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Молекулярно-динамические аспекты взаимодействия трансмембранного сегмента нейраминидазы-1 с перспективным пептидным перехватчиком
С. 108-108.
In book
Т. 2. , М. : Издательство "Перо", 2019
Kuznetsov A., Efremov R., Волынский П. Е., Acta Naturae 2015 Т. 7 № 4 С. 135-140
An efficient computational approach is developed to quantify the free energy of a spontaneous association of the α-helices of proteins in the membrane environment. The approach is based on the numerical decomposition of the free energy profiles of the transmembrane (TM) helices into components corresponding to protein-protein, protein-lipid, and protein-water interactions. The method was tested ...
Added: February 20, 2016
Kuznetsov Andrey S., Volynsky P., Efremov Roman G., , in : Computed Design for New Drugs and Materials. Molecular Dynamics of Nanoscale Phenomena. : NY : Nova Science Publishers, Inc., 2017. Ch. 5. P. 89-107.
Plasmatic membranes contain high amount of membrane proteins. They perform vital functions of life, so any disruptions in their structure result in pathologies and diseases. Studies of these proteins with experimental methods are very complicated and expensive, as they require the membrane environment. Despite considerable progress achieved so far in methods of structure determination and ...
Added: November 14, 2017
Bocharov E., Nadezhdin K., Urban A. et al., ACS Chemical Biology 2019 Vol. 14 No. 7 P. 1573-1582
Alzheimer’s disease is an age-related pathology associated with accumulation of amyloid-β peptides, products of enzymatic cleavage of amyloid-β precursor protein (APP) by secretases. Several familial mutations causing early onset of the disease have been identified in the APP transmembrane (TM) domain. The mutations influence production of amyloid-β, but the molecular mechanisms of this effect are ...
Added: August 8, 2019
Albrecht C., Kuznetsov A., Appert-Collin A. et al., Frontiers in Cell and Developmental Biology 2020 Vol. 8 P. 611121
Sialidases, or neuraminidases, are involved in several human disorders such as neurodegenerative, infectious and cardiovascular diseases, and cancers. Accumulative data have shown that inhibition of neuraminidases, such as NEU1 sialidase, may be a promising pharmacological target, and selective inhibitors of NEU1 are therefore needed to better understand the biological functions of this sialidase. In the ...
Added: December 14, 2020
Bocharov E. V., Lesovoy D. M., Bocharova O. V. et al., Biochimica et Biophysica Acta - General Subjects 2018 Vol. 1862 No. 6 P. 1410-1420
Background: Prior studies of the human growth hormone receptor (GHR) revealed a distinct role of spatial rearrangements of its dimeric transmembrane domain in signal transduction across membrane. Detailed structural information obtained in the present study allowed elucidating the bases of such rearrangement and provided novel insights into receptor functioning.
Methods: We investigated the dimerization of recombinant ...
Added: April 5, 2018
Kuznetsov A., Efremov R., В кн. : Тезисы докладов XXVI Международной конференции "Математика. Компьютер. Образование". МКО-2019. : [б.и.], 2019. С. 45-45.
Transmembrane (TM) helices are one of the most common structural elements in membrane proteins. Their interaction in lipid environment governs the formation of protein spatial structure formation and functioning in normal and pathology. Receptor tyrosine kinases are a wide class of protein molecules having single helix as their TM domain, so dimerization process is crucial ...
Added: November 1, 2019
Bershatsky Y., Kuznetsov A., Idiatullina A. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 4 Article 3906
Human InsR, IGF1R, and IRR receptor tyrosine kinases (RTK) of the insulin receptor
subfamily play an important role in signaling pathways for a wide range of physiological processes
and are directly associated with many pathologies, including neurodegenerative diseases. The
disulfide-linked dimeric structure of these receptors is unique among RTKs. Sharing high sequence
and structure homology, the receptors differ dramatically ...
Added: May 19, 2023
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
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., Bennasroune A., Maurice P. et al., FEBS Open Bio 2021 Vol. 11 No. Suppl.1 P. 219-219
The receptor tyrosine kinase (RTK) superfamily comprises many different cell-surface receptors having similar membrane organization and function with signal transduction occuring in the dimeric state. Insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) differ from other RTKs being constitutively homodimeric transmembrane glycoproteins, and molecular mechanisms of their activation still remain elusive. Current ...
