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Cryo-EM structure of the bullet-shaped GroEL-GroES complex at 3.6 Å resolution

Microscopy and Microanalysis 2021年第S1期27卷 1120-1121页

作者： Evgeny Pichkur Sofia Kudryavtseva Igor Yaroshevich Vladimir Muronetz Olga Sokolova Tatiana Stanishneva-Konovalova 1National Research Center “Kurchatov Institute” United States Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics United States Lomonosov Moscow State University United States Moscow Lomonosov University United States

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Search for Ligands Complementary to the 430-cavity of Influenza Virus Neuraminidase by Virtual Screening

Supercomputing Frontiers and Innovations

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Supercomputing Frontiers and Innovations 2022年第2期9卷 79-83页

作者： Nilov, Dmitry K. Schmidtke, Michaela Makarov, Vadim A. Svedas, Vytas K. Lomonosov Moscow State University Belozersky Institute of Physicochemical Biology Moscow Russia Lomonosov Moscow State University Research Computing Center Moscow Russia Department of Virology and Antiviral Therapy Jena University Hospital Jena Germany Research Center of Biotechnology of the Russian Academy of Sciences Moscow Russia Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Moscow Russia

An anthrapyrazole derivative STK663786 has been identified as a selective ligand of the socalled 430-cavity of influenza virus neuraminidase at virtual screening of a library of low-molecularweight compounds. It is able to form favorable contacts with hydrophobic residues as well as cation-interaction and hydrogen bonds with the polar Arg371 residue. The experimentally determined EC50 values have been found to be 19 and 30 μM for viruses H1N1 and H3N2, respectively. Complementarity of STK663786 to the 430-cavity adjacent to the sialic acid binding subsite in the active center of neuraminidase makes this compound a valuable structural fragment at construction of bifunctional inhibitors of the enzyme. © The Authors 2022. This paper is published with open access at ***

关键词： Viruses

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Translating from Na to Ca : Na/Ca-exchanger exerts Na -dependent control over astrocytic Ca oscillations

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The European Physical Journal Plus 2021年第7期136卷 1-16页

作者： Verisokin, Andrey Yu. Verveyko, Darya V. Kucherenko, Varvara V. Postnov, Dmitry E. Brazhe, Alexey R. Department of Theoretical Physics Kursk State University Kursk Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia Saratov State National Research University Saratov Russia Biological Faculty Lomonosov Moscow State University Moscow Russia Department of Molecular Neurobiology Institute of Bioorganic Chemistry RAS Moscow Russia

Recently accumulated evidences suggest that astrocyte signaling is in touch link with extracellular volume regulation and interstitial fluid drainage from the brain. Classical understanding of astrocyte activity is based on IP $$_3$$ -dependent calcium exchange with intracellular stores. Recent evidence shifts focus to calcium entry from extracellular space via multiple mechanisms and widens it to taking other ions into account. It has been hypothesized that Na/Ca-exchanger can translate activity-dependent Na $$^+$$ transients into modulation of Ca $$^{2+}$$ dynamics. We combine a model of IP $$_3$$ -based Ca $$^{2+}$$ dynamics with a model of Ca $$^{2+}$$ flow through Na/Ca-exchanger to provide theoretical insights into the possible effects of such modulation. We find that the exchanger can provide for bidirectional Na $$^+$$ -dependent modulation of the sensitivity to extracellular glutamate, oscillation amplitude and frequency modulation, as well as extending the available set of dynamical regimes. The extent of the emergent Na $$^+$$ sensitivity is predicted to be scaled by a morphology-dependent balance between the maximal flow through the exchanger and the rate of entry from intracellular stores.

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Modulatory effect of NCX on IP3-dependent Ca2+oscillations in astrocytes

Modulatory effect of NCX on IP3-dependent Ca2+oscillations i...

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Saratov Fall Meeting 2020 - Computations and Data Analysis: From Molecular Processes to Brain Functions

作者： Verisokin, Andrey Yu. Verveyko, Darya V. Kucherenko, Varvara V. Postnov, Dmitry E. Brazhe, Alexey R. Department of Theoretical Physics Kursk State University Radishcheva st. 33 Kursk305000 Russia Saratov State National Research University Astrakhanskaya st. 83 Saratov Russia Biological Faculty Lomonosov Moscow State University Leninskie Gory 1/24 Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Leninskie Gory 1/73 Moscow Russia Department of Molecular Neurobiology Institute of Bioorganic Chemistry RAS Miklukho-Maklay str 16/10 Moscow Russia

ISBN: (纸本)9781510645325

Most of the existing models of calcium dynamics of astrocytes do not take into account the effect of the Na/Ca- exchanger on the formation of calcium oscillations and their properties. However, recent experimental studies show that at an increased sodium concentration, the Na/Ca-exchanger works in the reverse mode, providing an additional calcium entry into the cell cytosol. In this work we study a model that simultaneously takes into account the IP3-mediated exchange with intracellular [Ca2+] stores and bidirectional [Ca2+] flow through Na/Ca-exchanger. We analyze the behavior of the system under stimulation with external glutamate- of the cell, explore the possible behavior regimes and reveal the effect of the cytosolic sodium concentration, the maximum current through the Na/Ca-exchanger, and the stimulus amplitude on the astrocytic calcium dynamics. © COPYRIGHT SPIE. Downloading of the abstract is permitted for personal use only.

