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Молекулярное моделирование биомембран и их комплексов с трансмембранными α-спиралями белков
С. 108-109.
In book
Якутск : Северо-Восточный федеральный университет им. М.К. Аммосова, 2017
Dolgoprudni : MIPT, 2018
The International Conference “BIOMEMBRANES 2018” was held at Moscow Institute of Physics and Technology (MIPT), Russia, Dolgoprudny on October 1st - 5th, 2018. A major goal of this conference is to provide up-to-date information about research on biomembranes and to consolidate cross-disciplinary international scientific efforts in this field. The speacers focused on cutting-edge problems of ...
Added: October 23, 2018
Bragin P. E., Kuznetsov A.S., Bocharova O. V. et al., Biochimica et Biophysica Acta - Biomembranes 2018 Vol. 1860 No. 12 P. 2486-2498
The interaction between the elements of the secondary structure is the key process, determining the spatial structure and activity of a membrane protein. The transmembrane (TM) helix-helix interaction is known to be especially important for the function of so-called type I or bitopic membrane proteins, which have small TM domains, consisting of a single ⍺-helix. ...
Added: September 25, 2018
Kuznetsov A., Efremov R., В кн. : Актуальные вопросы биологической физики и химии. БФФХ-2017: материалы XII международной научно-технической конференции, г. Севастополь, 2-6 октября 2017 г. : Севастополь : Федеральное государственное автономное образовательное учреждение высшего образования "Севастопольский государственный университет", 2017. С. 313-317.
Transmembrane domains of the most membrane proteins consist of single α-helices or their bundles. They take part in the functioning of receptors and ion channels and provide spatial structure formation. Thus, helix-helix interactions in lipid environment are involved in crucial processes of cell functioning. The concept of dimerization motifs representing protein-protein interactions as direct residue ...
Added: November 14, 2017
Maurice P., Baud S., Bocharova O. et al., Scientific Reports 2016 Vol. 6 No. 38363 P. 1-19
Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural ...
Added: March 15, 2017
Volynsky P. E., Nolde D.E., Zakharova G. S. et al., Scientific Reports 2019 Vol. 9 P. 413
How is a water-soluble globular protein able to spontaneously cross a cellular membrane? It is commonly accepted that it undergoes significant structural rearrangements on the lipid-water interface, thus acquiring membrane binding and penetration ability. In this study molecular dynamics (MD) simulations have been used to explore large-scale conformational changes of the globular viscumin A chain ...
Added: February 10, 2020
Logvenkov S. A., Штейн А. А., Российский журнал биомеханики 2013 Т. 17 № 4 С. 37-46
Basing on the information about the structure of the solution and asymptotic estimates in the problem of steady flow across the root, a system of algebraic relations similar to the commonly used compartment models is obtained. As compared with these, the method proposed has an important advantage making it possible to take into account the ...
Added: January 30, 2014
Kuznetsov A., Polyansky A., Fleck M. et al., Journal of Chemical Theory and Computation 2015 Vol. 11 No. 9 P. 4415-4426
The cell membrane is "stuffed" with proteins, whose transmembrane (TM) helical domains spontaneously associate to form functionally active complexes. For a number of membrane receptors, a modulation of TM domains' oligomerization has been shown to contribute to the development of severe pathological states, thus calling for detailed studies of the atomistic aspects of the process. ...
Added: October 8, 2015
Kuznetsov A., Efremov R., В кн. : Физико-химические механизмы и регуляция процессов трансформации энергии в биологических структурах. : Ижевск : Ижевский институт компьютерных исследований, 2017. Гл. 1.1. С. 9-32.
В главе 1.1 (Кузнецов, Ефремов) рассмотрены теоретические подходы к изучению мембранных белков (МБ), которые являются важнейшим компонентом плазматической мембраны клетки. Они выполняют жизненно важные функции, а нарушения в их работе приводят к развитию патологических состояний. Изучение МБ экспериментальными методами требует особых подходов и техник, поскольку для их функционирования необходимо сохранение мембранного окружения. Поэтому несмотря на ...
Added: November 14, 2017
Efremov R., Konshina A., Dubovskii P., Current Medicinal Chemistry 2013 Vol. 21 No. 3 P. 270-287
Natural polycationic membrane-active peptides typically lack disulfide bonds and exhibit fusion, cell-penetrating, antimicrobial activities. They are mostly unordered in solution, but adopt a helical structure, when bound to phospholipid membranes. Structurally different are cardiotoxins (or cytotoxins, СTs) from cobra venom. They are fully b-structured molecules, characterized by the three-finger fold (TFF). Affinity of CTs to ...