Added: August 30, 2021
Efremov R., Albrecht C., Appert-Collin A. et al., Frontiers in Oncology 2020 Vol. 10 P. 519
Cellular functions are regulated by extracellular signals such as hormones,
neurotransmitters, matrix ligands, and other chemical or physical stimuli. Ligand
binding on its transmembrane receptor induced cell signaling and the recruitment of
several interacting partners to the plasma membrane. Nowadays, it is well-established
that the transmembrane domain is not only an anchor of these receptors to the
membrane, but it ...
Added: September 1, 2020
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
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
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
Kuznetsov A., Zamaletdinov M., Bershatsky Y. et al., Biochimica et Biophysica Acta - Biomembranes 2020 Vol. 1862 No. 11 P. 183417
Despite the biological significance of insulin signaling, the molecular mechanisms of activation of the insulin receptor (IR) and other proteins from its family remain elusive. Current hypothesis on signal transduction suggests ligand-triggered structural changes in the extracellular domain followed by transmembrane (TM) domains closure and dimerization leading to trans-autophosphorylation and kinase activity in intracellular segments ...
Added: August 27, 2020
Bocharov E. V., Mineev K. S., Pavlov K. V. et al., Biochimica et Biophysica Acta - Biomembranes 2017 Vol. 1859 No. 4 P. 561-576
Interaction between transmembrane helices often determines biological activity of membrane proteins. Bitopic proteins, a broad subclass of membrane proteins, form dimers containing two membrane-spanning helices. Some aspects of their structure-function relationship cannot be fully understood without considering the protein-lipid interaction, which can determine the protein conformational ensemble. Experimental and computer modeling data concerning transmembrane parts ...
Added: February 15, 2017
Kuznetsov A., Efremov R., В кн. : Сборник научных трудов VI съезда биофизиков России. Т. 1.: Краснодар : Полиграфическое объединение «Плехановец», 2019. С. 165-165.
Рецепторные тирозинкиназы семейства ErbB —это белки, играющие ключевую роль в процессахделения и дифференцировки клеток. Их природными лигандами являются различные гормоны и факторы роста. В то же время, выявлен ряд мутаций, приводящий к спонтанной активации рецепторов ErbB и развитию патологических состояний организма. В частности, рецептор ErbB2 также известен как Neu-онкоген, поскольку для многих видов рака выявлен ...
Added: November 1, 2019
Bocharov E. V., Bragin P. E., Pavlov K. V. et al., Biochemistry 2017 Vol. 56 No. 12 P. 1697-1705
The epidermal growth factor receptor (EGFR) family is an important class of receptor tyrosine kinases, mediating a variety of cellular responses in normal biological processes and in pathological states of multicellular organisms. Different modes of dimerization of the human EGFR transmembrane domain (TMD) in different membrane mimetics recently prompted us to propose a novel signal ...
Added: May 19, 2017
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
Kuznetsov A., Efremov R., В кн. : Актуальные вопросы биологической физики и химии. БФФХ-2016: материалы XI международной научной-технической конференции, г. Севастополь, 25-29 апреля 2016 г. Т. 1. Вып. 1.: Севастополь : Федеральное государственное автономное образовательное учреждение высшего образования "Севастопольский государственный университет", 2016. С. 250-254.
Here we present a combined method to study mutual effects of a protein and a membrane upon the
dimerization of transmembrane (TM) α-helical peptides. The approach is based on the numerical decomposition of
dimerization free energy profiles for TM helices into components corresponding to different interaction types and on the
mapping of the distribution of the average lipid ...
Added: November 14, 2017
Gylmiyarova F., Ryskina E.A., Kolotyeva N. et al., , in : Blood Groups. : IntechOpen, 2019. Ch. 5. P. 63-77.
This work presents a research of intermolecular interactions on the example of the antigen antibody interactions of the ABO system. This model could be successfully used in the future due to the lack of knowledge in the area of the ABO antigen’s behavior as a biomolecule and the integration of these structures into chain of ...
Added: October 23, 2020
Kuznetsov Andrey S., Smirnov Kirill V., Antonov M. Y. et al., , in : AIP Conference Proceedings. Vol. 1907: Proceedings of the 8th International Conference on Mathematical Modeling (ICMM-2017).: Melville : AIP Publishing LLC, 2017. Ch. 030023. P. 030023-1-030023-5.
Helical segments are common structural elements of membrane proteins. Dimerization and oligomerization of transmembrane (TM) α-helices provides the framework for spatial structure formation and protein-protein interactions. The membrane itself also takes part in the protein functioning. There are some examples of the mutual influence of the lipid bilayer properties and embedded membrane proteins. This work ...
Added: October 23, 2018