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Article ; Online: Myelin basic protein antagonizes the SARS-CoV-2 protein ORF3a-induced autophagy inhibition.

Saratov, George A / Belogurov, Alexey A / Kudriaeva, Anna A

2024

Abstract: Inhibition of autophagy is one of the hallmarks of the SARS-CoV-2 infection. Recently it was reported that SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes via interaction with VPS39 thus preventing binding of homotypic fusion ... ...

Abstract	Inhibition of autophagy is one of the hallmarks of the SARS-CoV-2 infection. Recently it was reported that SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes via interaction with VPS39 thus preventing binding of homotypic fusion and protein sorting (HOPS) complex to RAB7 GTPase. Here we report that myelin basic protein (MBP), a major structural component of the myelin sheath, binds ORF3a and is colocalized with it in mammalian cells. Co-expression of MBP with ORF3a restores autophagy in mammalian cells, inhibited by viral protein. Our data suggest that basic charge of MBP drives suppression of ORF3a-induced autophagy inhibition as its deaminated variants lost ability to bind ORF3a and counteract autophagy blockade. These results together with our recent findings, indicating that MBP interacts with structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3) and Sec1/Munc18-1 family members, may suggest protective role of the MBP in terms of the maintaining of protein traffic and autophagosome-lysosome fusion machinery in oligodendrocytes during SARS-CoV-2 infection. Finally, our data may indicate that deimination of MBP observed in the patients with multiple sclerosis (MS) may contribute to the previously reported worser outcomes of COVID-19 and increase of post-COVID-19 neurologic symptoms in patients with MS.
Language	English
Publishing date	2024-05-02
Publishing country	France
Document type	Journal Article
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2024.04.011
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Article ; Online: Topology of Ubiquitin Chains in the Chromatosomal Environment of the E3 Ubiquitin Ligase RNF168.

Kudriaeva, Anna A / Yakubova, Lyudmila A / Saratov, George A / Vladimirov, Vasiliy I / Lipkin, Valeriy M / Belogurov, Alexey A

Biochemistry. Biokhimiia

2024 Volume 88, Issue 12, Page(s) 2063–2072

Abstract: Genome stability is critical for normal functioning of cells, it depends on accuracy of DNA replication, chromosome segregation, and DNA repair. Cellular defense mechanisms against DNA damage are important for preventing cancer development and aging. The ...

Abstract	Genome stability is critical for normal functioning of cells, it depends on accuracy of DNA replication, chromosome segregation, and DNA repair. Cellular defense mechanisms against DNA damage are important for preventing cancer development and aging. The E3 ubiquitin ligase RNF168 of the RING superfamily is an essential component of the complex responsible for ubiquitination of the H2A/H2A.X histones near DNA double-strand breaks, which is a key step in attracting repair factors to the damage site. In this study, we unequivocally showed that RNF168 does not have the ability to directly distinguish architecture of polyubiquitin chains, except for the tropism of its two ubiquitin-binding domains UDM1/2 to K63 ubiquitin chains. Analysis of intracellular chromatosomal environment of the full-length RNF168 and its domains using the ligand-induced bioluminescence resonance energy transfer (BRET) revealed that the C-terminal part of UDM1 is associated with the K63 ubiquitin chains; RING and the N-terminal part of UDM2 are sterically close to the K63- and K48-ubiquitin chains, while the C-terminal part of UDM1 is co-localized with all possible ubiquitin variants. Our observations together with the available structural data suggest that the C-terminal part of UDM1 binds the K63 polyubiquitin chains on the linker histone H1; RING and the N-terminal part of UDM2 are located in the central part of nucleosome and sterically close to H1 and K48-ubiquitinated alternative substrates of RNF168, such as JMJD2A/B demethylases, while the C-terminal part of UDM1 is in the region of activated ubiquitin residue associated with E2 ubiquitin ligase, engaged by RNF168.
MeSH term(s)	Ubiquitin-Protein Ligases/genetics ; Ubiquitin/metabolism ; Polyubiquitin/genetics ; Polyubiquitin/metabolism ; Ubiquitination ; DNA Repair ; DNA Damage
Chemical Substances	Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Ubiquitin ; Polyubiquitin (120904-94-1)
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S000629792312009X
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Article ; Online: Control of Genome through Variative Nature of Histone-Modifying Ubiquitin Ligases.

Bacheva, Anna V / Gotmanova, Nataliya N / Belogurov, Alexey A / Kudriaeva, Anna A

Biochemistry. Biokhimiia

2021 Volume 86, Issue Suppl 1, Page(s) S71–S95

Abstract: Covalent attachment of ubiquitin residue is not only the proteasomal degradation signal, but also a widespread posttranslational modification of cellular proteins in eukaryotes. One of the most important targets of the regulatory ubiquitination are ... ...

