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The accuracy of the rapid equilibrium assumption in steady-state enzyme kinetics in the case of a multipath arbitrary enzyme mechanism with a number of equilibrium segments

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Biophysics (Russian Federation) 2016年第3期61卷 373-379页

作者： Vrzheshch, P.V. Faculty of Bioengineering and Bioinformatics Moscow State University International Biotechnological Center Moscow 119991 Russian Federation

A quantitative evaluation of the accuracy of the rapid-equilibrium assumption in steady-state enzyme kinetics was obtained for a multipath arbitrary enzyme mechanism with a number of equilibrium segments. Explicit expressions for estimating the contribution of any equilibrium segment to the accuracy of the rapid-equilibrium assumption were obtained. This allowed us to determine the accuracy of the rapid-equilibrium assumption (Δ) in general: 1 + Δ = (1 + Δ₁)(1 + Δ₂).. (1 + Δ_k), where Δ₁, Δ₂,.., Δ_k is the contribution of each individual equilibrium segment. The accuracy depends only on the structure and properties of equilibrium segments, which have been accounted for in the rapid-equilibrium assumption, but it is independent of the number of paths in the mechanism of the enzymatic reaction and on the structure and properties of the remaining part (steady-state) of the kinetic scheme. © 2016, Pleiades Publishing, Inc.

关键词： accuracy of assumption equilibrium segments graph theory multipath enzyme mechanisms rapid-equilibrium assumption steady-state enzyme kinetics

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[Statistical methods of comparative genomic analysis based on diffusion processes].

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Biofizika 2013年第2期58卷 203-209页

作者： Soldatov, R.A. Mironov, A.A. Institute for Information Transmission Problems Russian Academy of Sciences Moscow Russia Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russia

Comparative genomics is a powerful tool of genome functional specificity predictions and investigation of evolution specificity. Background of a large field of bioinformatics investigations is a computation of different scores of sequences and comparing them with a threshold. Comparative genomic analysis involves scores comparing for orthological groups of genetic objects. In this paper we represent a statistical approach to comparative genomic analysis, that based on investigation of diffusion in sequence space determined by neutral evolution of sequences. Using this approach we represent several statistics for selection pressure estimation and analyze statistics for several biological problems. We formulate technology of statistics applying to obtain new biological information. This approach is represented as Java-class library.

关键词： comparative genomics diffusion process molecular evolution phenotype selection

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Ultrastructure of yeast cell Saccharomyces cerevisiae after amiodarone treatment

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Cell and Tissue Biology 2010年第1期4卷 90-95页

作者： Ozhovan, S.M. Knorre, D.A. Severin, F.F. Bakeeva, L.E. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russian Federation Belozerskii Institute of Physical-Chemical Biology Moscow State University Moscow Russian Federation

The ultrastrcutre of Saccharomyces cerevisiae cells (wild-type and ysp2 mutant cells) was studied after amiodarone treatment. Amiodarone is used as a pharmaceutical substance for treating a number of diseases;however, it is known that amiodarone causes structural and functional disturbances in patient tissues. Here, the peculiarities of the amiodarone effect are studied in Saccharomyces cerevisiae yeast, in which amiodarone has been shown to cause apoptosis. Electron-microscopic study of yeast cells after amiodarone treatment reveals a significant increase in the number of lipid particles, which can lead to the formation of a structural complex by interacting with cell membranous organelles. Amiodarone causes the appearance of small and slightly swollen mitochondria. Chromatin displacement to the periphery of the nucleus, nuclear sectioning, and nuclear envelope disturbances are observed in the cells under these conditions. The detected changes int eh ultrastructure of the cell in Saccharomyces cerevisiae are considered to be a specific response to phospholipidosis and apoptosis caused by amiodarone. © 2010 Pleiades Publishing, Ltd.

关键词： Amiodarone Apoptosis Cell ultrastructure Lipid particles (LP) Phospholipidosis Yeast Saccharomyces cerevisiae

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Volatilomics and Lipidomics revealed flavoring mechanism in baijiu brewed from diverse Sorghum varieties

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Food Chemistry 2025年 485卷 144503页

