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Article ; Online: How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities.

Nevinsky, Georgy A

International journal of molecular sciences

2021 Volume 22, Issue 3

Abstract: X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and ... ...

Abstract	X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes-replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein from
MeSH term(s)	Animals ; Antibodies/metabolism ; DNA/metabolism ; DNA Glycosylases/metabolism ; DNA Helicases/metabolism ; DNA Ligases/metabolism ; DNA Topoisomerases, Type I/metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; DNA-Directed DNA Polymerase/metabolism ; Deoxyribonuclease EcoRI/metabolism ; Humans ; Lactalbumin/metabolism ; Lactoferrin/metabolism ; Proteins/metabolism ; Rec A Recombinases/metabolism ; Serum Albumin, Human/metabolism
Chemical Substances	Antibodies ; Proteins ; DNA (9007-49-2) ; Lactalbumin (9013-90-5) ; Rec A Recombinases (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Deoxyribonuclease EcoRI (EC 3.1.21.-) ; DNA Glycosylases (EC 3.2.2.-) ; Lactoferrin (EC 3.4.21.-) ; DNA Helicases (EC 3.6.4.-) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18) ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; DNA Ligases (EC 6.5.1.-) ; Serum Albumin, Human (ZIF514RVZR)
Language	English
Publishing date	2021-01-29
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22031369
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Autoantibodies-Abzymes with Phosphatase Activity in Experimental Autoimmune Encephalomyelitis Mice.

Urusov, Andrey E / Aulova, Kseniya S / Nevinsky, Georgy A

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 6

Abstract: The exact mechanisms of MS (multiple sclerosis) evolution are still unknown. However, the development of EAE (experimental autoimmune encephalomyelitis simulating human MS) in C57BL/6 mice occurs due to the violation of bone marrow hematopoietic stem ... ...

Abstract	The exact mechanisms of MS (multiple sclerosis) evolution are still unknown. However, the development of EAE (experimental autoimmune encephalomyelitis simulating human MS) in C57BL/6 mice occurs due to the violation of bone marrow hematopoietic stem cell differentiation profiles, leading to the production of toxic for human autoantibody splitting MBP (myelin basic protein), MOG (mouse oligodendrocyte glycoprotein), five histones, DNA, and RNA. Here, we first analyzed the changes in the relative phosphatase activity of IgGs from C57BL/6 mice blood over time, corresponding to three stages of EAE: onset, acute, and remission. Antibodies have been shown to catalyze the hydrolysis of
MeSH term(s)	Mice ; Humans ; Animals ; Encephalomyelitis, Autoimmune, Experimental/pathology ; Autoantibodies ; Myelin-Oligodendrocyte Glycoprotein ; Histones ; Mice, Inbred C57BL ; Antibodies, Catalytic ; DNA ; Phosphoric Monoester Hydrolases
Chemical Substances	Autoantibodies ; Myelin-Oligodendrocyte Glycoprotein ; Histones ; Antibodies, Catalytic ; DNA (9007-49-2) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2024-03-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules29061382
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Article ; Online: Essential Protective Role of Catalytically Active Antibodies (Abzymes) with Redox Antioxidant Functions in Animals and Humans.

Tolmacheva, Anna S / Nevinsky, Georgy A

International journal of molecular sciences

2022 Volume 23, Issue 7

Abstract: During the life of aerobic organisms, the oxygen resulting from numerous reactions is converted into reactive oxygen species (ROS). Many ROS are dangerous due to their high reactivity; they are strong oxidants, and react with various cell components, ... ...

Abstract	During the life of aerobic organisms, the oxygen resulting from numerous reactions is converted into reactive oxygen species (ROS). Many ROS are dangerous due to their high reactivity; they are strong oxidants, and react with various cell components, leading to their damage. To protect against ROS overproduction, enzymatic and non-enzymatic systems are evolved in aerobic cells. Several known non-enzymatic antioxidants have a relatively low specific antioxidant activity. Superoxide dismutases, catalase, glutathione peroxidase, glutathione S-transferase, thioredoxin, and the peroxiredoxin families are the most important enzyme antioxidants. Artificial antibodies catalyzing redox reactions using different approaches have been created. During the past several decades, it has been shown that the blood and various biological fluids of humans and animals contain natural antibodies that catalyze different redox reactions, such as classical enzymes. This review, for the first time, summarizes data on existing non-enzymatic antioxidants, canonical enzymes, and artificial or natural antibodies (abzymes) with redox functions. Comparing abzymes with superoxide dismutase, catalase, peroxide-dependent peroxidase, and H
MeSH term(s)	Animals ; Antioxidants/chemistry ; Catalase ; Glutathione Peroxidase ; Humans ; Hydrogen Peroxide ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species ; Superoxide Dismutase
Chemical Substances	Antioxidants ; Reactive Oxygen Species ; Hydrogen Peroxide (BBX060AN9V) ; Catalase (EC 1.11.1.6) ; Glutathione Peroxidase (EC 1.11.1.9) ; Superoxide Dismutase (EC 1.15.1.1)
Language	English
Publishing date	2022-03-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23073898
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Article ; Online: How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities

