1
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Widmalm G. Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy. JACS AU 2024; 4:20-39. [PMID: 38274261 PMCID: PMC10807006 DOI: 10.1021/jacsau.3c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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Affiliation(s)
- Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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2
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Nedielkov R, Möller HM. Detecting and Characterizing Interactions of Metabolites with Proteins by Saturation Transfer Difference Nuclear Magnetic Resonance (STD NMR) Spectroscopy. Methods Mol Biol 2023; 2554:123-139. [PMID: 36178624 DOI: 10.1007/978-1-0716-2624-5_9] [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: 06/16/2023]
Abstract
Saturation transfer difference (STD) nuclear magnetic resonance (NMR) spectroscopy is an established technique for detecting and characterizing the binding of small molecules, such as metabolites, to biological macromolecules like proteins and nucleic acids. STD NMR allows detection of binding in complex mixtures of potential ligands, which is often used for library screening in the pharmaceutical industry but may also be beneficial for binding studies with metabolite mixtures. The nature of the ligand is normally restricted to small molecules in terms of NMR spectroscopy, and the size of the macromolecule on the other side should be larger than 10-15 kDa. This technique is especially applicable to detecting binders of intermediate to low affinity with the dissociation constant (KD) above 1 μM. In this chapter, we focus on recent developments and the applications of STD NMR to studying interactions of natural products and metabolites, in particular. The reader is also referred to excellent reviews of the field and the literature cited therein. This chapter also provides a detailed experimental protocol for performing the STD NMR measurement based on the example of the subunit A of the Na+-transporting NADH/ubiquinone oxidoreductase (Na+-NQR) from V. cholerae interacting with its natural quinone substrate and inhibitors.
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Affiliation(s)
- Ruslan Nedielkov
- University of Potsdam, Institute for Chemistry, Potsdam, Germany.
| | - Heiko M Möller
- University of Potsdam, Institute for Chemistry, Potsdam, Germany
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3
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Peters T, Creutznacher R, Maass T, Mallagaray A, Ogrissek P, Taube S, Thiede L, Uetrecht C. Norovirus-glycan interactions - how strong are they really? Biochem Soc Trans 2022; 50:347-359. [PMID: 34940787 PMCID: PMC9022987 DOI: 10.1042/bst20210526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022]
Abstract
Infection with human noroviruses requires attachment to histo blood group antigens (HBGAs) via the major capsid protein VP1 as a primary step. Several crystal structures of VP1 protruding domain dimers, so called P-dimers, complexed with different HBGAs have been solved to atomic resolution. Corresponding binding affinities have been determined for HBGAs and other glycans exploiting different biophysical techniques, with mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being most widely used. However, reported binding affinities are inconsistent. At the extreme, for the same system MS detects binding whereas NMR spectroscopy does not, suggesting a fundamental source of error. In this short essay, we will explain the reason for the observed differences and compile reliable and reproducible binding affinities. We will then highlight how a combination of MS techniques and NMR experiments affords unique insights into the process of HBGA binding by norovirus capsid proteins.
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Affiliation(s)
- Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Thorben Maass
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Patrick Ogrissek
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Stefan Taube
- Institute of Virology and Cell Biology, University of Lübeck, 23562 Lübeck, Germany
| | - Lars Thiede
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg & Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
| | - Charlotte Uetrecht
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg & Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
- School of Life Sciences, University of Siegen, 57076 Siegen & Deutsches Elektronensynchrotron (DESY), 22607 Hamburg & European XFEL GmbH, 22869 Schenefeld, Germany
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4
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Cañada FJ, Canales Á, Valverde P, de Toro BF, Martínez-Orts M, Phillips PO, Pereda A. Conformational and Structural characterization of carbohydrates and their interactions studied by NMR. Curr Med Chem 2021; 29:1147-1172. [PMID: 34225601 DOI: 10.2174/0929867328666210705154046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/30/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. The versatility of Nuclear Magnetic Resonance spectroscopy (NMR) often makes it the preferred choice to study glycans and carbohydrates in solution media. The most basic NMR parameters, namely chemical shifts, coupling constants and nuclear Overhauser effects, allow defining short or repetitive chain sequences and characterize their structures and local geometries either in the free state or when interacting with other biomolecules, rendering additional information on the molecular recognition processes. The increased accessibility to carbohydrate molecules extensively or selectively labeled with 13C boosts the resolution and detail that analyzed glycan structures can reach. In turn, structural information derived from NMR, complemented with molecular modeling and theoretical calculations can also provide dynamic information on the conformational flexibility of carbohydrate structures. Furthermore, using partially oriented media or paramagnetic perturbations, it has been possible to introduce additional long-range observables rendering structural information on longer and branched glycan chains. In this review, we provide examples of these studies and an overview of the recent and most relevant NMR applications in the glycobiology field.
