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Xue Y, Nestor G. Determination of Amide Cis/Trans Isomers in N-Acetyl-d-glucosamine: Tailored NMR Analysis of the N-Acetyl Group Conformation. Chembiochem 2022; 23:e202200338. [PMID: 35713405 PMCID: PMC9541821 DOI: 10.1002/cbic.202200338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/17/2022] [Indexed: 11/14/2022]
Abstract
N‐Acetyl‐d‐glucosamine (GlcNAc) is one of the most common amino sugars in nature, but the conformation of its N‐acetyl group has drawn little attention. We report herein the first identification of NH protons of the amide cis forms of α‐ and β‐GlcNAc by NMR spectroscopy. Relative quantification and thermodynamic analysis of both cis and trans forms was carried out in aqueous solution. The NH protons were further utilized by adapting protein NMR experiments to measure eight J‐couplings within the N‐acetyl group, of which six are sensitive to the H2‐NH conformation and two are sensitive to the amide conformation. For amide cis and trans forms, the orientation between H2 and NH was determined as anti conformation, while a small percentage of syn conformation was predicted for the amide trans form of β‐GlcNAc. This approach holds great promise for the detailed conformational analysis of GlcNAc in larger biomolecules, such as glycoproteins and polysaccharides.
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Affiliation(s)
- Yan Xue
- Swedish University of Agricultural Sciences: Sveriges lantbruksuniversitet, Department of Molecular Sciences, SWEDEN
| | - Gustav Nestor
- Swedish University of Agricultural Sciences, Department of Molecular Sciences, Almas allé 5, Box 7015, 750 07, Uppsala, SWEDEN
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2
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Furevi A, Ruda A, Angles d’Ortoli T, Mobarak H, Ståhle J, Hamark C, Fontana C, Engström O, Apostolica P, Widmalm G. Complete 1H and 13C NMR chemical shift assignments of mono-to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER. Carbohydr Res 2022; 513:108528. [DOI: 10.1016/j.carres.2022.108528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 02/02/2023]
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3
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Plazinski W, Roslund MU, Säwén E, Engström O, Tähtinen P, Widmalm G. Tautomers of N-acetyl-d-allosamine: an NMR and computational chemistry study. Org Biomol Chem 2021; 19:7190-7201. [PMID: 34382051 DOI: 10.1039/d1ob01139a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
d-Allosamine is a rare sugar in Nature but its pyranoid form has been found α-linked in the core region of the lipopolysaccharide from the Gram-negative bacterium Porphyromonas gingivalis and in the chitanase inhibitor allosamidin, then β-linked and N-acetylated. In water solution the monosaccharide N-acetyl-d-allosamine (d-AllNAc) shows a significant presence of four tautomers arising from pyranoid and furanoid ring forms and anomeric configurations. The furanoid ring forms both showed 3JH1,H2≈ 4.85 Hz and to differentiate the anomeric configurations a series of chemical shift anisotropy/dipole-dipole cross-correlated relaxation NMR experiments was performed in which the α-anomeric form showed notable different relaxation rates for its components of the H1 doublet, thereby making it possible to elucidate the anomeric configuration of each of the furanoses. The conformational preferences of the different forms of d-AllNAc were investigated by 3JHH, 2JCH and 3JCH coupling constants from NMR experiments, molecular dynamics simulations and density functional theory calculations. The pyranose form resides in the 4C1 conformation and the furanose ring form has the majority of its conformers located on the South-East region of the pseudorotation wheel, with a small population in the Northern hemisphere. The tautomeric equilibrium was quite sensitive to changes in temperature, where the β-anomer of the pyranoid ring form decreased upon a temperature increase while the other forms increased.
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Affiliation(s)
- Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
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Abstract
The conformation of a molecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less established for carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or material properties. In this Minireview, recent achievements in the structural characterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.