作者： Zhu, Hui Li, Linjuan Ma, Yi Luo, Huibo El-Sappah, Ahmed H. Liu, Ying Sun, Xiaoke Pan, Shijiang Mehmood, Muhammad Aamer Sun, Yong Wang, Ning Sichuan Province Engineering Technology Research Center of Liquor-Making Grains School of Bioengineering Sichuan University of Science and Engineering Yibin644000 China Liquor Making Biotechnology and Intelligent Manufacturing of Key Laboratory of China National Light Industry Yibin644000 China State Key Laboratory of Food Science and Resources Nanchang University Nanchang330047 China College of Agriculture Forestry and Food Engineering Yibin University Yibin644000 China Genetics Department Faculty of Agriculture Zagazig University Zagazig44511 Egypt Sichuan Yibin Hengshengfu Liquor Industry Group Co. Ltd Yibin644000 China Yibin City Agricultural and Rural Bureau Yibin644000 China Department of Bioinformatics and Biotechnology Government College University Faisalabad Faisalabad Pakistan

Sorghum is crucial in Baijiu brewing. Previous studies have shown that glutinous sorghum (LS) and non-glutinous sorghum (FS) significantly affect Zaopei's lipid metabolism and lipids affect flavor perception. This study aimed to explore the quality differences in Baijiu brewed with different sorghum varieties and the effects of lipids. Sensory evaluation, volatilomics, and lipidomics were used to analyze differences in flavors and lipids. The results showed that significant differences in flavor existed between the two types of Baijiu. The aged flavor of LS was more pronounced and its mouthfeel was smoother. However, the FS showed a more intense aroma release. In addition, FA 18:1;O3 (fatty acyls), acetaldehyde, and ethyl caprylate contributed to the smoothness and softness of Baijiu. These results suggest that the lipid composition of Baijiu affects its aroma and taste, thus providing a reference basis for selecting suitable raw sorghum materials to enhance the quality of Baijiu. © 2025 The Author(s)

关键词： Flavor compounds

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High-performance computing in bioinformatic analysis of protein superfamilies to design enzymes with new properties 1

High-performance computing in bioinformatic analysis of prot...

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1st Russian Conference on Supercomputing Days 2015, RuSCDays 2015

作者： Suplatov, D. Popova, N. Kopylov, K. Shegai, M. Voevodin, V. Švedas, V. Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physicochemical Biology Russia Faculty of Computational Mathematics and Cybernetics Russia Faculty of Chemistry Russia Research Computing Center Russia

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Effect of 4-(Trifluoromethoxy)phenylhydrazone Carbonyl Cyanide (FCCP) on FcεRI-Dependent Cytokine Production by RBL-2H3 Cells

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Moscow University Biological Sciences Bulletin 2023年第2期78卷 66-73页

作者： Pavlyuchenkova, A.N. Smirnov, M.S. Chelombitko, M.A. Belozersky Institute of Physicochemical Biology Moscow State University Moscow 119992 Russian Federation Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119992 Russian Federation

Abstract: Mast cells (MCs) play a key role in the development of allergic diseases. The interaction of antigens with immunoglobulin E and the subsequent binding of these complexes to the FcεRI receptor, which ultimately leads to rapid exocytosis of granules and subsequent production of cytokines, play a major role in MC activation in an allergy. There are data on the role of the mitochondrial membrane potential in the FcεRI-dependent activation of MCs. Thus, the use of classical uncouplers of oxidative phosphorylation reduces the level of MC degranulation. However, their effect on the production of MC cytokines has not been studied. In this work, it was demonstrated that pretreatment of RBL-2H3 MC with the uncoupler carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP) leads to a decrease not only in the level of FcεRI-dependent degranulation but also in the production of TNFα and IL-4 cytokines. At the same time, FCCP prevents the phosphorylation of the LAT adapter molecule, as well as the Erk1/2 kinase, which may underlie the inhibitory effect of the uncoupler on the FcεRI-dependent activation of RBL-2H3 cell line. The data obtained indicate that the mitochondrial membrane potential plays an important role in the FcεRI-dependent activation of MCs, and the uncoupling of oxidative phosphorylation and respiration of mitochondria with the help of uncouplers can be used to regulate this process. © 2023, Allerton Press, Inc.

关键词： allergy FCCP FcεRI-dependent activation mast cells mitochondria uncouplers

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Fluorescently controlled investigation of super-enhancers with CRISPR interference and CRISPR prime editing systems

Fluorescently controlled investigation of super-enhancers wi...

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2024 International Conference Laser Optics, ICLO 2024

作者： Orlova, N.N. Gladkova, M.G. Ashniev, G.A. Orlov, A.V. Prokhorov General Physics Institute of the Russian Academy of Sciences Moscow Russia Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Moscow Russia

ISBN: (纸本)9798350390674

In the evolving landscape of genomic research, our study delves into the intricate exploration of super-enhancers, pivotal and controversial elements exerting profound influence over gene expression. Utilizing CRISPR interference and CRISPR prime editing systems, our work yields promising results and opens avenues for future research to refine and expand these approaches across diverse cell types. © 2024 IEEE.