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Affiliation(s)
- Francisco Javier Cañada
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Pablo Valverde
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Beatriz Fernández de Toro
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Mónica Martínez-Orts
- Departamento de Química Orgánica I, Facultad Ciencias Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, C.P. 28040 Madrid, Spain
| | - Paola Oquist Phillips
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Amaia Pereda
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
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5
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Dülfer J, Yan H, Brodmerkel MN, Creutznacher R, Mallagaray A, Peters T, Caleman C, Marklund EG, Uetrecht C. Glycan-Induced Protein Dynamics in Human Norovirus P Dimers Depend on Virus Strain and Deamidation Status. Molecules 2021; 26:molecules26082125. [PMID: 33917179 PMCID: PMC8067865 DOI: 10.3390/molecules26082125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
Noroviruses are the major cause of viral gastroenteritis and re-emerge worldwide every year, with GII.4 currently being the most frequent human genotype. The norovirus capsid protein VP1 is essential for host immune response. The P domain mediates cell attachment via histo blood-group antigens (HBGAs) in a strain-dependent manner but how these glycan-interactions actually relate to cell entry remains unclear. Here, hydrogen/deuterium exchange mass spectrometry (HDX-MS) is used to investigate glycan-induced protein dynamics in P dimers of different strains, which exhibit high structural similarity but different prevalence in humans. While the almost identical strains GII.4 Saga and GII.4 MI001 share glycan-induced dynamics, the dynamics differ in the emerging GII.17 Kawasaki 308 and rare GII.10 Vietnam 026 strain. The structural aspects of glycan binding to fully deamidated GII.4 P dimers have been investigated before. However, considering the high specificity and half-life of N373D under physiological conditions, large fractions of partially deamidated virions with potentially altered dynamics in their P domains are likely to occur. Therefore, we also examined glycan binding to partially deamidated GII.4 Saga and GII.4 MI001 P dimers. Such mixed species exhibit increased exposure to solvent in the P dimer upon glycan binding as opposed to pure wildtype. Furthermore, deamidated P dimers display increased flexibility and a monomeric subpopulation. Our results indicate that glycan binding induces strain-dependent structural dynamics, which are further altered by N373 deamidation, and hence hint at a complex role of deamidation in modulating glycan-mediated cell attachment in GII.4 strains.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; (J.D.); (H.Y.)
| | - Hao Yan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; (J.D.); (H.Y.)
| | - Maxim N. Brodmerkel
- Department of Chemistry—BMC, Uppsala University, 75105 Uppsala, Sweden; (M.N.B.); (E.G.M.)
| | - Robert Creutznacher
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany; (R.C.); (A.M.); (T.P.)
| | - Alvaro Mallagaray
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany; (R.C.); (A.M.); (T.P.)
| | - Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany; (R.C.); (A.M.); (T.P.)
| | - Carl Caleman
- Department of Physics and Astronomy, Uppsala University, 75105 Uppsala, Sweden;
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Erik G. Marklund
- Department of Chemistry—BMC, Uppsala University, 75105 Uppsala, Sweden; (M.N.B.); (E.G.M.)
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany; (J.D.); (H.Y.)