Georgy A. Nevinsky

International Journal of Molecular Sciences, Vol 22, Iss 3, p

2021 Volume 1369

Abstract	X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes—replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein from Escherichia coli , human 8-oxoguanine-DNA glycosylase, human apurinic/apyrimidinic endonuclease, RecA protein, and DNA-ligase), and five DNA-recognizing proteins (RNA helicase, human lactoferrin, alfa-lactalbumin, human blood albumin, and IgGs against DNA). The relative contributions of structural elements of DNA fragments “covered” by globules of enzymes and proteins to the total affinity of DNA have been evaluated. Thermodynamic and catalytic factors providing discrimination of unspecific and specific DNAs by these enzymes on the stages of primary complex formation following changes in enzymes and DNAs or RNAs conformations and direct processing of the catalysis of the reactions were found. General regularities of recognition of nucleic acid by DNA-dependent enzymes, proteins, and antibodies were established.
Keywords	different enzymes and proteins ; anti-DNA antibodies ; general regularities of DNA recognition ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612 ; 572
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Experimental Autoimmune Encephalomyelitis of Mice: IgGs from the Sera of Mice Hydrolyze miRNAs.

Nevinsky, Georgy A / Urusov, Andrey E / Aulova, Kseniya S / Ermakov, Evgeny A

International journal of molecular sciences

2023 Volume 24, Issue 5

Abstract: It was shown that the spontaneous development of experimental encephalomyelitis (EAE) in C57BL/6 mice occurs due to changes in the profile of bone marrow stem cells differentiation. This leads to the appearance of lymphocytes producing antibodies-abzymes ...

Abstract	It was shown that the spontaneous development of experimental encephalomyelitis (EAE) in C57BL/6 mice occurs due to changes in the profile of bone marrow stem cells differentiation. This leads to the appearance of lymphocytes producing antibodies-abzymes that hydrolyze DNA, myelin basic protein (MBP), and histones. The activity of abzymes in the hydrolysis of these auto-antigens slowly but constantly increases during the spontaneous development of EAE. Treatment of mice with myelin oligodendrocyte glycoprotein (MOG) leads to a sharp increase in the activity of these abzymes with their maximum at 20 days (acute phase) after immunization. In this work, we analyzed changes in the activity of IgG-abzymes hydrolyzing (pA)
MeSH term(s)	Mice ; Animals ; Encephalomyelitis, Autoimmune, Experimental ; Histones/metabolism ; Mice, Inbred C57BL ; Myelin-Oligodendrocyte Glycoprotein ; MicroRNAs ; Antibodies, Catalytic ; DNA
Chemical Substances	Histones ; Myelin-Oligodendrocyte Glycoprotein ; MicroRNAs ; Antibodies, Catalytic ; DNA (9007-49-2)
Language	English
Publishing date	2023-02-23
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/ijms24054433
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Article ; Online: Autoantibody-Abzymes with Catalase Activity in Experimental Autoimmune Encephalomyelitis Mice.

Urusov, Andrey E / Tolmacheva, Anna S / Aulova, Kseniya S / Nevinsky, Georgy A

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 3

Abstract: The exact mechanisms of the evolution of multiple sclerosis are still unknown. At the same time, the development in C57BL/6 mice of experimental autoimmune encephalomyelitis (EAE, simulating human multiple sclerosis) happens as a result of the violation ... ...

