1
|
Smith MJ, Gates EL, Widmalm G, Adams RW, Morris GA, Nilsson M. Resolving the complexity in human milk oligosaccharides using pure shift NMR methods and CASPER. Org Biomol Chem 2023; 21:3984-3990. [PMID: 37186244 DOI: 10.1039/d3ob00421j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Human milk oligosaccharides belong to an important class of bioactive molecules with diverse effects on the development of infants. NMR is capable of providing vital structural information about oligosaccharides which can aid in determining structure-function relationships. However, this information is often concealed by signal overlap in 1H spectra, due to the narrow chemical shift range and signal multiplicity. Signal overlap in oligosaccharide spectra can be greatly reduced, and resolution improved, by utilising pure shift methods. Here the benefits of combining pure shift methods with the CASPER computational approach to resonance assignment in oligosaccharides are demonstrated.
Collapse
Affiliation(s)
- Marshall J Smith
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK.
| | - Emma L Gates
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK.
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Ralph W Adams
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK.
| | - Gareth A Morris
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK.
| | - Mathias Nilsson
- Department of Chemistry, University of Manchester, Manchester, M13 9PL, UK.
| |
Collapse
|
2
|
Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
Collapse
Affiliation(s)
- Carolina Fontana
- Departamento
de Química del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| |
Collapse
|
3
|
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]
|
4
|
Kupče Ē, Yong JRJ, Widmalm G, Claridge TDW. Parallel NMR Supersequences: Ten Spectra in a Single Measurement. JACS AU 2021; 1:1892-1897. [PMID: 34841408 PMCID: PMC8611666 DOI: 10.1021/jacsau.1c00423] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Indexed: 05/05/2023]
Abstract
The principles employed in parallel NMR and MRI are applied to NMR supersequences yielding as many as ten 2D NMR spectra in one measurement. We present a number of examples where two NOAH (NMR by Ordered Acquisition using 1H-detection) supersequences are recorded in parallel, thus dramatically increasing the information content obtained in a single NMR experiment. The two parallel supersequences entangled by time-sharing schemes (IPAP-seHSQC, HSQC-COSY, and HSQC-TOCSY) incorporate also modified (sequential and/or interleaved) conventional pulse schemes (modules), including HMBC, TOCSY, COSY, CLIP-COSY, NOESY, and ROESY. Such parallel supersequences can be tailored for specific applications, for instance, the analysis and characterization of molecular structure of complex organic molecules from a single measurement. In particular, the CASPER software was used to establish the structure of a tetrasaccharide, β-LNnTOMe, with a high degree of confidence from a single measurement involving a parallel NOAH-5 supersequence.
Collapse
Affiliation(s)
- Ēriks Kupče
- Bruker
UK Ltd, R&D, Banner
Lane, Coventry CV4 9GH, United Kingdom
| | - Jonathan R. J. Yong
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Tim D. W. Claridge
- Department
of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| |
Collapse
|
5
|
High-throughput and high-sensitivity N-Glycan profiling: A platform for biopharmaceutical development and disease biomarker discovery. Anal Biochem 2021; 623:114205. [PMID: 33891963 DOI: 10.1016/j.ab.2021.114205] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/11/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023]
Abstract
Protein glycosylation contributes to critical biological function of glycoproteins. Glycan analysis is essential for the production of biopharmaceuticals as well as for the identification of disease biomarkers. However, glycans are highly heterogeneous, which has considerably hampered the progress of glycomics. Here, we present an improved 96-well plate format platform for streamlined glycan profiling that takes advantage of rapid glycoprotein denaturation, deglycosylation, fluorescent derivatization, and on-matrix glycan clean-up. This approach offers high sensitivity with consistent identification and quantification of diverse N-glycans across multiple samples on a high-throughput scale. We demonstrate its capability for N-glycan profiling of glycoproteins from various sources, including two recombinant monoclonal antibodies produced from Chinese Hamster Ovary cells, EG2-hFc and rituximab, polyclonal antibodies purified from human serum, and total glycoproteins from human serum. Combined with the complementary information obtained by sequential digestion from exoglycosidase arrays, this approach allows the detection and identification of multiple N-glycans in these complex biological samples. The reagents, workflow, and Hydrophilic interaction liquid chromatography with fluorescence detection (HILIC-FLD), are simple enough to be implemented into a straightforward user-friendly setup. This improved technology provides a powerful tool in support of rapid advancement of glycan analysis for biopharmaceutical development and biomarker discovery for clinical disease diagnosis.