关键词： Sodium

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A Hybrid of Bat Algorithm and Minimization of Metabolic Adjustment for Succinate and Lactate Production 14th

A Hybrid of Bat Algorithm and Minimization of Metabolic Adju...

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14th International Conference on Practical Applications of Computational Biology and bioinformatics, PACBB 2020

作者： Man, Mei Yen Mohamad, Mohd Saberi Choon, Yee Wen Ismail, Mohd Arfian Artificial Intelligence and Bioinformatics Research Group Faculty of Computing Universiti Teknologi Malaysia SkudaiJohor81310 Malaysia Institute for Artificial Intelligence and Big Data Universiti Malaysia Kelantan City Campus Pengkalan Chepa Kota BharuKelantan16100 Malaysia Faculty of Bioengineering and Technology Universiti Malaysia Kelantan Jeli Campus JeliKelantan17600 Malaysia College of Computing and Applied Sciences Universiti Malaysia Pahang Lebuhraya Tun Razak Gambang KuantanPahang Darul Makmur26300 Malaysia

ISBN: (纸本)9783030545673

The elementary concept of metabolic engineering is to manipulate those potential genes to augment the yields of metabolite production by restructuring and deregulating the metabolic networks. However, the yields of biochemical products are far below their theoretical maximums, although many conventional methods that have been introduced. These conventional methods had encountered problems in getting stuck at a local minimum. This paper proposes a hybrid of the Bat Algorithm (BAT) and the Minimization of Metabolic Adjustment (MOMA) to predict an ideal set of solutions in order to improve the production of succinate and lactate. The dataset utilized in this paper was the Escherichia coli core model, which is the subset of the iAF1260 E. coli metabolic network. The experimental results include the production rate, growth rate, and a list of knockout genes. From the comparative analysis, BATMOMA has better performance in terms of production rate compared to previous works, proving that it has the potential for resolving genetic engineering problems. © 2021, The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Metabolic engineering

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Accuracy Enhancement of L-Band EPR Tooth Dosimetry by Implementing Multiple Harmonic Detection

SSRN

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SSRN 2024年

作者： Oh, Jeonghun Koo, Chang Uk Park, Jong In Choi, Kwon Lee, Junyoung Hirata, Hiroshi Ye, Sung-Joon Program in Biomedical Radiation Sciences Graduate School of Convergence Science and Technology Seoul National University Seoul08826 Korea Republic of Ionizing Radiation Metrology Group Korea Research Institute of Standards and Science Daejeon34113 Korea Republic of Research Institute for Convergence Science Seoul National University Seoul08826 Korea Republic of Division of Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Sapporo060–0814 Japan Department of Applied Bioengineering Graduate School of Convergence Science and Technology Seoul National University Seoul08826 Korea Republic of Advanced Institute of Convergence Technology Seoul National University Suwon16629 Korea Republic of Biomedical Research Institute Seoul National University Hospital Seoul03080 Korea Republic of

In a large-scale radiation accident, the swift classification of individuals exposed to high levels of radiation is crucial to minimize casualties. In-vivo tooth dosimetry using L-band electron paramagnetic resonance (EPR) spectroscopy is a promising method for this purpose, as it can estimate individual exposure levels rapidly and non-invasively. However, the accuracy of dose estimation associated with this technique remains a great challenge. To enhance the accuracy, digital multiple harmonic detection (MHD) was incorporated into a home-built L-band EPR spectrometer. This approach enabled the utilization of information present in higher harmonics of EPR signals, which has been often discarded in traditional EPR spectroscopy. Acquired multiple harmonic spectra were reconstructed to the first derivative spectrum to merge information and mitigate the signal broadening. The modulation amplitude varied in a range of 0.3 to 0.7 mT to maximize the accuracy. In a 0.5-minute measurement at 0.6 mT, the standard error of inverse prediction (SEIP) was reduced to 0.57 Gy from 0.71 Gy. The statistical significancy of the enhancement was validated. In conclusion, the accuracy enhanced by this MHD can contribute to improving the efficiency of triage systems in the aftermath of a mass radiation accident. © 2024, The Authors. All rights reserved.

关键词： Paramagnetic resonance

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Particle-Based Segmentation Of Extended Objects On Curved Biological Membranes

Particle-Based Segmentation Of Extended Objects On Curved Bi...

