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Технология «динамического молекулярного портрета» в вычислительном анализе белков и биомембран
С. 58-58.
In book
Т. 2. , М. : Издательство "Перо", 2019
Zamaletdinov M., Kuznetsov A., Maurice P. et al., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 27-047. P. 262-262.
Insulin receptor (IR) family is represented by three membrane proteins participating in organism development, growth, and vital activity. Modulation of the functioning of these receptors by external agents looks very perspective from a pharmaceutical point of view. Although IR is well studied, little is known about the role of its transmembrane (TM) domain in receptor ...
Added: November 1, 2019
Festa P., Pardalos P. M., Annals of Operations Research 2012 P. 663-682
Computational molecular biology has emerged as one of the most exciting interdisciplinary fields. It has currently benefited from concepts and theoretical results obtained by different scientific research communities, including genetics, biochemistry, and computer science. In the past few years it has been shown that a large number of molecular biology problems can be formulated as ...
Added: January 9, 2013
Urban A., Bocharov E., Nadezhdin K. et al., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 31-016. P. 299-299.
Bitopic proteins having only one helical transmembrane (TM) domain are a class of biologically significant membrane proteins, including the type I receptors and amyloid precursor protein (APP), which are involved in regulating the homeostasis of human organism and recognized as substrate by c-secretase. Amyloid Ab-peptides forming plaques in brain during Alzheimer disease (AD) are the ...
Added: November 1, 2019
Pham S. K., Antipov D., Sirotkin Alexander et al., Journal of Computational Biology 2013 Vol. 20 No. 4 P. 359-371
One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in ...
Added: March 21, 2014
Коншина А. Г., Krylov N., Efremov R., В кн. : Сборник научных трудов VI съезда биофизиков России. Т. 1.: Краснодар : Полиграфическое объединение «Плехановец», 2019. С. 160-161.
Изучение влияния мембранногоокруженияна работу различныхбелок-мембранныхкомплексов (трансмембранных каналов, рецепторов) являетсяодним из актуальныхнаправленийсовременнойструктурнойбиологии. Изменения в структурных параметрах бислоя, в частности,локальные возмущения геометрии, подвижности липидов при встраивании небольших мембрано-активных полипептидовмогут представлять особый интерес с точки зренияконтролируемого изменения активности рецепторных систем клетки. Подобная модуляция активности показана экспериментальнона клетках, обработанных цитотоксинами[1].Однако получить детальную информацию о механизме встраивания пептида-модулятора и локальных ...
Added: November 1, 2019
Panina I., Chugunov A., Krylov N. et al., В кн. : Сборник научных трудов VI съезда биофизиков России. Т. 1.: Краснодар : Полиграфическое объединение «Плехановец», 2019. С. 83-84.
Устойчивость микроорганизмов к применяемым в клинической практике антибиотикам является серьезной проблемой медицины во всем мире. В связи с этим одной из актуальных задач современной фармакологии является поиск или дизайн новых антибактериальных веществ, свободных от бремени резистентности. Перспективными кандидатами для разработки новых лекарств являются антимикробные пептиды (АМП). Среди всего разнообразия АМП особое внимание привлекают пептиды, мишенью ...
Added: November 1, 2019
Albrecht C., Dhaideh Z., Appert-Collin A. et al., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 31-006. P. 295-296.
Elastin is an essential component of numerous human tissues and plays a critical role in elasticity of skin, lungs and arteries. During vascular aging, the elastin network is degraded generating elastin-derived peptides (EDP). The ERC (Elastin Receptor Complex) is a membrane heterotrimeric receptor composed, amongst others, of a membrane-bound neuraminidase, NEU-1. Binding of EDP to ...
Added: November 1, 2019
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
Osmakov D., Belozerova O., Koshelev S. et al., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 15-014. P. 183-183.
Acid-sensing ion channels (ASICs), members of the family of
amiloride-sensitive degenerin/epithelial
Na + -channels, are expressed in neurons of both the peripheral and central nervous
system. Among six currently known isoforms of mammalian
ASICs, two, namely ASIC1a and ASIC3 are widespread and
have the largest physiological contribution such as synaptic plasticity, learning and memory as well as pain perception and
inflammation ...
Added: November 1, 2019
Efremov R., Koromyslova A., Chugunov A., Journal of Chemical Information and Modeling 2014 Vol. 54 No. 4 P. 1189-1199
Molecular surfaces are one of the key players in processes of bimolecular recognition and interaction. Nowadays, state of the art methods exist for visualizing molecule surface and surface distributed properties in three-dimensional space. However, such visual information could only be analyzed by human eye and therefore prompt to be biased and onerous in case of ...
