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GPR55 Receptor Activation by the N-Acyl Dopamine Family Lipids Induces Apoptosis in Cancer Cells via the Nitric Oxide Synthase (nNOS) Over-Stimulation
International Journal of Molecular Sciences. 2021. Vol. 22. No. 2. P. 622.
Akimov M., Gamisonia A., Dudina P., Gretskaya N., Gaydaryova A., Kuznetsov A., Zinchenko G., Bezuglov V.
Polyansky A., Roman G. Efremov, Computational and Structural Biotechnology Journal 2023 Vol. 21 P. 2837-2844
Constitutive activation of receptor tyrosine kinases (RTKs) via different mutations has a strong impact on the development of severe human disorders, including cancer. Here we propose a putative activation scenario of RTKs, whereby transmembrane (TM) mutations can also promote higher-order oligomerization of the receptors that leads to the subsequent ligand-free activation. We illustrate this scenario ...
Added: May 19, 2023
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
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
Antipova M. L., Petrenko V. E., Odintsova E. G., Journal of Supercritical Fluids 2018 No. 139 P. 19-29
The study of the selective solvation of hydroxycinnamic acids (para-coumaric, caffeic) by a polar cosolvent
(acetone, methanol) in supercritical carbon dioxide at T=328 K, ρ=0.772 g/cm3 has been carried out using
the molecular dynamics and quantum-chemical calculations. It has been shown that the selective solvation of the
solute occurs by the formation of hydrogen-bonded complexes with a cosolvent. ...
Added: November 19, 2021
Стройлов В. С., Панова М. А., Toukach P., International Journal of Molecular Sciences 2020 Vol. 21 No. 20 Article 7626
Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular ...
Added: January 31, 2022
Goncharuk M., Baleeva N., Nolde Dmitry E. et al., Communications Biology 2022 Vol. 5 Article 706
“Fluorescence-Activating and absorption-Shifting Tag” (FAST) is a well-studied fluorogenactivating
protein with high brightness and low size, able to activate a wide range of
fluorogens. This makes FAST a promising target for both protein and fluorogen optimization.
Here, we describe the structure-based rational design of the enhanced FAST mutants,
optimized for the N871b fluorogen. Using the spatial structure of the ...
Added: August 1, 2022
Pyrkova D. V., Tarasova N. K., Krylov N. et al., Journal of Biomolecular Structure and Dynamics 2013 Vol. 31 No. 1 P. 87-95
Delineation and analysis of lateral clustering of lipids in model bilayers is an important step toward understanding of the physical processes underlying formation of lipid domains and rafts in cell membranes. Computer modeling methods represent a powerful tool to address the problem since they can detect clusters of only few lipid molecules – this issue ...
Added: November 14, 2013
Nikita A. Kosarim, Armeev G., Alexey K. Shaytan et al., Supercomputing Frontiers and Innovations 2022 Vol. 9 No. 2 P. 56-67
The nucleosome is the basic unit of eukaryotic DNA compaction. It consists of about 147 base pairs wrapped around an octamer of histone proteins. Nucleosomal dynamics provides the availability of packaged DNA for various factors that carry out the vital processes associated with chromatin. It is not completely known how the structure and dynamics of ...
Added: September 4, 2023
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
Goryacheva E., Efremov R., Krylov N. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 7 Article 6403
The rapid development of new microscopy techniques for cell biology has exposed the
need for genetically encoded fluorescent tags with special properties. Fluorescent biomarkers of the
same color and spectral range and different fluorescent lifetimes (FLs) became useful for fluorescent
lifetime image microscopy (FLIM). One such tag, the green fluorescent protein BrUSLEE (Bright
Ultimately Short Lifetime Enhanced Emitter), having ...
Added: May 19, 2023
Efremov R., Нольде Д. Е., Волынский П. Е. et al., Scientific Reports 2019 Vol. 9 No. 413 P. 1-12
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 6, 2019
Dubovskii P., Dubinnyi M., Konshina A. et al., Biochemistry 2017 Vol. 56 No. 34 P. 4468-4477
Today, recombinant proteins are quite widely used in biomedical and biotechnological applications. At the same time, the question about their full equivalence to the native analogues remains unanswered. To gain additional insight into this problem, intimate atomistic details of a relatively simple protein, small and structurally rigid recombinant cardiotoxin I (CTI) from cobra Naja oxiana ...