- European XFEL GmbH, 22869 Schenefeld, Germany
- Correspondence:
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6
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NMR Experiments Shed New Light on Glycan Recognition by Human and Murine Norovirus Capsid Proteins. Viruses 2021; 13:v13030416. [PMID: 33807801 PMCID: PMC8001558 DOI: 10.3390/v13030416] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Glycan–protein interactions are highly specific yet transient, rendering glycans ideal recognition signals in a variety of biological processes. In human norovirus (HuNoV) infection, histo-blood group antigens (HBGAs) play an essential but poorly understood role. For murine norovirus infection (MNV), sialylated glycolipids or glycoproteins appear to be important. It has also been suggested that HuNoV capsid proteins bind to sialylated ganglioside head groups. Here, we study the binding of HBGAs and sialoglycans to HuNoV and MNV capsid proteins using NMR experiments. Surprisingly, the experiments show that none of the norovirus P-domains bind to sialoglycans. Notably, MNV P-domains do not bind to any of the glycans studied, and MNV-1 infection of cells deficient in surface sialoglycans shows no significant difference compared to cells expressing respective glycans. These findings redefine glycan recognition by noroviruses, challenging present models of infection.
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7
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Garber JM, Hennet T, Szymanski CM. Significance of fucose in intestinal health and disease. Mol Microbiol 2021; 115:1086-1093. [PMID: 33434389 DOI: 10.1111/mmi.14681] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
The deoxyhexose sugar L-fucose is important for many biological processes within the human body and the associated microbiota. This carbohydrate is abundant in host gut mucosal surfaces, numerous microbial cell surface structures, and some dietary carbohydrates. Fucosylated oligosaccharides facilitate the establishment of a healthy microbiota and provide protection from infection. However, there are instances where pathogens can also exploit these fucosylated structures to cause infection. Furthermore, deficiencies in host fucosylation are associated with specific disease outcomes. This review focuses on our current understanding of the impact of fucosylation within the mucosal environment of the gastrointestinal tract with a specific emphasis on the mediatory effects in host-microbe interactions.
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Affiliation(s)
- Jolene M Garber
- Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Christine M Szymanski
- Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, USA
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8
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Derya SM, Spiegel H, Hanisch FG, Morozov V, Schroten H, Jennewein S, Parschat K. Biotechnologically produced fucosylated oligosaccharides inhibit the binding of human noroviruses to their natural receptors. J Biotechnol 2020; 318:31-38. [PMID: 32387450 DOI: 10.1016/j.jbiotec.2020.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/10/2020] [Accepted: 05/01/2020] [Indexed: 01/17/2023]
Abstract
Norovirus infections cause severe gastroenteritis in millions of people every year. Infection requires the recognition of histo-blood group antigens (HBGAs), but such interactions can be inhibited by human milk oligosaccharides (HMOs), which act as structurally-similar decoys. HMO supplements could help to prevent norovirus infections, but the industrial production of complex HMOs is challenging. Here we describe a large-scale fermentation process that yields several kilograms of lacto-N-fucopentaose I (LNFP I). The product was synthesized in Escherichia coli BL21(DE3) cells expressing a recombinant N-acetylglucosaminyltransferase, β(1,3)galactosyltransferase and α(1,2)fucosyltransferase. Subsequent in vitro enzymatic conversion produced HBGA types A1 and B1 for norovirus inhibition assays. These carbohydrates inhibited the binding of GII.17 virus-like particles (VLPs) to type A1 and B1 trisaccharides more efficiently than simpler fucosylated HMOs, which were in turn more effective than any non-fucosylated structures. However, we found that the simpler fucosylated HMOs were more effective than complex molecules such as LNFP I when inhibiting the binding of GII.17 and GII.4 VLPs to human gastric mucins and mucins from human amniotic fluid. Our results show that complex fucosylated HMOs can be produced by large-scale fermentation and that a combination of simple and complex fucosylated structures is more likely to prevent norovirus infections.
