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A novel non-canonical PIP-box mediates PARG interaction with PCNA
Nucleic Acids Research. 2017. Vol. 45. No. 16. P. 9741–9759.
Polyansky A.
Poly(ADP-ribose) glycohydrolase (PARG) regulates cellular poly(ADP-ribose) (PAR) levels by rapidly cleaving glycosidic bonds between ADP-ribose units. PARG interacts with proliferating cell nuclear antigen (PCNA) and is strongly recruited to DNA damage sites in a PAR- and PCNA-dependent fashion. Here we identified PARG acetylation site K409 that is essential for its interaction with PCNA, its localization within replication foci and its recruitment to DNA damage sites. We found K409 to be part of a non-canonical PIP-box within the PARG disordered regulatory region. The previously identified putative N-terminal PIP-box does not bind PCNA directly but contributes to PARG localization within replication foci. X-ray structure and MD simulations reveal that the PARG non-canonical PIP-box binds PCNA in a manner similar to other canonical PIP-boxes and may represent a new type of PIP-box. While the binding of previously described PIP-boxes is based on hydrophobic interactions, PARG PIP-box binds PCNA via both stabilizing hydrophobic and fine-tuning electrostatic interactions. Our data explain the mechanism of PARG-PCNA interaction through a new PARG PIP-box that exhibits non-canonical sequence properties but a canonical mode of PCNA binding.
Nersisyan A., Frontiers in Molecular Biosciences 2026 Vol. 13 Article 1995001
Antiviral activity is commonly summarized using endpoint measures such as EC50 or EC90, yet these quantities emerge from a dynamic biological system and depend on viral replication kinetics, host-cell properties, experimental design, and the assay used to quantify infection. Infectious-virus titers, viral RNA, infected-cell fractions, viability measurements, and immune readouts capture different components of the ...
Added: October 15, 2026
Тукачев Н. В., González-Jiménez M., Ramakrishnan G. et al., Physical Chemistry Chemical Physics 2021 Vol. 23 No. 23 P. 13250–13260
Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands ...
Added: October 14, 2026
Батова О. Н., Савинецкая Л. Е., Проявка С. В. et al., Nature Conservation Research. Заповедная наука 2026 Т. 11 № 4 С. 25–39
Spermophilus suslicus is a threatened species listed in Red Data Books at all levels (from regional Red Data
Books to the IUCN Red List of Threatened Species), and it currently requires special conservation activity.
Over the past 30–50 years, its range has changed from continuous to mosaic, and its population has declined
everywhere. In 2015, in Russia experimental ...
Added: October 13, 2026
Temereva E., Zoologischer Anzeiger 2026 Vol. 325 P. 182–195
Brachiopoda is a group of animals, that is still insufficiently studied at the ultrastructural level, despite the significance of ultrastructure of tissues and organs for analysing the functional morphology, reconstructing the organisation and biology of numerous extinct brachiopods, and establishing relationships among major taxa. In the present study, we provide a revised reconstruction of the ...
Added: October 11, 2026
Ekaterina D. Riumina, Klink G. V., Alekseeva E. et al., PNAS, США 2026 Vol. 123 No. 35 P. 1–20
The role of escape from the cytotoxic T cell (CTL) response in SARS-CoV-2 evolution remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants whose mutations reduce presentation by the HLA class I alleles common in human populations. We find that 35% of mutations that are characteristic of the variants of concern, and ...
Added: October 2, 2026
Aly Ismailov, Poptsova M., Plos One 2026 Vol. 21 No. 9 Article e0355902
Added: October 2, 2026
Knyazev E., Чеботарева О. Е., М.: Издательский дом НИУ ВШЭ, 2026.
This teaching and learning guide provides a concise overview of the theoretical and practical aspects of the basic skills required to work in a biological laboratory. It also includes protocols for practical classes conducted as part of the introductory professional training placement for first-year students in the Bachelor’s programme in Cell and Molecular Biotechnology at ...
Added: September 30, 2026
Ryskina H., Knyazev E., Вопросы биологической, медицинской и фармацевтической химии 2026 Т. 29 № 9 С. 84–91
Introduction. The active integration of rapidly developing omics and computer technologies in the 21st century has led to a breakthrough in understanding the principles of the functioning of living systems. One of the dynamically developing integrative areas in biology is biological modeling. The fundamental paradigm has been the methodology that allows for the prediction of ...
Added: September 29, 2026
Lin Z., Duan K., Wan R. et al., Advanced Science 2026 P. 1–13
Targeted protein degradation represents a promising therapeutic strategy, yet its broader application is often limited by the scarcity of usable E3 ligases. Glutathione peroxidase 4 (GPX4) is a key target for inducing ferroptosis, but achieving sustained and potent inhibition remains challenging with conventional enzymatic inhibitors. Herein, we report the first small‐molecule GPX4 degraders that incorporate ...
Added: September 26, 2026
Diachkova E., Nikulin D., Кубкин Я. В. et al., American Journal of Respiratory and Critical Care Medicine 2026 Vol. 212
Accurate classification of a patient with pulmonary hypertension (PH) into one of five groups is fundamental for appropriate disease management strategies. The time from disease onset to correct diagnosis is unacceptably long in many cases. Chronic thromboembolic pulmonary hypertension (CTEPH) develops as a consequence of venous thromboemboli, resulting in a more pronounced hereditary predisposition to ...
Added: September 23, 2026
Xu Y., Ryabov F., Alexandrov I. et al., USA 2026 Vol. 6 No. 8 Article 101324
Центромеры обеспечивают расхождение хромосом, однако организацию их хроматина в пределах повторяющейся альфа-сателлитной ДНК долгое время было трудно изучать. Для решения этой задачи мы создали гаплотип-разрешённые аннотации сателлитной ДНК для полной диплоидной сборки генома человека T2T-HG002. Затем с помощью метода направленного метилирования с секвенированием длинных прочтений (DiMeLo-seq) мы картировали центромерный белок A (CENP-A), модификацию H3K9me3 и ...