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Affiliation(s)
- Yang Yu
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax-Planck-Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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Suzuki T, Yanaka S, Watanabe T, Yan G, Satoh T, Yagi H, Yamaguchi T, Kato K. Remodeling of the Oligosaccharide Conformational Space in the Prebound State To Improve Lectin-Binding Affinity. Biochemistry 2019; 59:3180-3185. [PMID: 31553574 DOI: 10.1021/acs.biochem.9b00594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We developed an approach to improve the lectin-binding affinity of an oligosaccharide by remodeling its conformational space in the precomplexed state. To develop this approach, we used a Lewis X-containing oligosaccharide interacting with RSL as a model system. Using an experimentally validated molecular dynamics simulation, we designed a Lewis X analogue with an increased population of conformational species that were originally very minor but exclusively accessible to the target lectin without steric hindrance by modifying the nonreducing terminal galactose, which does not directly contact the lectin in the complex. This Lewis X mimetic showed 17 times higher affinity for the lectin than the native counterpart. Our approach, complementing the lectin-bound-state optimizations, offers an alternative strategy to create high-affinity oligosaccharides by increasing populations of on-pathway metastable conformers.
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Affiliation(s)
- Tatsuya Suzuki
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Tokio Watanabe
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Gengwei Yan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Hirokazu Yagi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Takumi Yamaguchi
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.,Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.,School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
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Martínez-Gómez E, Ståhle J, Gil-Ramírez Y, Zúñiga-Ripa A, Zaccheus M, Moriyón I, Iriarte M, Widmalm G, Conde-Álvarez R. Genomic Insertion of a Heterologous Acetyltransferase Generates a New Lipopolysaccharide Antigenic Structure in Brucella abortus and Brucella melitensis. Front Microbiol 2018; 9:1092. [PMID: 29887851 PMCID: PMC5981137 DOI: 10.3389/fmicb.2018.01092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/07/2018] [Indexed: 12/31/2022] Open
Abstract
Brucellosis is a bacterial zoonosis of worldwide distribution caused by bacteria of the genus Brucella. In Brucella abortus and Brucella melitensis, the major species infecting domestic ruminants, the smooth lipopolysaccharide (S-LPS) is a virulence factor. This S-LPS carries a N-formyl-perosamine homopolymer O-polysaccharide that is the major antigen in serodiagnostic tests and is required for virulence. We report that the Brucella O-PS can be structurally and antigenically modified using wbdR, the acetyl-transferase gene involved in N-acetyl-perosamine synthesis in Escherichia coli O157:H7. Brucella constructs carrying plasmidic wbdR expressed a modified O-polysaccharide but were unstable, a problem circumvented by inserting wbdR into a neutral site of chromosome II. As compared to wild-type bacteria, both kinds of wbdR constructs expressed shorter O-polysaccharides and NMR analyses showed that they contained both N-formyl and N-acetyl-perosamine. Moreover, deletion of the Brucella formyltransferase gene wbkC in wbdR constructs generated bacteria producing only N-acetyl-perosamine homopolymers, proving that wbdR can replace for wbkC. Absorption experiments with immune sera revealed that the wbdR constructs triggered antibodies to new immunogenic epitope(s) and the use of monoclonal antibodies proved that B. abortus and B. melitensis wbdR constructs respectively lacked the A or M epitopes, and the absence of the C epitope in both backgrounds. The wbdR constructs showed resistance to polycations similar to that of the wild-type strains but displayed increased sensitivity to normal serum similar to that of a per R mutant. In mice, the wbdR constructs produced chronic infections and triggered antibody responses that can be differentiated from those evoked by the wild-type strain in S-LPS ELISAs. These results open the possibilities of developing brucellosis vaccines that are both antigenically tagged and lack the diagnostic epitopes of virulent field strains, thereby solving the diagnostic interference created by current vaccines against Brucella.
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Affiliation(s)
- Estrella Martínez-Gómez
- Instituto de Salud Tropical, Instituto de Investigación Sanitaria de Navarra, Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Yolanda Gil-Ramírez
- Instituto de Salud Tropical, Instituto de Investigación Sanitaria de Navarra, Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Amaia Zúñiga-Ripa
- Instituto de Salud Tropical, Instituto de Investigación Sanitaria de Navarra, Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Mona Zaccheus
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Ignacio Moriyón
- Instituto de Salud Tropical, Instituto de Investigación Sanitaria de Navarra, Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Maite Iriarte
- Instituto de Salud Tropical, Instituto de Investigación Sanitaria de Navarra, Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Raquel Conde-Álvarez
- Instituto de Salud Tropical, Instituto de Investigación Sanitaria de Navarra, Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
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