Collapse
|
6
|
Knaack W, Hölzl G, Gisch N. Structural Analysis of Glycosylglycerolipids Using NMR Spectroscopy. Methods Mol Biol 2021; 2295:249-272. [PMID: 34047981 DOI: 10.1007/978-1-0716-1362-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Glycosylglycerolipids are essential components of plant and bacterial membranes. These lipids exert central roles in physiological processes such as photosynthesis in plants or to maintain membrane stability in bacteria. They are composed of a glycerol backbone esterified with two fatty acids at the sn-1 and sn-2 positions, and carbohydrate moieties connected via a glycosidic bond at the sn-3 position. Nuclear magnetic resonance (NMR) spectroscopy is a state-of-the-art technique to determine the nature of the bound carbohydrates as well as their anomeric configurations. Here we describe the analysis of intact glycosylglycerolipids by NMR spectroscopy to determine structural details of their sugar head groups without the need of chemical derivatization.
Collapse
Affiliation(s)
- Wiebke Knaack
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Georg Hölzl
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz Lung Center, Borstel, Germany.
| |
Collapse
|
7
|
Lisacek F, Mariethoz J, Alocci D, Rudd PM, Abrahams JL, Campbell MP, Packer NH, Ståhle J, Widmalm G, Mullen E, Adamczyk B, Rojas-Macias MA, Jin C, Karlsson NG. Databases and Associated Tools for Glycomics and Glycoproteomics. Methods Mol Biol 2017; 1503:235-264. [PMID: 27743371 DOI: 10.1007/978-1-4939-6493-2_18] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (SugarBind).
Collapse
Affiliation(s)
- Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Pauline M Rudd
- NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
| | - Jodie L Abrahams
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Matthew P Campbell
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Nicolle H Packer
- Biomolecular Frontiers Research Centre, Macquarie University, North Ryde, NSW, Australia
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Barbara Adamczyk
- NIBRT GlycoScience Group, NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co., Dublin, Ireland
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Miguel A Rojas-Macias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30, Gothenburg, Sweden.
| |
Collapse
|
8
|
Unique lipid anchor attaches Vi antigen capsule to the surface of Salmonella enterica serovar Typhi. Proc Natl Acad Sci U S A 2016; 113:6719-24. [PMID: 27226298 DOI: 10.1073/pnas.1524665113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Polysaccharide capsules are surface structures that are critical for the virulence of many Gram-negative pathogenic bacteria. Salmonella enterica serovar Typhi is the etiological agent of typhoid fever. It produces a capsular polysaccharide known as "Vi antigen," which is composed of nonstoichiometrically O-acetylated α-1,4-linked N-acetylgalactosaminuronic acid residues. This glycan is a component of currently available vaccines. The genetic locus for Vi antigen production is also present in soil bacteria belonging to the genus Achromobacter Vi antigen assembly follows a widespread general strategy with a characteristic glycan export step involving an ATP-binding cassette transporter. However, Vi antigen producers lack the enzymes that build the conserved terminal glycolipid characterizing other capsules using this method. Achromobacter species possess a Vi antigen-specific depolymerase enzyme missing in S enterica Typhi, and we exploited this enzyme to isolate acylated Vi antigen termini. Mass spectrometry analysis revealed a reducing terminal N-acetylhexosamine residue modified with two β-hydroxyl acyl chains. This terminal structure resembles one half of lipid A, the hydrophobic portion of bacterial lipopolysaccharides. The VexE protein encoded in the Vi antigen biosynthesis locus shares similarity with LpxL, an acyltransferase from lipid A biosynthesis. In the absence of VexE, Vi antigen is produced, but its physical properties are altered, its export is impaired, and a Vi capsule structure is not assembled on the cell surface. The structure of the lipidated terminus dictates a unique assembly mechanism and has potential implications in pathogenesis and vaccine production.
Collapse
|