1
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Tamuli R, Nguyen T, Macdonald JR, Pierens GK, Fisher GM, Andrews KT, Adewoyin FB, Omisore NO, Odaibo AB, Feng Y. Isolation and In Vitro and In Vivo Activity of Secondary Metabolites from Clerodendrum polycephalum Baker against Plasmodium Malaria Parasites. JOURNAL OF NATURAL PRODUCTS 2023; 86:2661-2671. [PMID: 37972998 DOI: 10.1021/acs.jnatprod.3c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Chemical investigation of the antimalarial medicinal plant Clerodendrum polycephalum led to the isolation of five new diterpenoids, including ajugarins VII-X (1-4) and teuvincenone K (5), along with four known compounds, namely, 12,16-epoxy-6,11,14,17-tetrahydroxy-17(15 → 16)-abeo-5,8,11,13,15-abietapentaen-7-one (6), methyl pheophorbide A (7), loliolide (8), and acacetin (9). The chemical structures of the new compounds were elucidated using NMR spectroscopy, mass spectrometry, circular dichroism, as well as density functional theory calculations. All compounds were evaluated for in vitro activity against Plasmodium falciparum 3D7 malaria parasites with methyl pheophorbide A (7) showing the strongest activity (IC50 4.49 μM). Subsequent in vivo testing in a Plasmodium berghei chemosuppression model showed that compound 7 significantly attenuated peripheral blood parasitemia, leading to 79% and 87% chemosuppression following oral doses at 10 and 20 mg/kg, respectively.
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Affiliation(s)
- Roktima Tamuli
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Jacinta R Macdonald
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Gillian M Fisher
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Katherine T Andrews
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Francis B Adewoyin
- Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Osun State 220282, Nigeria
| | - Nusrat O Omisore
- Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Osun State 220282, Nigeria
| | - Alexander B Odaibo
- Department of Zoology, Faculty of Science, University of Ibadan, Ibadan, Oyo State 200005, Nigeria
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
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2
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Fittolani G, Tyrikos-Ergas T, Poveda A, Yu Y, Yadav N, Seeberger PH, Jiménez-Barbero J, Delbianco M. Synthesis of a glycan hairpin. Nat Chem 2023; 15:1461-1469. [PMID: 37400598 PMCID: PMC10533408 DOI: 10.1038/s41557-023-01255-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
The primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
| | - Yang Yu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Simpson Querrey Institute, Northwestern University, Evanston, IL, USA
| | - Nishu Yadav
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain
- Centro de Investigación Biomedica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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3
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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.
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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,
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4
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Dal Colle MCS, Fittolani G, Delbianco M. Synthetic Approaches to Break the Chemical Shift Degeneracy of Glycans. Chembiochem 2022; 23:e202200416. [PMID: 36005282 PMCID: PMC10087674 DOI: 10.1002/cbic.202200416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/24/2022] [Indexed: 01/25/2023]
Abstract
NMR spectroscopy is the leading technique for determining glycans' three-dimensional structure and dynamic in solution as well as a fundamental tool to study protein-glycan interactions. To overcome the severe chemical shift degeneracy of these compounds, synthetic probes carrying NMR-active nuclei (e. g., 13 C or 19 F) or lanthanide tags have been proposed. These elegant strategies permitted to simplify the complex NMR analysis of unlabeled analogues, shining light on glycans' conformational aspects and interaction with proteins. Here, we highlight some key achievements in the synthesis of specifically labeled glycan probes and their contribution towards the fundamental understanding of glycans.