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Affiliation(s)
- Sami M Derya
- Jennewein Biotechnologie GmbH, 53619 Rheinbreitbach, Germany.
| | - Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 52074 Aachen, Germany.
| | - Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty, University of Cologne, 50931 Köln, Germany.
| | - Vasily Morozov
- Pediatric Infectious Disease Unit, University Children's Hospital Mannheim, 68167 Mannheim, Germany.
| | - Horst Schroten
- Pediatric Infectious Disease Unit, University Children's Hospital Mannheim, 68167 Mannheim, Germany.
| | - Stefan Jennewein
- Jennewein Biotechnologie GmbH, 53619 Rheinbreitbach, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, 52074 Aachen, Germany.
| | - Katja Parschat
- Jennewein Biotechnologie GmbH, 53619 Rheinbreitbach, Germany.
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9
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A post-translational modification of human Norovirus capsid protein attenuates glycan binding. Nat Commun 2019; 10:1320. [PMID: 30899001 PMCID: PMC6428809 DOI: 10.1038/s41467-019-09251-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/27/2019] [Indexed: 01/06/2023] Open
Abstract
Attachment of human noroviruses to histo blood group antigens (HBGAs) is essential for infection, but how this binding event promotes the infection of host cells is unknown. Here, we employ protein NMR experiments supported by mass spectrometry and crystallography to study HBGA binding to the P-domain of a prevalent virus strain (GII.4). We report a highly selective transformation of asparagine 373, located in an antigenic loop adjoining the HBGA binding site, into an iso-aspartate residue. This spontaneous post-translational modification (PTM) proceeds with an estimated half-life of a few days at physiological temperatures, independent of the presence of HBGAs but dramatically affecting HBGA recognition. Sequence conservation and the surface-exposed position of this PTM suggest an important role in infection and immune recognition for many norovirus strains. Attachment of human noroviruses to histo blood group antigens (HBGAs) is essential for infection. Here the authors report that an asparagine residue located near the HBGA-attachment site can convert into an iso-aspartate residue through spontaneous deamidation and influence HBGA recognition.
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10
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Abdelkarim H, Hitchinson B, Banerjee A, Gaponenko V. Advances in NMR Methods to Identify Allosteric Sites and Allosteric Ligands. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:171-186. [PMID: 31707704 DOI: 10.1007/978-981-13-8719-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
NMR allows assessment of protein structure in solution. Unlike conventional X-ray crystallography that provides snapshots of protein conformations, all conformational states are simultaneously accessible to analysis by NMR. This is a significant advantage for discovery and characterization of allosteric effects. These effects are observed when binding at one site of the protein affects another distinct site through conformational transitions. Allosteric regulation of proteins has been observed in multiple physiological processes in health and disease, providing an opportunity for the development of allosteric inhibitors. These compounds do not directly interact with the orthosteric site of the protein but influence its structure and function. In this book chapter, we provide an overview on how NMR methods are utilized to identify allosteric sites and to discover novel inhibitors, highlighting examples from the field. We also describe how NMR has contributed to understanding of allosteric mechanisms and propose that it is likely to play an important role in clarification and further development of key concepts of allostery.
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Affiliation(s)
- Hazem Abdelkarim
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ben Hitchinson
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
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11
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Blaum BS, Neu U, Peters T, Stehle T. Spin ballet for sweet encounters: saturation-transfer difference NMR and X-ray crystallography complement each other in the elucidation of protein-glycan interactions. Acta Crystallogr F Struct Biol Commun 2018; 74:451-462. [PMID: 30084394 PMCID: PMC6096479 DOI: 10.1107/s2053230x18006581] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/28/2018] [Indexed: 03/11/2023] Open
Abstract
Biomolecular NMR spectroscopy has limitations in the determination of protein structures: an inherent size limit and the requirement for expensive and potentially difficult isotope labelling pose considerable hurdles. Therefore, structural analysis of larger proteins is almost exclusively performed by crystallography. However, the diversity of biological NMR applications outperforms that of any other structural biology technique. For the characterization of transient complexes formed by proteins and small ligands, notably oligosaccharides, one NMR technique has recently proven to be particularly powerful: saturation-transfer difference NMR (STD-NMR) spectroscopy. STD-NMR experiments are fast and simple to set up, with no general protein size limit and no requirement for isotope labelling. The method performs best in the moderate-to-low affinity range that is of interest in most of glycobiology. With small amounts of unlabelled protein, STD-NMR experiments can identify hits from mixtures of potential ligands, characterize mutant proteins and pinpoint binding epitopes on the ligand side. STD-NMR can thus be employed to complement and improve protein-ligand complex models obtained by other structural biology techniques or by purely computational means. With a set of protein-glycan interactions from our own work, this review provides an introduction to the technique for structural biologists. It exemplifies how crystallography and STD-NMR can be combined to elucidate protein-glycan (and other protein-ligand) interactions in atomic detail, and how the technique can extend structural biology from simplified systems amenable to crystallization to more complex biological entities such as membranes, live viruses or entire cells.
