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Activation of Bacterial F-ATPase by LDAO: Deciphering the Molecular Mechanism

Biochemistry (Moscow) 2025年第3期90卷 374-388页

作者： Bruman, Sofya M. Zubareva, Valeria M. Shugaeva, Tatiana E. Lapashina, Anna S. Feniouk, Boris A. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow 119991 Russian Federation Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University Moscow 119991 Russian Federation

Abstract: Proton FOF1 ATP synthase catalyzes the formation of ATP from ADP and inorganic phosphate coupled with transmembrane proton transfer using the energy of the protonmotive force (pmf). As pmf decreases, the dir... 详细信息

Abstract: Proton F_OF₁ ATP synthase catalyzes the formation of ATP from ADP and inorganic phosphate coupled with transmembrane proton transfer using the energy of the protonmotive force (pmf). As pmf decreases, the direction of the reaction is reversed and the enzyme generates pmf, transferring protons across the membrane using the energy of ATP hydrolysis. ATPase activity of the enzyme can be suppressed by ADP in a non-competitive manner (ADP-inhibition), and in a number of bacteria, it can be inhibited by conformational changes in the regulatory C-terminal domain of the ε subunit. Lauryldimethylamine oxide (LDAO), a zwitterionic detergent, is known to attenuate both of these inhibitory mechanisms, significantly increasing the ATPase activity of the enzyme. For this reason, LDAO is sometimes used for semi-quantitative estimation of the enzyme’s susceptibility to these regulatory mechanisms. However, the binding site of LDAO in ATP synthase remains unknown. The mechanism by which the detergent counteracts ADP-inhibition and the inhibition involving the ε subunit is also unclear. We performed molecular docking and predicted that LDAO binding might occur at the catalytic site of ATP synthase, whether empty or containing nucleotides. Molecular dynamics simulations showed that LDAO could affect the mobility of the loop in the β subunit (residues β404-415 in Escherichia coli ATP synthase) near the catalytic site. Mutagenesis of residue β409 in the E. coli enzyme and the corresponding β419 residue in the Bacillus subtilis ATP synthase revealed that the type of side chain of this residue indeed affects LDAO-dependent stimulation of ATPase activity. We also found that LDAO activates the enzyme more strongly in the presence of 100 mM sulfate compared to sulfate-free medium. This phenomenon is likely due to the enhancement of ADP-inhibition of the enzyme by sulfate. © Pleiades Publishing, Ltd. 2025.

关键词： ADP-inhibition ATP-synthase Bacillus subtilis Escherichia coli F-ATPase FOF1 LDAO regulation sulfate

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Developing a Head-Attached Interface Device for Closed-Loop Transcranial Ultrasound Stimulation in the Mouse Brain

Developing a Head-Attached Interface Device for Closed-Loop ...

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18th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2025

作者： Furukawa, Ryo Murakami, Shuichi Tateno, Takashi Bioengineering and Bioinformatics Graduate School of Information Science and Technology Hokkaido University Kita 14 Nishi 9 Kita-ku Hokkaido Sapporo060-0814 Japan Osaka Research Institute of Industrial Science and Technology 2-7-1 Ayumino Izumi Osaka594-1157 Japan Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Kita 14 Nishi 9 Kita-ku Hokkaido Sapporo060-0814 Japan

Transcranial ultrasound stimulation (TUS), which can be used to noninvasively stimulate local and deep brain areas, holds significant promise for clinical applications. However, TUS apparatus is typically constructed with several components, including a relatively large single-element ultrasound (US) transducer, a waveguide, and a driving source. These components pose challenges when conducting experiments with freely moving small animals, especially in the context of wearable devices. Additionally, conventional open-loop stimulation systems do not allow for the simultaneous monitoring of neural activity, which can sometimes result in the overactivation of neural responses. In this study, we developed a head-mounted piezoelectric micromachined ultrasound transducer (PMUT) array with integrated monitoring electrodes to serve as a TUS interface for mice. To determine effective array patterns for optimal US beam profiles, we first conducted beamforming simulations. We then microfabricated the PMUT arrays according to the results of these simulations. Subsequently, we performed electroencephalographic (EEG) recordings to evaluate the potential of TUS in mice while simultaneously monitoring neural activities. Finally, we discuss future applications of a closed loop TUS system in the treatment of brain diseases. © 2025 by SCITEPRESS– Science and Technology Publications, Lda.