Added: September 23, 2026
Hebbar P., Ryabov F., Alexandrov I. et al., Cell 2026 Vol. 189 P. 4891–4908.e12
The common marmoset is a New World monkey widely used to study primate evolution and human disease. We present a telomere-to-telomere (T2T) reference assembly for the species, plus three near-T2T haplotypes. These resolve previously inaccessible regions, including the centromeres, sex chromosomes, subterminal satellites, acrocentric chromosomes, and the major histocompatibility complex (MHC). We find marmoset centromeres ...
Added: September 23, 2026
Shaitan A., Ke Y., Shutao C. et al., 2026 No. 24 Article 181
Background Therapeutic peptides exert pivotal effects in diverse biological processes, and have attracted significant interest in the field of biomedicine in recent years. However, most existing methods often fail to adequately capture the intricate interactions among amino acid residues and the contextual dependencies within peptide sequences, which hampers the extraction of deep semantic representations and ...
Added: September 18, 2026
Anton Rogachev, Sysoeva O., Frontiers in Systems Neuroscience 2025 Vol. 19 Article 1658243
Added: September 17, 2026
Vladimir Staroverov, Alexei Galatenko, Evgeny Knyazev et al., PeerJ 2024 Vol. 12 Article e16964
Within-host infection dynamics of Omicron dramatically differs from previous variants of SARS-CoV-2. However, little is still known about which parameters of virus-cell interplay contribute to the observed attenuated replication and pathogenicity of Omicron. Mathematical models, often expressed as systems of differential equations, are frequently employed to study the infection dynamics of various viruses. Adopting such ...
Added: March 20, 2024
Лобаева Т. А., Смирнова К. В., Жданов Д. Д. et al., М.: ООО "Ваш формат", 2024.
Биология для студентов-медиков: общая биология, молекулярная биология, генетика
В сборнике приводится краткое теоретическое введение к каждому разделу, даны основные термины и понятия дисциплины, собраны тематические задания различного уровня сложности по 8 темам биологии, включая ситуационные, расчетные, практико-ориентированные, клинические и другие типы задач и упражнений, характерные для использования в образовательном процессе студентов-медиков. Пособие соответствует требованиям ФГОС ВО ...
Added: March 11, 2024
Poptsova M., Умеренков Д., Fedorov A. et al., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.
Flipons – non-B DNA conformations – have been shown to play an important role in various
genomic processes. Flipons identification and localization is difficult due to their dynamic
nature. We developed deep learning approaches to identify non-B DNA secondary structures
using available information from thousands of omics data sets. We created DeepZ models
based on CNN and RNN, and ...
Added: November 30, 2023
Kuzin I., В кн.: МЕТОД: Московский ежегодник трудов из обществоведческих дисциплинВып. 11: Вслед за Дарвином. Эволюция знания об эволюции и самого феномена развития.: М.: ИНИОН РАН, 2021. С. 406–421.
This article examines the prospects for the ideas outlined in the monograph by Lily E. Kay «Who Wrote the Book of Life? History of the Genetic Code». Firstly, it is argued that this book is an important contribution to the cultural history of science. L.E. Kay connects the formation of molecular biology in the mid ...
Added: November 1, 2022
Nizhny Novgorod: Lobachevsky State University of Nizhny Novgorod (UNN), 2021.
Leading scientists from all over the world will meet together to discuss topical problems in the field of neuroscience and artificial intelligence. ...
Added: May 4, 2022
NY: Association for Computing Machinery (ACM), 2021.
Continuing the annual tradition, the conference focuses on interdisciplinary research linking computer science, mathematics, statistics, biology, bioinformatics, biomedical informatics, and health informatics. ...
Added: December 7, 2021
Polyansky A., FEBS Letters 2018 Vol. 592 No. 17 P. 2901–2916
Despite their importance, our understanding of noncovalent RNA–protein interactions is incomplete. This especially concerns the binding between RNA and unstructured protein regions, a widespread class of such interactions. Here, we review the recent experimental and computational work on RNA–protein interactions in an unstructured context with a particular focus on how such interactions may be shaped ...
Added: November 26, 2019
Polyansky A., Journal of Chemical Theory and Computation 2018 Vol. 14 P. 3796–3810
The recently developed NMR techniques enable estimation of protein configurational entropy change from the change in the average methyl order parameters. This experimental observable, however, does not directly measure the contribution of intramolecular couplings, protein main-chain motions, or angular dynamics. Here, we carry out a self-consistent computational analysis of the impact of these missing contributions ...
Added: November 26, 2019
Polyansky A., Journal of Chemical Theory and Computation 2017 Vol. 13 P. 4504–4513
In order to fully understand the microscopic origins of binding specificity between nucleic acids and proteins, it is imperative to study the dependence of the binding preferences between nucleobases and protein side chains on the properties of the environment. Here, we employ molecular dynamics simulations and umbrella sampling to derive the potentials of mean force ...
Added: November 26, 2019
Polyansky A., Nucleic Acids Research 2019 Vol. 47 No. 21 P. 11077–11089
To address the structural and dynamical consequences of amino-acid attachment at 2′- or 3′-hydroxyls of the terminal ribose in oligoribonucleotides, we have performed an extensive set of molecular dynamics simulations of model aminoacylated RNA trinucleotides. Our simulations suggest that 3′-modified trinucleotides exhibit higher solvent exposure of the aminoacylester bond and may be more susceptible to ...
Added: November 22, 2019