPS2 mixtures with E.

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Virtual electrophoresis in proteomics can be used to search localization of proteins and their proteoforms (especially those existing in low concentrations), to identify proteoforms found in experiments etc. Although the problem of predicting the isoelectric point is well studied, the need of electrophoretic shift correction is usually ignored. Researchers simply use the brutto molecular weight of the protein.

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There were two sources of ionizing irradiation after the atomic bombings of Hiroshima and Nagasaki: (1) initial gamma-neutron irradiation at the moment of detonation and (2) residual radioactivity. Residual radioactivity consisted of two components: radioactive fallout containing fission products, including radioactive fissile materials from nuclear device, and neutron-activated radioisotopes from materials on the ground. The dosimetry systems DS86 and DS02 were mainly devoted to the assessment of initial radiation exposure to neutrons and gamma rays, while only brief considerations were given for the estimation of doses caused by residual radiation exposure.

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A universal model of inhibition of neuraminidases from various influenza virus strains by a particular has been developed. It is based on known 3D data for neuraminidases from three influenza virus strains (A/Tokyo/3/67, A/tern/Australia/G70C/75, B/Lee/40) and modeling of 3D structure of neuraminidases from other strains (A/PR/8/34 è A/Aichi/2/68). Using docking and molecular dynamics, we have modeled 235 enzyme-ligand complexes for 89 compounds with known IC50 values.

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The method of electron paramagnetic resonance (EPR) dosimetry using extracted teeth has been applied to human tooth enamel to obtain individual absorbed doses of residents of settlements in the vicinity of the central axis of radioactive fallout trace from the contaminating surface nuclear test on 7 August 1962. Most of the settlements (Kurchatov, Akzhar, Begen, Buras, Grachi, Mayskoe, Semenovka) are located from 70 to 120 km to the North-East from the epicenter of the explosion at the Semipalatinsk Nuclear Test Site (SNTS). This region is basically an agricultural region.

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The cytotoxic activity of synthetic progestins (pregna-D'-pentaranes) II-V full agonists of the progesterone receptor (PR) for PR-positive and PR-negative cells of human breast carcinoma was studied. These compounds were more active in the PR-positive MCF-7 cells than in the PR-negative MDA-MB-453 cells. Cytotoxic effects of tested compounds against normal epithelial MDCK cells were not found.

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The aim of the study is to determine the average intensity and variation of the native background signal amplitude (NSA) and of the solar light-induced signal amplitude (LSA) in electron paramagnetic resonance (EPR) spectra of tooth enamel for different kinds of teeth and different groups of people. These values are necessary for determination of the intensity of the radiation-induced signal amplitude (RSA) by subtraction of the expected NSA and LSA from the total signal amplitude measured in L-band for in vivo EPR dosimetry. Variation of these signals should be taken into account when estimating the uncertainty of the estimated RSA.

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This review elucidates the data on etiology and pathogenesis of functional (unulcerous) dyspepsia, clinical features, diagnostic, therapeutic and prophylactic approaches to this pathology.

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The changes in the nomenclature of species in the genus Staphylococcus, including the most pathogenic cluster of the coagulase-positive staphylococci, are represented. Presently, besides S. aureus, this cluster consists of 6 species: S.

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ProteoCat is a computer program has been designed to help researchers in the planning of large-scale proteomic experiments. The central part of this program is the subprogram of hydrolysis simulation that supports 4 proteases (trypsin, lysine C, endoproteinases AspN and GluC). For the peptides obtained after virtual hydrolysis or loaded from data file a number of properties important in mass-spectrometric experiments can be calculated or predicted.

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