Added: November 13, 2017
Контаров Н. А., Grishunina S., Балаев Н. В. et al., Инфекция и иммунитет 2013 Т. 3 № 4 С. 376-378
In the study the mathematical analysis of viruses reproduction in cell culture using the Marchuk' mathematical model to predict reproduction of virus in one or another cell cultures has been conducted. The obtained theoretical results are corresponded to the experimental data on reproduction od rubella virus in cell cultures of RK-13 and BHK-21. The sum ...
Added: May 9, 2016
Chugunov A.O., Volynsky P. E., Krylov N.A. et al., Scientific Reports 2016 Vol. 6 P. 33112
Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of ...
Added: February 10, 2020
Nolde D., Krylov N., Телегин П. Н. et al., Труды НИИСИ РАН 2018 Т. 7 № 4 С. 157-161
The performance of molecular dynamics software package Gromacs was measured on various
hardware: desktop computers, clusters based on x84_64 processors or many integrated core processors, and
heterogeneous system with gaming graphic cards or general purpose GPU systems. The optimal choice of hardware
for molecular dynamics simulations is discussed. ...
Added: February 10, 2020
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
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
Panina I., Balandin S., Tsarev A. et al., International Journal of Molecular Sciences 2023 Vol. 24 No. 2 P. 1
To date, a number of lantibiotics have been shown to use lipid II — a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria — as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin (Lchα), previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding ...
Added: February 21, 2023
Lohan S., Konshina A. G., Efremov R. et al., Journal of Medicinal Chemistry 2023 Vol. 66 No. 1 P. 855-874
A series of small (7- to 12-mer) amphipathic cationic peptides were designed and synthesized with the ultimate goal of creating a set of short helical peptides with broad-range bactericidal activity and good selectivity toward the bacterial cells. Activity analysis identified a lead 12-mer peptide 8b with broad spectrum activity against Gram-positive (MIC=3.1-6.2 µg/mL) and Gram-negative ...
Added: February 21, 2023
Aseev L. V., Chugunov A. O., Efremov R. et al., Journal of Bacteriology 2013 Vol. 195 No. 1 P. 95-104
Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct
phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants,
rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of ...
Added: November 14, 2013
Lohan S., Mandal D., Choi W. et al., Journal of Medicinal Chemistry 2022 Vol. 65 No. 1 P. 665-687
We report the synthesis and antibacterial activities of a series of amphiphilic membrane-active peptides composed, in part, of various non-genetically coded hydrophobic amino acids. Lead cyclic peptides, 8C and 9C, showed broad-spectrum activity against drug-resistant Gram-positive (MIC=1.5-6.2 µg/mL) and Gram-negative (MIC=12.5-25 µg/mL) bacteria. Cytotoxicity study showed the predominant lethal action of the peptides against bacteria ...
Added: February 1, 2022
Panina I., Chugunov A., Nolde D. et al., FEBS Open Bio 2021 Vol. 11 No. Suppl.1 P. 356-356
Given the challenge of global antibiotic resistance, the development of new medications is indispensable. Lipid II - bacterial cell wall precursor – is a promising pharmaceutical target for innovative antibiotics, whereas lantibiotic nisin, effectively capturing lipid II’s conservative pyrophosphate group, is a potential prototype of a new generation of antibiotics. Because the structure of membrane-bound ...
Added: August 31, 2021
Philip V Toukach, Scherbinina S. I., Frank M., Glycobiology 2022 Vol. 32 No. 6 P. 460-468
Population analysis in terms of glycosidic torsion angles is frequently used to reveal preferred conformers of glycans. However, due to high structural diversity and flexibility of carbohydrates, conformational characterization of complex glycans can be a challenging task. Herein we present a conformation module of oligosaccharide fragments occurring in natural glycan structures developed on the platform ...
Added: October 24, 2022
Nadezhdin K., Neuberger A., Trofimov Y. et al., Nature Structural and Molecular Biology 2021 Vol. 28 P. 564-572
Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open ...
Added: August 24, 2021