Abstract	The exact mechanisms of the evolution of multiple sclerosis are still unknown. At the same time, the development in C57BL/6 mice of experimental autoimmune encephalomyelitis (EAE, simulating human multiple sclerosis) happens as a result of the violation of bone marrow hematopoietic stem cell differentiation profiles integrated with the production of toxic auto-antibodies splitting the basic myelin protein, myelin oligodendrocyte glycoprotein (MOG), histones, and DNA. It has been shown that IgGs from the plasma of healthy humans and autoimmune patients oxidize many different compounds due to their peroxidase (H
MeSH term(s)	Animals ; Humans ; Mice ; Antibodies, Catalytic ; Autoantibodies ; Catalase ; DNA ; Encephalomyelitis, Autoimmune, Experimental ; Histones ; Hydrogen Peroxide ; Mice, Inbred C57BL ; Multiple Sclerosis ; Myelin-Oligodendrocyte Glycoprotein
Chemical Substances	Antibodies, Catalytic ; Autoantibodies ; Catalase (EC 1.11.1.6) ; DNA (9007-49-2) ; Histones ; Hydrogen Peroxide (BBX060AN9V) ; Myelin-Oligodendrocyte Glycoprotein
Language	English
Publishing date	2023-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28031330
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Article: Natural Antibodies Produced in Vaccinated Patients and COVID-19 Convalescents Recognize and Hydrolyze Oligopeptides Corresponding to the S-Protein of SARS-CoV-2.

Timofeeva, Anna M / Sedykh, Sergey E / Sedykh, Tatyana A / Nevinsky, Georgy A

Vaccines

2023 Volume 11, Issue 9

Abstract: The S-protein is the major antigen of the SARS-CoV-2 virus, against which protective antibodies are generated. The S-protein gene was used in adenoviral vectors and mRNA vaccines against COVID-19. While the primary function of antibodies is to bind to ... ...

Abstract	The S-protein is the major antigen of the SARS-CoV-2 virus, against which protective antibodies are generated. The S-protein gene was used in adenoviral vectors and mRNA vaccines against COVID-19. While the primary function of antibodies is to bind to antigens, catalytic antibodies can hydrolyze various substrates, including nucleic acids, proteins, oligopeptides, polysaccharides, and some other molecules. In this study, antibody fractions with affinity for RBD and S-protein (RBD-IgG and S-IgG) were isolated from the blood of COVID-19 patients vaccinated with Sputnik V. The fractions were analyzed for their potential to hydrolyze 18-mer oligopeptides corresponding to linear fragments of the SARS-CoV-2 S-protein. Here, we show that the IgG antibodies hydrolyze six out of nine oligopeptides efficiently, with the antibodies of COVID-19-exposed donors demonstrating the most significant activity. The IgGs of control donors not exposed to SARS-CoV-2 were found to be inactive in oligopeptide hydrolysis. The antibodies of convalescents and vaccinated patients were found to hydrolyze oligopeptides in a wide pH range, with the optimal pH range between 6.5 and 7.5. The hydrolysis of most oligopeptides by RBD-IgG antibodies is inhibited by thiol protease inhibitors, whereas S-IgG active centers generally combine several types of proteolytic activities. Ca
Language	English
Publishing date	2023-09-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines11091494
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Article ; Online: Identification of Antibody-Mediated Hydrolysis Sites of Oligopeptides Corresponding to the SARS-CoV-2 S-Protein by MALDI-TOF Mass Spectrometry.

Timofeeva, Anna M / Sedykh, Sergey E / Dmitrenok, Pavel S / Nevinsky, Georgy A

International journal of molecular sciences

2023 Volume 24, Issue 18

Abstract: Antibodies recognizing RBD and the S-protein have been previously demonstrated to be formed in humans after SARS-CoV-2 infection and vaccination with the Sputnik V adenovirus vaccine. These antibodies were found to be active when hydrolyzing FITC-labeled ...

Abstract	Antibodies recognizing RBD and the S-protein have been previously demonstrated to be formed in humans after SARS-CoV-2 infection and vaccination with the Sputnik V adenovirus vaccine. These antibodies were found to be active when hydrolyzing FITC-labeled oligopeptides corresponding to linear epitopes of the S-protein. The thin-layer chromatography method allows the relative accumulation of the reaction product to be estimated but cannot identify hydrolysis sites. This study used the MALDI-TOF MS method to establish oligopeptide hydrolysis sites. Using the MALDI-TOF MS method in combination with the analysis of known hydrolysis sites characteristic of canonical proteases allowed us to establish the unique hydrolysis sites inherent only to catalytically active antibodies. We have discovered two 12-mer oligopeptides to have six hydrolysis sites equally distributed throughout the oligopeptide. The other three oligopeptides were found to have two to three closely spaced hydrolysis sites. In contrast to trypsin and chymotrypsin proteases, the catalytically active antibodies of COVID-19 patients have their peptide bond hydrolyzed mainly after proline, threonine, glycine, or serine residues. Here, we propose a new high-throughput experimental method for analyzing the proteolytic activity of natural antibodies produced in viral pathology.
MeSH term(s)	Humans ; Hydrolysis ; SARS-CoV-2 ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; COVID-19 ; Antibodies ; Oligopeptides ; Peptide Hydrolases ; Antibodies, Viral
Chemical Substances	Antibodies ; Oligopeptides ; Peptide Hydrolases (EC 3.4.-) ; Antibodies, Viral
Language	English
Publishing date	2023-09-20
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/ijms241814342
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Article ; Online: Milk Exosomes: Next-Generation Agents for Delivery of Anticancer Drugs and Therapeutic Nucleic Acids.