Added: March 18, 2014
Polyansky A., Chugunov A., Volynsky P. et al., Bioinformatics 2014 Vol. 30 No. 6 P. 889-890
Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments; (ii) ranking and filtering of predicted structures according to respective values of a scoring function; (iii) visualization of predicted 3D dimer structures; ...
Added: May 15, 2014
Polyansky A., Kuznetsov A., Volynsky P. et al., , in : Biomembranes 2018. International Conference. 1-5 October 2018. Book of Abstracts. : Dolgoprudni : MIPT, 2018. P. 89-90.
A computational approach to the analysis of structural and dynamical properties of all components of model membranes - membrane proteins, lipids, water and ions - has been developed. It is established that local changes in the membrane environment play an important role in the binding of membrane-active peptides and peripherical membrane proteins, causing specific clustering ...
Added: October 23, 2018
Volynsky P., Maltseva D., Tabakmakher V. et al., Biomolecules 2022 Vol. 12 No. 2 Article 295
Structurally similar catalytic subunits A of ricin (RTA) and viscumin (MLA) exhibit cytotoxic activity through ribosome inactivation. Ricin is more cytotoxic than viscumin, although the molecular cause of this is still poorly understood. To shed more light on this problem, we used a combined biochemical / molecular modeling approach to assess the possible relationship between ...
Added: August 1, 2022
Yusipovich A., Parshina E., Baizhumanov A. A. et al., Instruments and Experimental Techniques 2021 Vol. 94 No. 6 P. 877-885
An automated interference microscope has been used to determine the rms amplitude of fluctuations of living cells in vitro. The geometric thickness of cells has been calculated based on the measured optical
path differences of light waves and the equivalent elastic constants of these cells have been estimated.
The determined rms amplitude of fluctuations of the optical ...
Added: November 15, 2021
Volynsky P., Efremov R., Mikhalev I. et al., Molecular Immunology 2017 Vol. 90 P. 87-97
Background
Human blood contains a big variety of natural antibodies, circulating throughout life at constant concentration. Previously, we have found natural antibodies capable of binding to trisaccharide Galα1-4Galβ1-4Glc (Pk) practically in all humans. Intriguingly, the same trisaccharide is a key fragment of glycosphingolipid globotriaosylceramide (Gb3Cer) – normal component of erythrocyte and endothelial cell membrane, i.e. the ...
Added: November 13, 2017
Бочаров Э. В., Лесовой Д. М., Минеев К. С. et al., В кн. : II объединенный научный форум: VI съезд физиологов СНГ, VI съезд биохимиков России, IX российский симпозиум «Белки и пептиды» (Сочи, Дагомыс, 1–6 октября 2019). Научные труды. Т. 2.: М. : Издательство "Перо", 2019. С. 45-46.
Биологическая функция битопных мембранных белков, имеющих только один трансмембранный (ТМ) сегмент, обеспечивается сетью разнообразных межмолекулярных взаимодействий в клеточной мембране. К этому классу белков принадлежат, например, рецепторы типа I, которые принимают непосредственное участие в развитии и поддержании гомеостаза тканей организма человека. Рецепторы эпидермального фактора роста (EGFR/HER) и гормона роста (GHR) служат удобными моделями рецепторов типа I, ...
Added: November 2, 2019
Коншина А. Г., Дубовский П. В., Efremov R., Journal of Chemical Information and Modeling 2021 Vol. 61 No. 1 P. 385-399
For many peripheral membrane-binding proteins (MBPs), especially β-structural ones, the precise molecular mechanisms of membrane insertion remain unclear. In most cases, only the terminal water-soluble and membrane-bound states have been elucidated, whereas potential functionally important intermediate stages are still not understood in sufficient detail. In this study we present one of the first successful attempts ...
Added: January 24, 2021
Kiselevsky D. B., Shagdarova B. T., Varlamov V. P. et al., Moscow University Biological Sciences Bulletin 2021 Vol. 76 No. 1 P. 14-19
The effect of low molecular weight chitosans with a molecular weight (MW) of 5, 6, 10, 25, and 45 kDa and a deacetylation degree (DD) of 85–99% obtained by chemical depolymerization and enzymatic hydrolysis on the cells of the epidermis of pea leaves was analyzed. Low molecular weight chitosans induced damage to guard cells' plasma membrane, ...
Added: October 14, 2022