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Affiliation(s)
- Marlene C S Dal Colle
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
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5
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Miao WG, Nguyen T, Iqbal J, Pierens GK, Ma L, Richardson DR, Wood SA, Mellick GD, Quinn RJ, Feng Y. Meeting the Challenge 2: Identification of Potential Chemical Probes for Parkinson's Disease from Ligusticum chuanxiong Hort Using Cytological Profiling. ACS Chem Neurosci 2022; 13:2565-2578. [PMID: 36018577 DOI: 10.1021/acschemneuro.1c00820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Traditional Chinese medicine (TCM) has been around for thousands of years and is increasingly gaining popularity in the Western world to treat various complex disorders including the incurable neurodegenerative condition, Parkinson's Disease (PD). One of the many directions in recent studies of PD is utilizing the phenotypic assay, or cytological profiling, to evaluate the phenotypic changes of PD-implicated cellular components in patient-derived olfactory neuroepithelial (hONS) cells, upon treating the cells with extracts or pure compounds. To obtain small molecules for studies utilizing PD phenotyping assays, Ligusticum chuanxiong Hort was selected for analysis as it is a popular Chinese herbal medicine used for treating PD-like symptoms. Fifty-three secondary metabolites, including six new compounds, were isolated from the ethanolic extract of L. chuanxiong; their structures were elucidated based on several spectroscopic techniques such as NMR, MS, Fourier transform infrared (FTIR), UV, and theoretical density functional theory (DFT) calculations. Cytological profiling of the afforded natural products against PD hONS cells revealed 34 compounds strongly perturbated the staining of several cellular organelles. In fact, greaterthan 1.5-fold change was observed compared to the control (dimethyl sulfoxide; DMSO), with early endosome, lysosome, and autophagosome (LC3b) being particularly affected. Given these biological compartments are closely related to PD pathogenesis, the results helped rationalize the traditional medicinal use of L. chuanxiong in PD treatment. Further, the hit compounds can serve as chemical probes to map the molecular pathways underlying PD, potentially leading to new therapeutic targets for PD.
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Affiliation(s)
- William Gang Miao
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Jamila Iqbal
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Linlin Ma
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Des R Richardson
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia.,School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
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6
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Soares CO, Grosso AS, Ereño-Orbea J, Coelho H, Marcelo F. Molecular Recognition Insights of Sialic Acid Glycans by Distinct Receptors Unveiled by NMR and Molecular Modeling. Front Mol Biosci 2021; 8:727847. [PMID: 34869580 PMCID: PMC8634706 DOI: 10.3389/fmolb.2021.727847] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
All cells are decorated with a highly dense and complex structure of glycan chains, which are mostly attached to proteins and lipids. In this context, sialic acids are a family of nine-carbon acidic monosaccharides typically found at the terminal position of glycan chains, modulating several physiological and pathological processes. Sialic acids have many structural and modulatory roles due to their negative charge and hydrophilicity. In addition, the recognition of sialic acid glycans by mammalian cell lectins, such as siglecs, has been described as an important immunological checkpoint. Furthermore, sialic acid glycans also play a pivotal role in host-pathogen interactions. Various pathogen receptors exposed on the surface of viruses and bacteria are responsible for the binding to sialic acid sugars located on the surface of host cells, becoming a critical point of contact in the infection process. Understanding the molecular mechanism of sialic acid glycans recognition by sialic acid-binding proteins, present on the surface of pathogens or human cells, is essential to realize the biological mechanism of these events and paves the way for the rational development of strategies to modulate sialic acid-protein interactions in diseases. In this perspective, nuclear magnetic resonance (NMR) spectroscopy, assisted with molecular modeling protocols, is a versatile and powerful technique to investigate the structural and dynamic aspects of glycoconjugates and their interactions in solution at the atomic level. NMR provides the corresponding ligand and protein epitopes, essential for designing and developing potential glycan-based therapies. In this review, we critically discuss the current state of knowledge about the structural features behind the molecular recognition of sialic acid glycans by different receptors, naturally present on human cells or pathogens, disclosed by NMR spectroscopy and molecular modeling protocols.
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Affiliation(s)
- Cátia Oliveira Soares
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Ana Sofia Grosso
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - June Ereño-Orbea
- CIC bioGUNE, Basque Research and Technology Alliance, Bizkaia Technology Park, Bilbao, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Helena Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal.,Department of Chemistry, UCIBIO-Applied Molecular Biosciences Unit, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
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7
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Methods for Measuring Exchangeable Protons in Glycosaminoglycans. Methods Mol Biol 2021. [PMID: 34626393 DOI: 10.1007/978-1-0716-1398-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.
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8
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Mindler K, Ostertag E, Stehle T. The polyfunctional polysialic acid: A structural view. Carbohydr Res 2021; 507:108376. [PMID: 34273862 DOI: 10.1016/j.carres.2021.108376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 12/15/2022]
Abstract
Polysialic acid (polySia), a homopolymer of α2,8-linked sialic acid residues, modifies a small number of proteins and has central functions in vertebrate signalling. Here, we review the regulatory functions of polySia in signalling processes and the immune system of adult humans, as well as functions based on their chemical properties. The main focus will be on the structure-function relationship of polySia with its interaction partners in humans. Recent studies have indicated that the degree of polymerisation is an important parameter that can guide the regulatory effect of polySia in addition to its binding to target proteins. Therefore, the structures of polySia in solution and bound to interaction partners are compared in order to identify the key factors that define binding specificity.
