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Оценка взаимного влияния белок-мембрана для рецепторных тирозинкиназ в компьютерном эксперименте
С. 53–54.
Kuznetsov A., Efremov R.
Receptor tyrosine kinases form an important class of membrane proteins that regulate cell life cycle and metabolism. Among wide variety of receptors, they have simple structure with single alpha-helix crossing the membrane. This transmembrane domain is functionalm as dimeric state conformation defines active/inactive state of the receptor. The lipid environment can modulate functioning of such proteins, but the exact details are not well described yet. In addition to specific interactions with certain types of lipids, cholesterol and gangliosides, there are non-specific ones, since physico-chemical parameters are dependent on local lipid composition around protein molecule. However, there are opposite hypotheses about what is the driving force of heterogeneities formation in the membrane: lipid molecules themselves or membrane proteins embedded in the bilayer. To answer the question on mutual influence of proteins and their lipid environment, we used atomistic computer modeling: molecular dynamics simulations followed by a detailed analysis of intermolecular contacts to identify key amino acid residues that determine protein-lipid interactions. It was shown that the number of protein-lipid contacts depends on the conformation of the dimeric state, and their distribution over the monolayers is asymmetric. The results of the work will help in understanding the mechanism of signal transduction by receptor tyrosine kinases and finding ways to influence their activity.
In book
Вып. 27: Двадцать седьмая международная конференция "Математика. Компьютер. Образование." Симпозиум с международным участием "Биофизика сложных систем, вычислительная и системная биология, молекулярное моделирование". , Ижевск: Ижевский институт компьютерных исследований, 2020.
Goryashchenko A., Mozhaev AA, Serova O. et al., Biomolecules 2020 Vol. 10 No. 7 P. 1060–0
To study the structure and function of the pH-regulated receptor tyrosine kinase insulin receptor-related receptor (IRR), а member of the insulin receptor family, we obtained six mouse monoclonal antibodies against the recombinant IRR ectodomain. These antibodies were characterized in experiments with exogenously expressed full-length IRR by Western blotting, immunoprecipitation, and immunocytochemistry analyses. Utilizing a previously ...
Added: February 4, 2024
Yaremenko I., Belyakova Y., Radulov P. et al., Journal of Organic Chemistry 2023 Vol. 88 No. 19 P. 13782–13795
Relief of stereoelectronic frustration drives the acid-catalyzed three-component condensation of β,δ′-triketones with hydrazides and H2O2 to the direction where both nucleophiles and all three electrophilic carbons are involved in the formation of a tricyclic sp3-rich ring system that includes four heteroatoms. The otherwise inaccessible tricyclic N-substituted aminoperoxides are prepared rapidly and selectively from relatively simple ...
Added: October 24, 2023
Zelenina A. I., Gordeev I. S., Kolotova L., Journal of Non-Crystalline Solids 2023 Vol. 606 Article 122215
Plasmonic nanoobjects have many applications from biosensors to electronic device components. The most promising method for obtaining such objects is the laser printing method due to the possibility of controlling the resulting structure by experimental conditions. In this work, the influence of laser printing initial parameters and Al content on silicon-aluminum nanoparticles (NPs) structure were investigated by a combination ...
Added: June 28, 2023
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
Kondratyuk N., Pisarev V., Успехи физических наук 2023 Т. 193 № 4 С. 437–461
Predictive models for the shear viscosity of liquids and gases together with the exact equations of state have a great importance for the problems of hydrodynamic modeling of processes occurring in nature, industrial plants and mechanisms. This review aims to consider the currently proposed theoretical, including atomistic modeling, and empirical approaches for predicting the viscosity ...
Added: August 9, 2022
Kolotova L., Starikov S., Journal of Nuclear Materials 2017 Vol. 495 P. 111–117
In irradiation of swift heavy ions, the defects formation frequently takes place in crystals. High energy
transfer into the electronic subsystem and relaxations processes lead to the formation of structural
defects and cause specific effects, such as the track formation. There is a large interest to understanding
of the mechanisms of defects/tracks formation due to the heating of ...
Added: January 28, 2022
Starikov S., Kolotova L., Scripta Materialia 2016 Vol. 113 P. 27–30
Using molecular dynamics simulations, we study the structural properties of body-centered cubic (BCC) and
body-centered tetragonal (BCT) phases of U–Mo alloys. The local positions of uranium atoms in the BCC phase
correspond to the BCT structure. Thus, the BCC lattice exhibits cubic symmetry only on the scale of several
interatomic spacings, and it is therefore more correct to ...