关键词： Closed loop systems

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De Novo Gene Birth

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Molecular Biology 2025年第1期59卷 17-25页

作者： Aristova, E.O. Volkhin, I.A. Denisova, A.A. Nikitin, P.A. Petrukhin, E.R. Faculty of Bioengineering and Bioinformatics Moscow State University Moscow 119234 Russian Federation Life Sciences Research Center Moscow Institute of Physics and Technology (National Research University) Moscow oblast Dolgoprudny 141700 Russian Federation Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow 119071 Russian Federation

Abstract: According to classic ideas, new genes emerge from old genes by duplication or horizontal transfer. Analyses of a large number of genomes in recent decades have shown that some genes have no visible homologs and have presumably emerged de novo from previously noncoding sequences. The review considers possible mechanisms of de novo gene formation, the properties of protein sequences encoded by such genes, and features of their expression and selection. The problem of identification of de novo arising gene is discussed separately. © Pleiades Publishing, Ltd. 2025.

关键词： de novo gene orphan gene pervasive transcription pervasive translation

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Integrating computational and experimental insights into osmolyte-driven activation of Geobacillus kaustophilus L-asparaginase for acrylamide mitigation

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Journal of Molecular Liquids 2025年 423卷

作者： Özdemir, F.İnci Servili, Burak Demirtaş, Özge Şükür, Gözde Tülek, Ahmet Yildirim, Deniz Gebze Technical University Department of Molecular Biology and Genetics Kocaeli Gebze41400 Turkey Kadir Has University of Science and Engineering Bioinformatics and Genetics Program İstanbul Fatih35430 Turkey Iğdır University Postgraduate Education Institute Department of Bioengineering and Sciences Iğdır Merkez76000 Turkey Cukurova University Faculty of Ceyhan Engineering Department of Chemical Engineering Adana Ceyhan01950 Turkey

Osmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V.

关键词： Maltose

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MIXL1 activation in endoderm differentiation of human induced pluripotent stem cells

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Stem Cell Reports 2025年第5期20卷

作者： Osteil, Pierre Withey, Sarah Santucci, Nicole Aryamanesh, Nader Pang, Ignatius Salehin, Nazmus Sun, Jane Qin, Annie Su, Jiayi Knowles, Hilary Li, Xiucheng Bella Cai, Simon Wolvetang, Ernst Tam, Patrick P.L. Embryology Research Unit Children's Medical Research Institute University of Sydney Sydney Australia School of Medical Sciences Faculty of Medicine and Health University of Sydney Sydney Australia Australian Institute for Bioengineering and Nanotechnology University of Queensland Brisbane Australia Bioinformatics Group Children's Medical Research Institute University of Sydney Sydney Australia

Human induced pluripotent stem cells (hiPSCs) possess the ability to differentiate into a multitude of cell and tissue types but display heterogeneous propensity of differentiation into specific lineage. Characterization of the transcriptome of 11 hiPSC lines showed that activation of MIXL1 at the early stage of stem cell differentiation correlated with higher efficacy in generating definitive endoderm and advancing differentiation and maturation of endoderm derivatives. Enforced expression of MIXL1 in the endoderm-inefficient hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity to generate the requisite stem cell products. © 2025 The Author(s)

关键词： 2D gastruloids differentiation endoderm human induced pluripotent stem cells MIXL1 scRNA-seq

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[New relations for steady-state enzyme kinetics and their application to rapid equilibrium assumption]

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Biofizika 2013年第6期58卷 953-960页

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

With the use of a graph theory new relations for steady-state enzyme kinetics are derived and strictly proved for the arbitrary mechanism of an enzyme-catalysed reaction containing a reversible segment. Using these relations, a general principle for rapid equilibrium assumption is formulated and proved: the reversible bound segment can be considered as an equilibrium segment only when the values of the base trees that are not proper to this segment can be neglected (within a prescribed accuracy) in relation to the values of the base trees that belong to this segment. In contrast with the foreign base trees the base trees that are proper to the segment have the following properties: the tree that is directed to the base within this segment does not contain the edges leaving this segment;and the tree that is directed to the base outside the segment contains only one edge leaving this segment. Equilibrium variations are assessed for steady-state intermediates concentrations of the equilibrium segment, numerical expressions are obtained for the accuracy of determination of the intermediates concentrations as well as for the accuracy of determination of the rate of enzyme-catalysed reaction in case of using rapid equilibrium assumption.

关键词： approximation accuracy Cha's method enzyme kinetics graph theory rapid equilibrium assumption steady-state kinetics

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The accuracy of rapid equilibrium assumption in steady-state enzyme kinetics is the function of equilibrium segment structure and properties

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Biofizika 2015年第2期60卷 262-269页

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

Quantitative evaluation of the accuracy of the rapid equilibrium assumption in the steady-state enzyme kinetics was obtained for an arbitrary mechanism of an enzyme-catalyzed reaction. This evaluation depends only on the structure and properties of the equilibrium segment, but doesn't depend on the structure and properties of the rest (stationary part) of the kinetic scheme. The smaller the values of the edges leaving equilibrium segment in relation to values of the edges within the equilibrium segment, the higher the accuracy of determination of intermediate concentrations and reaction velocity in a case of the rapid equilibrium assumption.