关键词： Gene expression

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Ten percent of conserved miRNA-binding sites in vertebrates are misaligned

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Biophysics (Russian Federation) 2017年第1期62卷 38-42页

作者： Prosvirov, K.A. Mironov, A.A. Soldatov, R.A. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119234 Russian Federation Institute for Information Transmission Problems Russian Academy of Sciences Moscow 127051 Russian Federation

MiRNAs are small endogenous noncoding RNAs that inhibit protein expression at the translation level via complementary binding to a specific site in the mRNA. Most of the functional binding sites (miRNA nucleotides 2–7) located within the 3' untranslated region are conserved. These sites are predicted using the methods of comparative genomics, primarily, multiple sequence alignment. However, multiple sequence alignments are prone to accumulating errors due to strong divergence of species. Moreover, in the course of evolution, binding sites can migrate along the sequence. The aim of this work was to estimate the portion of conserved miRNA-binding sites that cannot be predicted using the existing tools because of these phenomena. The concept of L-conserved sites is introduced: a site is termed L-conserved if it is present in each sequence in the alignment within a frame of length L. We observed a significant increase in the number of additionally detected conserved sites without loss of sensitivity. The effect of species divergence on this increase was also evaluated. © 2017, Pleiades Publishing, Inc.

关键词： comparative genomics miRNA multiple sequence alignment

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Parameters that affect estimation of nucleolar proteins' mobility in living cells by the FRAP method with the example of protein fibrillarin

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Cell and Tissue Biology 2012年第2期6卷 128-136页

作者： Barygina, V.V. Mironova, A.A. Zatsepina, O.V. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russian Federation Faculty of Biology Moscow State University Moscow Russian Federation Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russian Federation

The fluorescence recovery after photobleaching (FRAP) method, in combination with confocal laser scanning microscopy, represents one of the basic approaches to studying the properties of proteins in living mammalian cells. However, the data of different authors on the dynamic properties of the same protein and even in cells of the same type can differ greatly. Until now, the reasons for such discrepancies have not been specifically analyzed. In the present work, using the example of nucleolar protein fibrillarin fused with EGFP, we studied the effect of the area of the irradiated region (the region of interest (ROI)) and temperature conditions of experiments on the main dynamic characteristics of the protein-the portion of the mobile fraction of protein and the half-recovery time of fluorescence after photobleaching (t _1/2). The obtained results have shown that both parameters affect markedly the estimation of the fibrillarin-EGFP mobility in HeLa cells. It was concluded that, in FRAP experiments the ROI area can be standardized and, where possible, minimized. In addition, when analyzing the dynamic characteristics of the nucleolar proteins, which participate in the temperature-dependent enzymatic reactions, it is necessary to maintain standard temperature conditions. © 2012 Pleiades Publishing, Ltd.

关键词： area of ROI photobleaching fibrillarin fluorescence half-recovery time (t 1/2) FRAP mobile protein fraction temperature conditions

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Semantic Knowledge Graph Network Features for Drug Repurposing 10

Semantic Knowledge Graph Network Features for Drug Repurposi...

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10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4LS 2017

作者： Malas, Tareq B. Kudrin, Roman Starikov, Sergei Thoen, Peter A.C. Peters, Dorien J.M. Roos, Marco Hettne, Kristina M. Department of Human Genetics Leiden University Medical Center Leiden2300 RC Netherlands Faculty of Bioengineering and Bioinformatics Moscow State University Moscow119234 Russia

Given the significant time and financial costs of developing a commercial drug, it remains important to constantly reform the drug discovery pipeline with novel technologies that can narrow the candidates down to the most promising lead compounds for clinical testing. Computational approaches are used to expedite the drug discovery processes. Semantic knowledge graphs can assist these computational approaches, because they connect different biological databases and reflect the relationships between genes, pathways and diseases. Here, we took advantage of the Euretos Knowledge Platform (EKP), a commercial database that integrates more than 170 different biological resources including DrugBank, and evaluated the usefulness of the underlying semantic knowledge graphs to predict novel drug-disease associations. We extracted network-based features from the semantic knowledge graph and tested their ability to separate between the positive and negative data sets of drug-disease pairs. Our results showed that the extracted features such as the total number of intermediate concepts (count), the number of different semantic categories (diversity), and the predicates connecting a drug-disease pair were successful in separating the positive from the negative sets. These features provide a proof of concept for using semantic knowledge graphs for drug repurposing efforts. Our work reveals the added value of integrating different biological databases for solving complex biological questions.

关键词： Database systems

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