Abstract	Covalent attachment of ubiquitin residue is not only the proteasomal degradation signal, but also a widespread posttranslational modification of cellular proteins in eukaryotes. One of the most important targets of the regulatory ubiquitination are histones. Localization of ubiquitin residue in different regions of the nucleosome attracts a strictly determined set of cellular factors with varied functionality. Depending on the type of histone and the particular lysine residue undergoing modification, histone ubiquitination can lead both to transcription activation and to gene repression, as well as contribute to DNA repair via different mechanisms. An extremely interesting feature of the family of RING E3 ubiquitin ligases catalyzing histone ubiquitination is the striking structural diversity of the domains providing high specificity of modification very similar initial targets. It is obvious that further elucidation of peculiarities of the ubiquitination system involved in histone modification, as well as understanding of physiological role of this process in the maintenance of homeostasis of both single cells and the entire organism, will substantially expand the possibilities of treating a number of socially significant diseases.
MeSH term(s)	Animals ; Epigenesis, Genetic ; Gene Expression Regulation ; Histone Code ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Histones ; Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2021-04-08
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297921140066
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Article ; Online: MHC Class II Presentation in Autoimmunity.

Ishina, Irina A / Zakharova, Maria Y / Kurbatskaia, Inna N / Mamedov, Azad E / Belogurov, Alexey A / Gabibov, Alexander G

Cells

2023 Volume 12, Issue 2

Abstract: Antigen presentation by major histocompatibility complex class II (MHC-II) molecules is crucial for eliciting an efficient immune response by ... ...

Abstract	Antigen presentation by major histocompatibility complex class II (MHC-II) molecules is crucial for eliciting an efficient immune response by CD4
MeSH term(s)	Humans ; Autoimmunity ; CD4-Positive T-Lymphocytes ; Histocompatibility Antigens Class II/metabolism ; Autoimmune Diseases ; Antigen Presentation ; Autoantigens/metabolism
Chemical Substances	Histocompatibility Antigens Class II ; Autoantigens
Language	English
Publishing date	2023-01-14
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12020314
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Article ; Online: Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics.

Smirnova, Evgeniya V / Rakitina, Tatiana V / Ziganshin, Rustam H / Saratov, George A / Arapidi, Georgij P / Belogurov, Alexey A / Kudriaeva, Anna A

Cells

2023 Volume 12, Issue 6

Abstract: Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, ... ...

Abstract	Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (
MeSH term(s)	Biotin ; Myelin Basic Protein/metabolism ; Myelin Sheath/metabolism ; Proteins ; Proteomics/methods ; Protein Interaction Maps
Chemical Substances	Biotin (6SO6U10H04) ; Myelin Basic Protein ; Proteins
Language	English
Publishing date	2023-03-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12060944
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Article ; Online: Myelin Basic Protein Attenuates Furin-Mediated Bri2 Cleavage and Postpones Its Membrane Trafficking.

Smirnova, Evgeniya V / Timofeev, Vladimir I / Rakitina, Tatiana V / Petrenko, Dmitry E / Elmeeva, Olga S / Saratov, George A / Kudriaeva, Anna A / Bocharov, Eduard V / Belogurov, Alexey A

International journal of molecular sciences

2024 Volume 25, Issue 5

Abstract: Myelin basic protein (MBP) is the second most abundant protein in the central nervous system and is responsible for structural maintenance of the myelin sheath covering axons. Previously, we showed that MBP has a more proactive role in the ... ...

Abstract	Myelin basic protein (MBP) is the second most abundant protein in the central nervous system and is responsible for structural maintenance of the myelin sheath covering axons. Previously, we showed that MBP has a more proactive role in the oligodendrocyte homeostasis, interacting with membrane-associated proteins, including integral membrane protein 2B (ITM2B or Bri2) that is associated with familial dementias. Here, we report that the molecular dynamics of the in silico-generated MBP-Bri2 complex revealed that MBP covers a significant portion of the Bri2 ectodomain, assumingly trapping the furin cleavage site, while the surface of the BRICHOS domain, which is responsible for the multimerization and activation of the Bri2 high-molecular-weight oligomer chaperone function, remains unmasked. These observations were supported by the co-expression of MBP with Bri2, its mature form, and disease-associated mutants, which showed that in mammalian cells, MBP indeed modulates the post-translational processing of Bri2 by restriction of the furin-catalyzed release of its C-terminal peptide. Moreover, we showed that the co-expression of MBP and Bri2 also leads to an altered cellular localization of Bri2, restricting its membrane trafficking independently of the MBP-mediated suppression of the Bri2 C-terminal peptide release. Further investigations should elucidate if these observations have physiological meaning in terms of Bri2 as a MBP chaperone activated by the MBP-dependent postponement of Bri2 membrane trafficking.
MeSH term(s)	Animals ; Membrane Glycoproteins ; Furin/metabolism ; Myelin Basic Protein ; Membrane Proteins/metabolism ; Peptides ; Mammals/metabolism
Chemical Substances	Membrane Glycoproteins ; Furin (EC 3.4.21.75) ; Myelin Basic Protein ; Membrane Proteins ; Peptides
Language	English
Publishing date	2024-02-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25052608
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Article: CCR5/CXCR3 antagonist TAK-779 prevents diffuse alveolar damage of the lung in the murine model of the acute respiratory distress syndrome.