关键词： accuracy of assumption Cha method enzyme kinetics graph theory rapid equilibrium assumption steady-state kinetics

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Chemiresistive Sensors for Thrombin Assay Based on Nanosize Carbon Nanotube Films on Flexible Supports

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Biomedical Engineering 2018年第6期51卷 377-380页

作者： Komarov, I.A. Rubtsova, E.N. Lapashina, A.S. Golovin, A.V. Bobrinetskiy, I.I. MoscowZelenograd Russia Faculty of Bioengineering and Bioinformatics M. V. Lomonosov Moscow State University Moscow Russia

We present here results obtained during the developmental construction of a selective biological sensor based on carbon nanotubes chemically modified with specific aptamers. The sensory layer, consisting of a film of carbon nanotubes, on a flexible polymer substrate, provides high sensitivity for assay of the target proteins. The responses of the sensory structures to the target protein − thrombin and a reference protein, albumin − were studied. Selective estimation of thrombin after exposure of the sensor to albumin was demonstrated. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.

关键词： Carbon nanotubes

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Potassium homeostasis and signalling: from the whole plant to the subcellular level

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Quantitative Plant Biology 2025年 6卷 e13-e13页

作者： Wegner, Lars H. Pottosin, Igor Dreyer, Ingo Shabala, Sergey International Research Center for Environmental Membrane Biology School of Agriculture and Bioengineering Foshan University Foshan China Centro Universitario de Investigaciones Biomédicas Universidad de Colima Colima Mexico Electrical Signaling in Plants (ESP) Laboratory Center of Bioinformatics Simulation and Modeling (CBSM) Faculty of Engineering Universidad de Talca Talca Chile School of Biological Science University of Western Australia Crawley WA Australia

Potassium is an essential macronutrient required for plant growth and development. Over the recent decade, an important signalling role of K+ has emerged. Here, we discuss some aspects of such signalling at the variou... 详细信息

Potassium is an essential macronutrient required for plant growth and development. Over the recent decade, an important signalling role of K⁺ has emerged. Here, we discuss some aspects of such signalling at the various levels of plant functional organisation. The topic covered include: (1) mechanisms of long-distant K⁺ transport in the xylem and phloem and the molecular identity and regulation of K⁺ loading and unloading into plant vasculature;(2) essentiality and physiological roles of K⁺ cycling between shoots and roots;(3) plant sensing and signalling of low K⁺;(4) maintenance of K⁺ homeostasis at the cellular level;(5) stress-induced modulation of cytosolic K⁺ as a signal in plant adaptive responses to hostile environment;(6) stress-specific K⁺ signatures and mechanisms of their decoding by regulation of purine metabolism and H⁺-ATPase activity;(7) cytosolic K⁺ loss as a metabolic switch and a regulator of autophagy;and (8) vacuolar K⁺ transport and sensing. © 2025 The Author(s). Published by Cambridge University Press in association with John Innes Centre.

关键词： autophagy long-distance transport metabolic switch programmed cell death stress response

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Characterization of conformational flexibility in protein structures by applying artificial intelligence to molecular modeling

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Journal of Structural Biology 2025年第2期217卷

作者： Kopylov, Kirill Kirilin, Evgeny Voevodin, Vladimir Švedas, Vytas Lomonosov Moscow State University Research Computing Center Leninskie Gory 1-4 Moscow 119234 Russian Federation Lomonosov Moscow State University Belozersky Institute of Physicochemical Biology Leninskie Gory 1-40 Moscow 119992 Russian Federation Lomonosov Moscow State University Faculty of Bioengineering and Bioinformatics Leninskie Gory 1-73 Moscow 119991 Russian Federation Abu Dhabi United Arab Emirates

Recent AI applications have revolutionized the modeling of structurally unresolved protein regions, thereby complementing traditional computational methods. These state-of-the-art techniques can generate numerous candidate structures, significantly expanding the scope of structural biology. However, to effectively prioritize these models, a physics-based approach is required to assess the energy landscape. Such integration can bridge the gap between rapid model generation and precise determination of functional conformations. To address this challenge, we propose an integrated approach that combines molecular modeling with AI and HPC. Metadynamics simulations in latent space are used to explore potential energy landscapes based on initial approximations of flexible region structures derived from modeling tools such as AlphaFold, RosettaFold, Modeller, SwissModel, etc. The approach was validated by modeling folding of Trp-cage protein and conformational plasticity of ubiquitin. The predominant conformations of previously unresolved mobile regions in the active center of flavin-dependent 2-hydroxybiphenyl-3-monooxygenase (EC 1.14.13.44) were identified, while estimating the energy associated with these conformational changes. © 2025 Elsevier Inc.

关键词： 2-hydroxybiphenyl-3-monooxygenase substrate tunnel Hyperspherical latent space Modelled structure prioritization Protein conformational pathway Unresolved region modelling

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