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Affiliation(s)
- Bärbel S. Blaum
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Ursula Neu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Thomas Peters
- Institute of Chemistry and Metabolomics, University of Lübeck, 23562 Lübeck, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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12
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Taube S, Mallagaray A, Peters T. Norovirus, glycans and attachment. Curr Opin Virol 2018; 31:33-42. [DOI: 10.1016/j.coviro.2018.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 10/16/2022]
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13
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Wegener H, Mallagaray Á, Schöne T, Peters T, Lockhauserbäumer J, Yan H, Uetrecht C, Hansman GS, Taube S. Human norovirus GII.4(MI001) P dimer binds fucosylated and sialylated carbohydrates. Glycobiology 2018; 27:1027-1037. [PMID: 28973640 DOI: 10.1093/glycob/cwx078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/29/2017] [Indexed: 12/23/2022] Open
Abstract
Human noroviruses (HuNoV), members of the family Caliciviridae, are the major cause of acute viral gastroenteritis worldwide. Successful infection is linked to the ability of the protruding (P) domain of the viral capsid to bind histo-blood group antigens (HBGA). Binding to gangliosides plays a major role for many nonhuman calici- and noroviruses. Increasing evidence points to a broader role of sialylated carbohydrates such as gangliosides in norovirus infection. Here, we compare HBGA and ganglioside binding of a GII.4 HuNoV variant (MI001), previously shown to be infectious in a HuNoV mouse model. Saturation transfer difference nuclear magnetic resonance spectroscopy, native mass spectrometry (MS) and surface plasmon resonance spectroscopy were used to characterize binding epitopes, affinities, stoichiometry and dynamics, focusing on 3'-sialyllactose, the GM3 ganglioside saccharide and B antigen. Binding was observed for 3'-sialyllactose and various HBGAs following a multistep binding process. Intrinsic affinities (Kd) of fucose, 3'-sialyllactose and B antigen were determined for the individual binding steps. Stronger affinities were observed for B antigen over 3'-sialyllactose and fucose, which bound in the mM range. Binding stoichiometry was analyzed by native MS showing the presence of four B antigens or two 3'-sialyllactose in the complex. Epitope mapping of 3'-sialyllactose revealed direct interaction of α2,3-linked sialic acid with the P domain. The ability of HuNoV to engage multiple carbohydrates emphasizes the multivalent nature of norovirus glycan-specificity. Our findings reveal direct binding of a GII.4 HuNoV P dimer to α2,3-linked sialic acid and support a broader role of ganglioside binding in norovirus infection.
