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Your search keyword '"Knirel, Yuriy A"' showing total 1,424 results
Start Over Author "Knirel, Yuriy A" Publication Type Academic Journals
1,424 results on '"Knirel, Yuriy A"'

1. Cataloging natural sialic acids and other nonulosonic acids (NulOs), and their representation using the Symbol Nomenclature for Glycans.

Author

Frank, Martin, Lütteke, Thomas, Knirel, Yuriy, Schoenhofen, Ian, Varki, Ajit, Vinogradov, Evgeny, Woods, Robert, Zachara, Natasha, Zhang, Jian, Kamerling, Johannis, Neelamegham, Sriram, Toukach, Philip, Bolton, Evan, Chen, Xi, and Lewis, Amanda

Subjects
NulO, glycans, nonulosonic acid, sialic acid, symbol nomenclature, Animals, Sialic Acids, N-Acetylneuraminic Acid, Polysaccharides, Monosaccharides, Cataloging
Abstract

Nonulosonic acids or non-2-ulosonic acids (NulOs) are an ancient family of 2-ketoaldonic acids (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in a 3-deoxy form (referred to as sialic acids) or in a 3,9-dideoxy sialic-acid-like form. The former sialic acids are most common in the deuterostome lineage, including vertebrates, and mimicked by some of their pathogens. The latter sialic-acid-like molecules are found in bacteria and archaea. NulOs are often prominently positioned at the outermost tips of cell surface glycans, and have many key roles in evolution, biology and disease. The diversity of stereochemistry and structural modifications among the NulOs contributes to more than 90 sialic acid forms and 50 sialic-acid-like variants described thus far in nature. This paper reports the curation of these diverse naturally occurring NulOs at the NCBI sialic acid page (https://www.ncbi.nlm.nih.gov/glycans/sialic.html) as part of the NCBI-Glycans initiative. This includes external links to relevant Carbohydrate Structure Databases. As the amino and hydroxyl groups of these monosaccharides are extensively derivatized by various substituents in nature, the Symbol Nomenclature For Glycans (SNFG) rules have been expanded to represent this natural diversity. These developments help illustrate the natural diversity of sialic acids and related NulOs, and enable their systematic representation in publications and online resources.

Published
2023

14. Labeling of Polysaccharides with Biotin and Fluorescent Dyes.

Author

Tuzikov, Alexander, Shilova, Nadezhda, Ovchinnikova, Tatiana, Nokel, Alexey, Patova, Olga, Knirel, Yuriy, Chernova, Tatiana, Gorshkova, Tatiana, and Bovin, Nicolai

Subjects
POLYSACCHARIDES, BIOTIN, FLUORESCEIN isothiocyanate, CARBOXYL group, HYALURONIC acid, GLYCOLIPIDS, FLUORESCENT dyes
Abstract

Examples of labeling polysaccharides at hydroxyl groups are described in this paper, which are especially in demand for molecules with a blocked reducing end. The protocols presented are suitable for the microscale synthesis of labeled polysaccharides that do not require a chromatography step for isolation. Examples of hydroxyl labeling include (1) direct modification with fluorescein isothiocyanate; (2) reaction with a fluorescein-dichlorotriazine derivative; (3) reaction with biotin-dichlorotriazine; (4) indirect two-step modification (given for glycosphingolipid) with glutaric anhydride followed by amidation with aminospacered BODIPY or SuCy5. The labeling of carboxyl groups of hyaluronic acid with BODIPY is also described. The staining of plant tissue sections with biotinylated polysaccharide versus being fluorescein labeled is compared. [ABSTRACT FROM AUTHOR]

Published
2024
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22. New Obolenskvirus Phages Brutus and Scipio: Biology, Evolution, and Phage-Host Interaction.

Author

Evseev, Peter V., Shneider, Mikhail M., Kolupaeva, Lyubov V., Kasimova, Anastasia A., Timoshina, Olga Y., Perepelov, Andrey V., Shpirt, Anna M., Shelenkov, Andrey A., Mikhailova, Yulia V., Suzina, Natalia E., Knirel, Yuriy A., Miroshnikov, Konstantin A., and Popova, Anastasia V.

Subjects
VIRUS diversity, PAN-genome, BIOLOGY
Abstract

Two novel virulent phages of the genus Obolenskvirus infecting Acinetobacter baumannii, a significant nosocomial pathogen, have been isolated and studied. Phages Brutus and Scipio were able to infect A. baumannii strains belonging to the K116 and K82 capsular types, respectively. The biological properties and genomic organization of the phages were characterized. Comparative genomic, phylogenetic, and pangenomic analyses were performed to investigate the relationship of Brutus and Scipio to other bacterial viruses and to trace the possible origin and evolutionary history of these phages and other representatives of the genus Obolenskvirus. The investigation of enzymatic activity of the tailspike depolymerase encoded in the genome of phage Scipio, the first reported virus infecting A. baumannii of the K82 capsular type, was performed. The study of new representatives of the genus Obolenskvirus and mechanisms of action of depolymerases encoded in their genomes expands knowledge about the diversity of viruses within this taxonomic group and strategies of Obolenskvirus–host bacteria interaction. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5.