Chernov, Aleksandr S / Rodionov, Maksim V / Kazakov, Vitaly A / Ivanova, Karina A / Meshcheryakov, Fedor A / Kudriaeva, Anna A / Gabibov, Alexander G / Telegin, Georgii B / Belogurov, Alexey A

Frontiers in pharmacology

2024 Volume 15, Page(s) 1351655

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2024-02-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2024.1351655
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Article: Genetically engineered CD80-pMHC-harboring extracellular vesicles for antigen-specific CD4

Ishina, Irina A / Kurbatskaia, Inna N / Mamedov, Azad E / Shramova, Elena I / Deyev, Sergey M / Nurbaeva, Kamila S / Rubtsov, Yury P / Belogurov, Alexey A / Gabibov, Alexander G / Zakharova, Maria Y

Frontiers in bioengineering and biotechnology

2024 Volume 11, Page(s) 1341685

Abstract: The identification of low-frequency antigen-specific ... ...

Abstract	The identification of low-frequency antigen-specific CD4
Language	English
Publishing date	2024-01-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2023.1341685
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Article ; Online: Myelin Basic Protein Fragmentation by Engineered Human Proteasomes with Different Catalytic Phenotypes Revealed Direct Peptide Ligands of MS-Associated and Protective HLA Class I Molecules.

Saratov, George A / Vladimirov, Vasiliy I / Novoselov, Alexey L / Ziganshin, Rustam H / Chen, Guo / Baymukhametov, Timur N / Konevega, Andrey L / Belogurov, Alexey A / Kudriaeva, Anna A

International journal of molecular sciences

2023 Volume 24, Issue 3

Abstract: Proteasomes exist in mammalian cells in multiple combinatorial variants due to the diverse regulatory particles and exchange of catalytic subunits. Here, using biotin carboxyl carrier domain of transcarboxylase ... ...

Abstract	Proteasomes exist in mammalian cells in multiple combinatorial variants due to the diverse regulatory particles and exchange of catalytic subunits. Here, using biotin carboxyl carrier domain of transcarboxylase from
MeSH term(s)	Animals ; Humans ; Myelin Basic Protein/metabolism ; Proteasome Endopeptidase Complex ; Ligands ; Peptide Fragments ; Peptides/chemistry ; Multiple Sclerosis/genetics ; Immunodominant Epitopes ; HLA-A Antigens ; Mammals/metabolism
Chemical Substances	Myelin Basic Protein ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ligands ; Peptide Fragments ; Peptides ; Immunodominant Epitopes ; HLA-A Antigens
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24032091
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Article ; Online: Mutational pressure drives enhanced release of proteasome-generated public CD8+ T cell epitopes from SARS-CoV-2 RBD of Omicron and its current lineages

Kudriaeva, Anna A. / Butenko, Ivan O. / Saratov, George A. / Ri, Maxim / Mokrushina, Yuliana A. / Bondarev, Alexey A. / Evpak, Alena S. / Smirnov, Ivan V. / Matyushkina, Daria S. / Gabibov, Alexander G. / Govorun, Vadim M. / Belogurov, Alexey A.

medRxiv

Abstract: The COVID-19 pandemic was the most dramatic in the newest history with nearly 7 million deaths and global impact on mankind. Here we report binding index of 305 HLA class I molecules from 18,771 unique haplotypes of 28,104 individuals to 821 peptides ... ...

Abstract	The COVID-19 pandemic was the most dramatic in the newest history with nearly 7 million deaths and global impact on mankind. Here we report binding index of 305 HLA class I molecules from 18,771 unique haplotypes of 28,104 individuals to 821 peptides experimentally observed from spike protein RBD of 5 main SARS-CoV-2 strains hydrolyzed by human proteasomes with constitutive and immune catalytic phenotypes. Our data read that 4 point mutations in the hACE2-binding region RBD496-513 of Omicron B1.1.529 strain results in a dramatic increase of proteasome-mediated release of two public HLA class I epitopes. Global population analysis of HLA class I haplotypes, specific to these peptides, demonstrated decreased mortality of human populations enriched in these haplotypes from COVID-19 after but not before December, 2021, when Omicron became dominant SARS-CoV-2 strain. Noteworthy, currently circulating BA.2.86 and JN.1 lineages contain no amino acid substitutions in RBD496-513 thus preserving identified core epitopes.
Keywords	covid19
Language	English
Publishing date	2024-04-03
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.04.03.24305074
Database	COVID19

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