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IEEE International Symposium on Biomedical Imaging

作者： A. Solomatina Y. Kalaidzidis A. Cezanne K. Soans C. Norden M. Zerial I. F. Sbalzarini Faculty of Computer Science Technische Universität Dresden Dresden Germany Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany Center for Systems Biology Dresden Dresden Germany Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russia Cluster of Excellence Physics of Life TU Dresden Dresden Germany Instituto Gulbenkian de Ciência (IGC) Oeiras Portugal

We present a novel method for model-based segmentation of extended, blob-like objects on curved surfaces. Our method addresses several challenges arising when imaging curved biological membrane, such as out-of-membrane signal and geometry-induced background variations. We use a particle-based reconstruction of the membrane geometry, moment-conserving intensity interpolation from pixels to surface particles, and model-based in-surface segmentation. Our method denoises and deconvolves images, corrects for background variations, and quantifies the number, size, and intensity of segmented objects. We benchmark the accuracy of the method and present two applications to (1) neuroepithelial focal adhesion sites during optic cup morphogenesis in zebrafish and (2) reconstituted membrane domains bearing the small GTPase Rab5 on spherical beads.

关键词： Geometry Image segmentation Interpolation Surface reconstruction Biomedical optical imaging Biological system modeling Benchmark testing

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Erratum to:Study of GroEL Conformational Mobility by Cryo-Electron Microscopy and Molecular Dynamics

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Crystallography Reports 2022年第2期67卷 310-310页

作者： Panina, I. S. Mamchur, A. A. Yaroshevich, I. A. Zlenko, D. V. Pichkur, E. B. Kudryavtseva, S. S. Muronetz, V. I. Sokolova, O. S. Stanishneva-Konovalova, T. B. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russia Faculty of Biology Moscow State University Faculty of Biology Moscow Russia National Research Centre “Kurchatov Institute” Moscow Russia Faculty of Bioengineering and Bioinformatics Moscow State University Moscow Russia

An Erratum to this paper has been published: https://***/10.1134/S1063774521340058

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Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod

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Journal of biomolecular structure & dynamics [J Biomol Struct Dyn] 2019年第8期37卷 2049-2060页

作者： Suplatov Kopylov Sharapova Švedas a Faculty of Bioengineering and Bioinformatics Belozersky Institute of Physicochemical Biology Lomonosov Moscow State University Vorobjev hills Moscow Russia

Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the 'out' state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod's binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins. Communicated by Ramaswamy H. Sarma.

关键词： Inhibitor Doramapimod (BIRB-796) bioinformatic sequence/structure analysis of protein superfamilies direct and indirect competition with ATP human p38α (p38alpha) MAPK in DFG-in and DFG-out states long-timescale classical and accelerated molecular dynamics

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Interaction of phage chaperonin OBP domains with amyloidogenic proteins

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Archives of Biochemistry and Biophysics 2025年 110493页

作者： Evgeniia V. Leisi Darya V. Zyurkalova Uliana F. Dzhus Alexey D. Nikulin Sergei A. Golyshev Vladimir I. Muronetz Lidia P. Kurochkina Belozersky Research Institute of Physico-Chemical Biology Lomonosov Moscow State University Leninskie Gory 1 Bld 40 119991 Moscow Russia Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Leninskie Gory 1 Bld 73 119991 Moscow Russia Institute of Protein Research Russian Academy of Sciences Institutskaya street 4 Pushchino Moscow Region 142290 Russia

GroEL-like chaperonins encoded by bacterial viruses have unique features compared to other group I and II chaperonins. Here, the properties of the single-ring chaperonin of the bacteriophage OBP Pseudomonas fluorescens were further studied. To understand the role of the chaperonin domains in its function, two deletion variants of the chaperonin OBP were obtained. One represented the isolated apical domain (AD) only and the other was a chaperonin without apical domains (OBPΔAD). It was shown that removal of the apical domains slightly destabilises the chaperonin structure, but does not affect its heptameric assembly. In addition, the chaperonin without the apical domains retains its ATPase activity and exhibits the properties that are characteristic of the full-length chaperonin OBP. In the presence of ATP, the mutant chaperonin OBPΔAD protects the phage endolysin from thermal aggregation and promotes the fibrillation of two amyloidogenic proteins, α-synuclein and the prion protein. In the absence of ATP, OBPΔAD is able to bind α-synuclein monomers in the same way as the full-length chaperonin OBP, thus preventing their spontaneous fibrillation. The recombinant chaperonin apical domain, lacking ATPase activity, binds α-synuclein monomers independently of ATP presence, preventing amyloid formation. The results obtained suggest that, in mutant OBP, which lacks apical domains, substrate proteins, including non-specific ones, are capable of binding to the internal cavity formed by the other two chaperonin domains. The possible role of chaperonin domains in regulating the pathological transformation of amyloidogenic proteins is discussed.

关键词： ATPase activity Phage chaperonin amyloid transformation prion protein protein aggregation α-synuclein

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