Author

Lukianova, Anna A., Shneider, Mikhail M., Evseev, Peter V., Egorov, Mikhail V., Kasimova, Anastasiya A., Shpirt, Anna M., Shashkov, Alexander S., Knirel, Yuriy A., Kostryukova, Elena S., and Miroshnikov, Konstantin A.

Subjects
POLYSACCHARIDES, DEPOLYMERIZATION, KLEBSIELLA, KLEBSIELLA infections, KLEBSIELLA pneumoniae, DRUG resistance in bacteria, BACTERIOPHAGES
Abstract

Klebsiella pneumoniae is a pathogen associated with various infection types, which often exhibits multiple antibiotic resistance. Phages, or bacterial viruses, have an ability to specifically target and destroy K. pneumoniae, offering a potential means of combatting multidrug-resistant infections. Phage enzymes are another promising therapeutic agent that can break down bacterial capsular polysaccharide, which shields K. pneumoniae from the immune response and external factors. In this study, Klebsiella phage K5 was isolated; this phage is active against Klebsiella pneumoniae with the capsular type K21. It was demonstrated that the phage can effectively lyse the host culture. The adsorption apparatus of the phage has revealed two receptor-binding proteins (RBPs) with predicted polysaccharide depolymerising activity. A recombinant form of both RBPs was obtained and experiments showed that one of them depolymerised the capsular polysaccharide K21. The structure of this polysaccharide and its degradation fragments were analysed. The second receptor-binding protein showed no activity on capsular polysaccharide of any of the 31 capsule types tested, so the substrate for this enzyme remains to be determined in the future. Klebsiella phage K5 may be considered a useful agent against Klebsiella infections. [ABSTRACT FROM AUTHOR]

Published
2023
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37. Structures of cell-wall glycopolymers of Lactococcus lactis BIM B-1024

Author

Zdorovenko Evelina Leont’evna, Shashkov Alexander Stepanovich, Kadykova Alexandra Alexeevna, Fakhrutdinov Artem Nikolaevich, Kiseleva Elena Pavlovna, Plotnikava Danuta Tofilevna, Novik Galina Ivanovna, and Knirel Yuriy Alexandrovich

Subjects
Biotechnology, TP248.13-248.65
Abstract

Glycopolymers of two types were isolated from the cell wall of Lactococcus lactis BIM B-1024 by stepwise extraction with cold and hot 10% CCl3CO2H and separated by anion-exchange gel chromatography. The following structures of the glycopolymers were established by sugar analysis, dephosphorylation with 48% HF, 1D and 2D NMR spectroscopy, and ESI-MS:

Published
2017
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50. Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii.

Author

Timoshina, Olga Y., Kasimova, Anastasia A., Shneider, Mikhail M., Matyuta, Ilya O., Nikolaeva, Alena Y., Evseev, Peter V., Arbatsky, Nikolay P., Shashkov, Alexander S., Chizhov, Alexander O., Shelenkov, Andrey A., Mikhaylova, Yulia V., Slukin, Pavel V., Volozhantsev, Nikolay V., Boyko, Konstantin M., Knirel, Yuriy A., Miroshnikov, Konstantin A., and Popova, Anastasia V.

Subjects
GREATER wax moth, CRYSTAL structure, ANTIBACTERIAL agents, BACTERIOPHAGES, ACINETOBACTER baumannii, POLYSACCHARIDES
Abstract

Acinetobacter baumannii is a critical priority nosocomial pathogen that produces a variety of capsular polysaccharides (CPSs), the primary receptors for specific depolymerase-carrying phages. In this study, the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, APK14, APK16, APK86, APK127v, APK128, and one previously described Friunavirus phage, APK37.1, were characterized. For all TSDs, the mechanism of specific cleavage of corresponding A. baumannii capsular polysaccharides (CPSs) was established. The structures of oligosaccharide fragments derived from K9, K14, K16, K37/K3-v1, K86, K127, and K128 CPSs degradation by the recombinant depolymerases have been determined. The crystal structures of three of the studied TSDs were obtained. A significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type was shown in the example of recombinant TSD APK09_gp48. The data obtained will provide a better understanding of the interaction of phage–bacterial host systems and will contribute to the formation of principles of rational usage of lytic phages and phage-derived enzymes as antibacterial agents. [ABSTRACT FROM AUTHOR]

Published
2023
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