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Путешествия в «аномальные зоны» клетки с помощью вычислительной биофизики
С. 16–17.
Publication based on the results of:
In book
Т. 1. , Краснодар: Полиграфическое объединение «Плехановец», 2019.
Fedorova A., Jovišić N., Vallverdù J. et al., Advanced Electronic Materials 2024 Vol. 10 No. 12 Article 2400258
The energy efficiency of Artificial Intelligence (AI) systems is a crucial and actual issue that may have an important impact on an ecological, economic and technological level. Spiking Neural Networks (SNNs) are strongly suggested as valid candidates able to overcome Artificial Neural Networks (ANNs) in this specific contest. In this study, the proposal involves the ...
Added: December 12, 2024
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
Efremov R., 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. 58–58.
Детальный анализ меняющихся во времени свойств молекулярных поверхностей играет важную роль в процессах распознавания, взаимодействия и передачи сигналов в биомолекулярных системах. Технология «динамического молекулярного портрета» представляет собой современный подход к расчету, наглядной визуализации и сравнительному анализу различных физико-химических характеристик поверхности биомолекул. Эффективное использование таких подходов требует создания специальных методов компьютерной обработки, анализа и представления «молекулярных ...
Added: November 2, 2019
Волынский П. Е., Arbuzova A., Nolde D. 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 трудыТ. 1.: М.: Издательство "Перо", 2019. С. 141–141.
Функционирование многих белков, обладающих стабильной пространственной структурой в воде, часто связано с их переносом в клетку или из нее через липидную мембрану. Помимо белков, которые преодолевают такой барьер с помощью различных вспомогательных систем (например, транслоконов, мембранных переносчиков), некоторые белки способны спонтанно внедряться в мембрану с последующим проходом и рефолдингом на противоположной стороне липидного бислоя. Наиболее ...
Added: November 2, 2019
Коншина А. Г., Krylov N., Efremov R., В кн.: Сборник научных трудов VI съезда биофизиков РоссииТ. 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 РоссииТ. 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
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, 2019Vol. 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
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, 2019Vol. 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
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, 2019Vol. 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
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, 2019Vol. 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
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, 2019Vol. 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
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, 2019Vol. 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
Efremov R., Journal of Chemical Information and Modeling 2019 Vol. 59 No. 6 P. 2765–2775
Atomistic aspects of the structural organization, dynamics, and functioning of hydrated lipid bilayers - model cell membranes - are primarily governed by the fine balance of intermolecular interactions between all constituents of these systems. Besides the hydrophobic effect, which shapes the overall skeleton of lipid membranes, very important contribution to their behavior is made by ...
Added: August 7, 2019
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
NY: Nova Science Publishers, Inc., 2017.
In this book, the original papers have been collected that demonstrate the efficient use of the computer molecular dynamics (MD) simulation methods for the studying of nanoscale phenomena in the materials and life sciences. This volume contains the Proceedings of the International Symposium KSCMBS-2016 ”Khujand Symposium on Computational Materials and Biological Sciences” (10 th Japan–Russia ...
Added: November 14, 2017
Севастополь: Федеральное государственное автономное образовательное учреждение высшего образования "Севастопольский государственный университет", 2017.
The proceedings is a compilation of the reports of XI International science-technical
conference "Modern Trends in Biological Physics and Chemistry. BPPC-2017", organized by
Sevastopol State University 2-6 of October, 2017.
The proceedings contains materials of research papers, devoted to modern trends in
general and molecular biophysics, nanobiophysics, problems of modern biological,
biophysical and medicinal chemistry, and biophysical education.
The publication is ...
Added: November 14, 2017
Севастополь: Федеральное государственное автономное образовательное учреждение высшего образования "Севастопольский государственный университет", 2016.
The proceedings is a compilation of the reports of XI International science-technical conference "Modern Trends in Biological Physics and Chemistry. BPPC-2016", organized by Sevastopol State University 25-29 of April, 2016. The proceedings contains materials of research papers, devoted to modern trends in general and molecular biophysics, nanobiophysics, and problems of modern biological, biophysical and medicinal ...
Added: November 14, 2017
Chugunov A. O., Pyrkova D. V., Nolde D. E. et al., Scientific Reports 2013 Vol. 3 No. 1678
Bacterial cell wall is targeted by many antibiotics. Among them are lantibiotics, which realize their function via interaction with transmembrane lipid-II molecule — a chemically conserved part of the cell wall synthesis pathway. To investigate structural and dynamic properties of this molecule, we have performed a series of nearly microsecond-long molecular dynamics simulations (MD) of lipid-II ...
Added: November 13, 2013