Added: January 28, 2022
Damodaran K., Delaye J. -., Kalinichev A. G. et al., Acta Materialia 2022 Vol. 225 Article 117478
The role of Al in aluminosilicate glasses remains somewhat a mystery: at low concentrations, it increases the resistance to hydrolysis of the glass, whereas at high concentrations an opposite effect is observed. To understand the origin of the phenomenon on a fundamental atomistic scale, we performed 577 MD simulations and applied potential mean force (PMF) ...
Added: December 10, 2021
Yu K. B., Bowers G. M., Loganathan N. et al., Energy & Fuels 2021 Vol. 35 No. 20 P. 16515–16526
As global energy demand increases, natural gas recovery from source rocks is attracting considerable attention since recent development in shale extraction techniques has made the recovery process economically viable. Kerogens are thought to play an important role in gas recovery; however, the interactions between trapped shale gas and kerogens remain poorly understood due to the ...
Added: November 3, 2021
Eliseev I. E., Yudenko A. N., Vysochinskaya V. V. et al., F1000Research 2018 Vol. 7 Article 57
Background: The ability of ErbB3 receptor to functionally complement ErbB1-2 and induce tumor resistance to their inhibitors makes it a unique target in cancer therapy by monoclonal antibodies. Here we report the expression, purification and structural analysis of a new anti-ErbB3 single-chain antibody.
Methods: The VHH fragment of the antibody was expressed in E. coli SHuffle cells as ...
Added: September 24, 2021
Kalinichev A. G., , in: Computational Modeling in Clay MineralogyVol. 3.: Bari: Digilabs Pub., 2021. Ch. 2 P. 17–52.
The Chapter is based on the material of two invited lectures given by the author at the AIPEA School for Young Scientists “Computational Modeling In Clay Mineralogy”, Granada, Spain, July 2017, and the Workshop “Argilla Studium-2019”, Moscow, Russia, November 2019. ...
Added: September 5, 2021
Bari: Digilabs Pub., 2021.
ASYS, the AIPEA School for Young Scientists. ASYS was successfully convened at the Andalusian Institute of
Earth Sciences (CSIC-UGR, Granada, Spain) on July 15 and 16, 2017, under the supervision of Dr. Claro Ignacio
Sainz Díaz, researcher of this centre, and in close connection to the 16th International Clay Conference in Granada
(ICC 2017). Young and not so-young ...
Added: September 5, 2021
Cygan R. T., Greathouse J. A., Kalinichev A. G., Journal of Physical Chemistry C 2021 Vol. 125 No. 32 P. 17573–17589
As a general-purpose force field for molecular simulations of layered materials and their fluid interfaces, Clayff continues to see broad usage in atomistic computational modeling for numerous geoscience and materials science applications due to its (1) success in predicting properties of bulk nanoporous materials and their interfaces, (2) transferability to a range of layered and ...
Added: September 5, 2021
Mutisya S. M., Kalinichev A. G., Minerals 2021 Vol. 11 No. 5 Article 509
Geological carbon capture and sequestration (CCS) is a promising technology for curbing the global warming crisis by reduction of the overall carbon footprint. Degradation of cement wellbore casings due to carbonation reactions in the underground CO2 storage environment is one of the central issues in assessing the long-term success of the CCS operations. However, the ...
Added: September 5, 2021
Nikolskiy V., Stegailov V., , in: Parallel Computing: Technology Trends.: IOS Press, 2020. P. 565–573.
In this work, a new algorithm was developed for calculating the fourpoint water model TIP4P on graphics accelerators. It was designed as a part of the flexible molecular dynamics modeling package LAMMPS in the library module “GPU”. In this paper we describe two approaches to implement the TIP4P model for GPU: 1) to divide the ...
Added: March 27, 2020
Kuznetsov A., Efremov R., В кн.: Сборник научных трудов VI съезда биофизиков РоссииТ. 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
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
Stegailov V., Dlinnova E., Ismagilov T. et al., International Journal of High Performance Computing Applications 2019 Vol. 33 No. 3 P. 507–521
In this paper, we describe the Desmos supercomputer that consists of 32 hybrid nodes connected by a low-latency highbandwidth Angara interconnect with torus topology. This supercomputer is aimed at cost-effective classical molecular dynamics calculations. Desmos serves as a test bed for the Angara interconnect that supports 3D and 4D torus network topologies, and verifies its ...
Added: November 11, 2018
Kuznetsov Andrey S., Smirnov Kirill V., Antonov M. Y. et al., , in: AIP Conference ProceedingsVol. 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