Timofeeva, Anna M / Paramonik, Anastasia P / Sedykh, Sergey S / Nevinsky, Georgy A

International journal of molecular sciences

2023 Volume 24, Issue 12

Abstract: Exosomes are nanovesicles 40-120 nm in diameter secreted by almost all cell types and providing humoral intercellular interactions. Given the natural origin and high biocompatibility, the potential for loading various anticancer molecules and therapeutic ...

Abstract	Exosomes are nanovesicles 40-120 nm in diameter secreted by almost all cell types and providing humoral intercellular interactions. Given the natural origin and high biocompatibility, the potential for loading various anticancer molecules and therapeutic nucleic acids inside, and the surface modification possibility for targeted delivery, exosomes are considered to be a promising means of delivery to cell cultures and experimental animal organisms. Milk is a unique natural source of exosomes available in semi-preparative and preparative quantities. Milk exosomes are highly resistant to the harsh conditions of the gastrointestinal tract. In vitro studies have demonstrated that milk exosomes have an affinity to epithelial cells, are digested by cells by endocytosis mechanism, and can be used for oral delivery. With milk exosome membranes containing hydrophilic and hydrophobic components, exosomes can be loaded with hydrophilic and lipophilic drugs. This review covers a number of scalable protocols for isolating and purifying exosomes from human, cow, and horse milk. Additionally, it considers passive and active methods for drug loading into exosomes, as well as methods for modifying and functionalizing the surface of milk exosomes with specific molecules for more efficient and specific delivery to target cells. In addition, the review considers various approaches to visualize exosomes and determine cellular localization and bio-distribution of loaded drug molecules in tissues. In conclusion, we outline new challenges for studying milk exosomes, a new generation of targeted delivery agents.
MeSH term(s)	Animals ; Cattle ; Female ; Humans ; Exosomes/metabolism ; Milk/metabolism ; Antineoplastic Agents ; Drug Delivery Systems ; Drug Carriers/metabolism
Chemical Substances	Antineoplastic Agents ; Drug Carriers
Language	English
Publishing date	2023-06-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241210194
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Article: Multiple Sclerosis: Enzymatic Cross Site-Specific Recognition and Hydrolysis of H2A Histone by IgGs against H2A, H1, H2B, H3 Histones, Myelin Basic Protein, and DNA.

Nevinsky, Georgy A / Buneva, Valentina N / Dmitrienok, Pavel S

Biomedicines

2022 Volume 10, Issue 8

Abstract: Histones have a paramount role in chromatin remodeling and gene transcription. Free histones are damage-associated molecules in the blood; administration of histones to animals drives systemic inflammatory and toxic effects. Myelin basic protein (MBP) is ...

Abstract	Histones have a paramount role in chromatin remodeling and gene transcription. Free histones are damage-associated molecules in the blood; administration of histones to animals drives systemic inflammatory and toxic effects. Myelin basic protein (MBP) is the most crucial component of the axon myelin-proteolipid sheath. Antibodies-abzymes with different enzymatic activities are very toxic and an essential feature of some autoimmune diseases. Electrophoretically homogeneous IgGs against H1, H2A, H2B, H3, H4, MBP, and DNA were derived from sera of multiple sclerosis (MS) patients by several affinity chromatographies. Using MALDI-TOFF mass spectrometry, it was shown that IgGs against H2A split H2A at 12 sites; the number of H2A hydrolysis sites by antibodies against other antigens is different: H1 (19), H2B (11), H3 (15), H4 (9), MBP (10), and DNA (23), and they only partly match. Thus, the complex formation polyreactivity and the enzymatic cross-activity of pernicious humans IgGs against five histones, MBP, and DNA have been shown for the first time. The data obtained indicate that the formation of such polyspecific-polyreactive abzymes, whose single active center can recognize and hydrolyze different substrates, can occur due to the formation of antibodies against hybrid antigenic determinants consisting of several histone protein sequences. IgGs with high affinity for DNA with DNase and protease activities may be antibodies against DNA-histone complex antigenic determinants, including protein and DNA sequences. Polyreactive IgGs-abzymes against MBP, five histones, and DNA with extended cytotoxicity can play a very negative role in the pathogenesis of multiple sclerosis and probably other different diseases.
Language	English
Publishing date	2022-08-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines10081876
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