Added: May 15, 2014
Aliper E. T., Krylov Nikolay A., Nolde Dmitry E. et al., International Journal of Molecular Sciences 2022 Vol. 23(16) Article 9221
Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic
transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D
structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational
framework to model the spike TMD only based on its primary structure. We performed amino acid
sequence pattern matching and compared the molecular hydrophobicity potential ...
Added: August 25, 2022
Dubovskii P., Efremov R., Expert Review of Proteomics 2018 Vol. 15 No. 11 P. 873-886
Introduction: Being important representatives of various proteomes, membrane-active cationic peptides (CPs) are attractive objects as lead compounds in the design of new antibacterial, anticancer, antifungal, and antiviral molecules. Numerous CPs are found in insect and snake venoms, where many of them reveal cytolytic properties. Due to advances in omics technologies, the number of such peptides ...
Added: October 24, 2018
Panina I. S., Chugunov A., Efremov R., Russian Journal of Bioorganic Chemistry 2018 Vol. 44 No. 6 P. 653-664
The growing problem of antibiotic resistance in medicine raises the attention to antimicrobial substances that act on non-protein molecules, which have more conservative structure comparing to proteins or peptides. One of the most promising and studied targets is lipid II — the participant of the bacterial cell wall biosynthetic pathway. Lipid II is present in ...
Added: February 25, 2019
Данченко В. И., Давыдов А. А., Nikitin A. A., М. : Издательский отдел факультета ВМК МГУ им. М.В. Ломоносова, 2009
Added: September 24, 2013
Bocharov E., Lesovoy D., Pavlov K. et al., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 06-027. P. 130-130.
The human epidermal growth factor (EGFR/HER) and growth hormone (GHR) receptors serve as excellent models of type I receptors to illustrate how ligand-induced conformational rearrangements and specific dimerization of extracellular domains lead to the allosteric activation of the cytoplasmic domains via single-span transmembrane domain (TMD). We determined the alternative dimeric conformations of the EGFR and ...
Added: November 1, 2019
Kuznetsov A., Maurice P., Efremov R., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 27-068. P. 268-269.
Receptor tyrosine kinases (RTK) are vital players in cell signaling governing growth and proliferation. These integral membrane proteins work only in dimeric states, so the conformation of transmembrane dimer determines the signal transferred into cell. Here, we used modern molecular modeling techniques to study details of protein-protein and protein-lipid interactions in model systems containing monomers ...
Added: November 1, 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
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
Springer, 2019
In this paper, we study the Maximum Happy Vertices and the Maximum Happy Edges problems (MHV and MHE for short). Very recently, the problems attracted a lot of attention and were studied in Agrawal ’17, Aravind et al. ’16, Choudhari and Reddy ’18, Misra and Reddy ’17. Main focus of our work is lower bounds on the computational complexity ...
Added: October 29, 2019
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
Panina I., Chugunov A., Dmitry Nolde et al., , in : FEBS Open Bio Volume 9, Issue S1 Supplement: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019. Vol. 9: 44th FEBS Congress, From Molecules to Living Systems, Krakow, Poland, July 6‐11, 2019.: Oxford : Wiley, 2019. Ch. 27-069. P. 269-269.
The worldwide rapid emergence of resistant bacteria put at threat the efficacy of antibiotics, thus the development of novel antibacterial agents is urgently needed. The cell wall precursor lipid II consisting the chemically conservative pyrophosphate group represents a promising pharmaceutical target. Antimicrobial peptides, that target lipid II, i.e. lantibiotic nisin, could be excellent prototypes for ...
Added: November 1, 2019
Pardalos P. M., Pappalardo E., Stracquadanio G., Dordrecht, L., Heidelberg, NY : Springer, 2013
Optimization Approaches for Solving String Selection Problems provides an overview of optimization methods for a wide class of genomics-related problems in relation to the string selection problems. This class of problems addresses the recognition of similar characteristics or differences within biological sequences. Specifically, this book considers a large class of problems, ranging from the closest ...
Added: November 8, 2013
Panina I., Krylov N., Nolde D. et al., Scientific Reports 2020 Vol. 10 Article 8821
Antibiotics (AB) resistance is a major threat to global health, thus the development of novel AB classes is urgently needed. Lantibiotics (i.e. nisin) are natural compounds that effectively control bacterial populations, yet their clinical potential is very limited. Nisin targets membrane-embedded cell wall precursor — lipid II — via capturing its pyrophosphate group (PPi), which is unlikely ...
Added: June 1, 2020
Polyansky A., Nucleic Acids Research 2017 Vol. 45 No. 16 P. 9741-9759
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 ...
Added: November 26, 2019