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Affiliation(s)
- Henrik Wegener
- University of Lübeck, Institute of Virology and Cell Biology,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Álvaro Mallagaray
- University of Lübeck, Institute of Chemistry,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Tobias Schöne
- University of Lübeck, Institute of Chemistry,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Thomas Peters
- University of Lübeck, Institute of Chemistry,Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Julia Lockhauserbäumer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology,Martinistrasse 52, 20251 Hamburg, Germany
| | - Hao Yan
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology,Martinistrasse 52, 20251 Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Grant S Hansman
- German Cancer Research Center (DKFZ), CHS Foundation at the University of Heidelberg, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Stefan Taube
- University of Lübeck, Institute of Virology and Cell Biology,Ratzeburger Allee 160, 23562 Lübeck, Germany
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Fiege B, Leuthold M, Parra F, Dalton KP, Meloncelli PJ, Lowary TL, Peters T. Epitope mapping of histo blood group antigens bound to norovirus VLPs using STD NMR experiments reveals fine details of molecular recognition. Glycoconj J 2017; 34:679-689. [PMID: 28823097 DOI: 10.1007/s10719-017-9792-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/04/2017] [Accepted: 08/08/2017] [Indexed: 01/06/2023]
Abstract
Attachment of human noroviruses to histo blood group antigens (HBGAs) is thought to be critical for the infection process. Therefore, we have determined binding epitopes of synthetic type 1 to 6 blood group A- and B-tetrasaccharides binding to GII.4 human Norovirus virus like particles (VLPs) using STD NMR experiments. So far, little information is available from crystal structure analysis studies on the interactions of the reducing-end sugars with the protruding domain (P-domain) of the viral coat protein VP1. Here, we show that the reducing-end sugars make notable contacts with the protein surface. The type of glycosidic linkage, and the identity of the sugar at the reducing end modulate HBGA recognition. Most strikingly, type 2 structures yield only very poor saturation transfer indicating impeded binding. This observation is in accordance with previous mass spectrometry based affinity measurements, and can be understood based on recent crystal structure data of a complex of highly homologous GII.4 P-dimers with H-type 2 trisaccharide where the N-acetyl group of the reducing N-acetyl glucosamine residue points towards a loop comprising amino acids Q390 to H395. We suggest that in our case, binding of type 2 A- and B-tetrasaccharides leads to steric conflicts with this loop. In order to identify factors determining L-Fuc recognition, we also synthesized GII.4 VLPs with point mutations D391A and H395A. Prior studies had suggested that these residues, located in a second shell around the L-Fuc binding site, assist L-Fuc binding. STD NMR experiments with L-Fuc and B-trisaccharide in the presence of wild type and mutant VLPs yield virtually identical binding epitopes suggesting that these two mutations do not significantly alter HBGA recognition. Our study emphasizes that recognition of α-(1→2)-linked L-Fuc residues is a conserved feature of GII.4 noroviruses. However, structural variation of the HBGA core structures clearly modulates molecular recognition depending on the genotype.
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Affiliation(s)
- Brigitte Fiege
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Mila Leuthold
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany
- Molecular Virology, Heidelberg University Hospital, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Kevin P Dalton
- Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Peter J Meloncelli
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, The University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G G2, Canada
| | - Todd L Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning-Lemieux Chemistry Centre, The University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, T6G G2, Canada
| | - Thomas Peters
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry and Metabolomics, University of Luebeck, Ratzeburger Allee 160, 23562, Luebeck, Germany.
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Abstract
Noroviruses are the leading cause of acute gastroenteritis around the world. An individual living in the United States is estimated to develop norovirus infection five times in his or her lifetime. Despite this, there is currently no antiviral or vaccine to combat the infection, in large part because of the historical lack of cell culture and small animal models. However, the last few years of norovirus research were marked by a number of ground-breaking advances that have overcome technical barriers and uncovered novel aspects of norovirus biology. Foremost among them was the development of two different
in vitro culture systems for human noroviruses. Underappreciated was the notion that noroviruses infect cells of the immune system as well as epithelial cells within the gastrointestinal tract and that human norovirus infection of enterocytes requires or is promoted by the presence of bile acids. Furthermore, two proteinaceous receptors are now recognized for murine norovirus, marking the first discovery of a functional receptor for any norovirus. Recent work further points to a role for certain bacteria, including those found in the gut microbiome, as potential modulators of norovirus infection in the host, emphasizing the importance of interactions with organisms from other kingdoms of life for viral pathogenesis. Lastly, we will highlight the adaptation of drop-based microfluidics to norovirus research, as this technology has the potential to reveal novel insights into virus evolution. This review aims to summarize these new findings while also including possible future directions.
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Affiliation(s)
- Eric Bartnicki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Juliana Bragazzi Cunha
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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