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Structure type: oligomer
Trivial name: synthetic disaccharide
Contained glycoepitopes: IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_143253,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 4687
  Kang Y, Barbirz S, Lipowsky R, Santer M "Conformational Diversity of O-Antigen Polysaccharides of the Gram-Negative Bacterium Shigella flexneri Serotype Y" - Journal of Physical Chemistry B 118(9) (2014) 2523-2534
  

  O-Antigen polysaccharides constitute the outer protective layer of most Gram-negative bacteria, important for the bacterium's survival and adaption within its host. Although important for many functions, the three-dimensional structure of the dense polysaccharide coat remains to be elucidated. In this study, we present a systematic numerical investigation of O-antigen polysaccharide chains of Shigella flexneri serotype Y composed of one up to four tetrasaccharide repeat units. To bridge the gap between atomistic and coarse-grained levels of description, we employ a genuine multiscale modeling approach. It reveals that even for a few repeat units polymer-like flexibility emerges, which is furthermore complemented by extreme, hairpin-like conformations. These can facilitate the formation of metastable compact states, but this conclusion depends sensitively on the force field used to model the carbohydrates. Thus, our computational analysis represents an essential prerequisite for developing reliable coarse-grained models that may help visualizing changes in O-antigen coat morphology upon variations in chain length distribution or chemical composition of the polysaccharide characterizing a certain serotype.

  conformation, carbohydrates, structure, tetrasaccharide, host, variation, polysaccharide, serotype, O-antigen, analysis, O antigen, carbohydrate, chain, morphology, Shigella flexneri, level, conformational, bacteria, chemical, polysaccharides, Shigella, Gram-negative bacteria, function, gram negative bacteria, Gram-negative, formation, composition, change, protective, distribution, diversity, model, models, modeling, chain length, flexibility, force field, approach, systematic, layer, survival

  NCBI PubMed ID: 24559142
  Publication DOI: 10.1021/jp4111713
  Journal NLM ID: 101157530
  Publisher: Washington, DC: American Chemical Society
  Correspondence: mark.santer@mpikg.mpg.de
  Institutions: Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
  Methods: conformation analysis, MD simulations, molecular modeling, Monte Carlo simulations
  
   
  
  Shigella flexneri Y
  CSDB ID 30299 (all data & tools)

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Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_140630,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_151531,IEDB_153510,IEDB_423153,IEDB_885822,IEDB_983931,SB_192

• Article ID: 6128
  Popova AV, Shneider MM, Arbatsky NP, Kasimova AA, Senchenkova SN, Shashkov AS, Dmitrenok AS, Chizhov AO, Mikhailova YV, Shagin DA, Sokolova OS, Timoshina OY, Kozlov RS, Miroshnikov KA, Knirel YA "Specific interaction of novel Friunavirus phages encoding tailspike depolymerases with corresponding Acinetobacter baumannii capsular types" - Journal of Virology 95(5) (2021) e01714-20
  

  Acinetobacter baumannii is one of the most clinically important nosocomial pathogens. The World Health Organisation refers it to its <> category to develop new strategies for effective therapy. This microorganism is capable of producing structurally diverse capsular polysaccharides (CPSs), which serve as primary receptors for A. baumannii bacteriophages carrying polysaccharide-depolymerasing enzymes. In this study, eight novel bacterial viruses that specifically infect A. baumannii strains belonging to K2/K93, K32, K37, K44, K48, K87, K89 and K116 capsular types were isolated and characterized. The overall genomic architecture demonstrated that these viruses are representatives of the Friunavirus genus of the family Autographiviridae The linear double-stranded DNA phage genomes of 41,105-42,402 bp share high nucleotide sequence identity, except for genes encoding structural depolymerases or tailspikes which determine the host specificity. Deletion mutants lacking N-terminal domains of tailspike proteins were cloned, expressed and purified. The structurally defined CPSs of the phage bacterial hosts were cleaved with the specific recombinant depolymerases, and the resultant oligosaccharides that corresponded to monomers or/and dimers of the CPS repeats (K-units) were isolated. Structures of the derived oligosaccharides were established by nuclear magnetic resonance spectroscopy and high-resolution electrospray ionization mass spectrometry. The data obtained showed that all depolymerases studied were glycosidases that cleave specifically the A. baumannii CPSs by the hydrolytic mechanism, in most cases, by the linkage between the K-units.IMPORTANCE Acinetobacter baumannii, a nonfermentative, Gram-negative, aerobic bacterium, is one of the most significant nosocomial pathogens. The pathogenicity of A. baumannii is based on the cooperative action of many factors, one of them being the production of capsular polysaccharides (CPSs) that surround bacterial cells with a thick protective layer. Polymorphism of the chromosomal capsule loci is responsible for the observed high structural diversity of the CPSs. In this study, we describe eight novel lytic phages which have different tailspike depolymerases (TSDs) determining the interaction of the viruses with corresponding A. baumannii capsular types (K-types). Moreover, we elucidate the structures of oligosaccharide products obtained by cleavage of the CPSs by the recombinant depolymerases. We believe that as the TSDs determine phage specificity, the diversity of their structures should be taken into consideration as selection criteria for inclusion of certain phage candidate to the cocktail designed to control A. baumannii with different K-types

  structure, Acinetobacter baumannii, capsular polysaccharide, bacteriophage, glycosidase, capsular type, tailspike depolymerase

  NCBI PubMed ID: 33268523
  Publication DOI: 10.1128/JVI.01714-20
  Journal NLM ID: 0113724
  Correspondence: popova.av@mipt.ru; popova_nastya86@mail.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia, Central Scientific Research Institute of Epidemiology, Moscow, Russia, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, Russia, Pirogov Russian National Research Medical University, Moscow, Russia, Lomonosov Moscow State University, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, DNA techniques, GPC, phage depolymerisation, HR-ESI-MS, TEM, phage isolation, phage infection inhibition assay, phage genome analysis
  
   
  
  Acinetobacter baumannii K32 LUH5549
  CSDB ID 9737 (all data & tools)