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Affiliation(s)
- Katja Mindler
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076, Tübingen, Germany
| | - Elena Ostertag
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076, Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076, Tübingen, Germany.
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9
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Novakovic M, Battistel MD, Azurmendi HF, Concilio MG, Freedberg DI, Frydman L. The Incorporation of Labile Protons into Multidimensional NMR Analyses: Glycan Structures Revisited. J Am Chem Soc 2021; 143:8935-8948. [PMID: 34085814 PMCID: PMC8297728 DOI: 10.1021/jacs.1c04512] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Glycan structures
are often stabilized by a repertoire of hydrogen-bonded
donor/acceptor groups, revealing longer-lived structures that could
represent biologically relevant conformations. NMR provides unique
data on these hydrogen-bonded networks from multidimensional experiments
detecting cross-peaks resulting from through-bond (TOCSY) or through-space
(NOESY) interactions. However, fast OH/H2O exchange, and
the spectral proximity among these NMR resonances, hamper the use
of glycans’ labile protons in such analyses; consequently,
studies are often restricted to aprotic solvents or supercooled aqueous
solutions. These nonphysiological conditions may lead to unrepresentative
structures or to probing a small subset of accessible conformations
that may miss “active” glycan conformations. Looped,
projected spectroscopy (L-PROSY) has been recently shown to substantially
enhance protein NOESY and TOCSY cross-peaks, for 1Hs that
undergo fast exchange with water. This study shows that even larger
enhancements can be obtained for rapidly exchanging OHs in saccharides,
leading to the retrieval of previously undetectable 2D TOCSY/NOESY
cross-peaks with nonlabile protons. After demonstrating ≥300%
signal enhancements on model monosaccharides, these experiments were
applied at 1 GHz to elucidate the structural network adopted by a
sialic acid homotetramer, used as a model for α,2–8 linked
polysaccharides. High-field L-PROSY NMR enabled these studies at higher
temperatures and provided insight previously unavailable from lower-field
NMR investigations on supercooled samples, involving mostly nonlabile
nuclei. Using L-PROSY’s NOEs and other restraints, a revised
structural model for the homotetramer was obtained combining rigid
motifs and flexible segments, that is well represented by conformations
derived from 40 μs molecular dynamics simulations.
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Affiliation(s)
- Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Maria-Grazia Concilio
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, United States
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
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10
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Watson A, Simmermaker C, Aung E, Do S, Hackbusch S, Franz AH. NMR analysis and molecular dynamics conformation of α-1,6-linear and α-1,3-branched isomaltose oligomers as mimetics of α-1,6-linked dextran. Carbohydr Res 2021; 503:108296. [PMID: 33813322 DOI: 10.1016/j.carres.2021.108296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023]
Abstract
The conformational preferences of several α-1,6-linear and α-1,3-branched isomalto-oligosaccharides were investigated by NMR and MD-simulations. Right-handed helical structure contributed to the solution geometry in isomaltotriose and isomaltotetraose with one nearly complete helix turn and stabilizing intramolecular hydrogen bonds in the latter by MD-simulation. Decreased helix contribution was observed in α-1,3-glucopyranosyl- and α-1,3-isomaltosyl-branched saccharide chains. Especially the latter modification was predicted to cause a more compact structure consistent with literature rheology measurements as well as with published dextranase-resistant α-1,3-branched oligosaccharides. The findings presented here are significant because they shed further light on the conformational preference of isomalto-oligosaccharides and provide possible help for the design of dextran-based drug delivery systems or for the targeted degradation of capsular polysaccharides by dextranases in multi-drug resistant bacteria.
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Affiliation(s)
- Amelia Watson
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Cate Simmermaker
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ei Aung
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Stephen Do
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Sven Hackbusch
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Andreas H Franz
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
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11
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Hamagami H, Yamaguchi Y, Tanaka H. Chemical Synthesis of Residue-Selectively 13C and 2H Double-Isotope-Labeled Oligosaccharides as Chemical Probes for the NMR-Based Conformational Analysis of Oligosaccharides. J Org Chem 2020; 85:16115-16127. [PMID: 33107296 DOI: 10.1021/acs.joc.0c01939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The conformational analysis of oligosaccharide is a fundamental issue in glycobiology. NMR measurements of atom-selectively 13C-labeled oligosaccharides have provided valuable information concerning their conformation, which would not be possible using nonlabeled oligosaccharides. The amount of accessible information from an atom-selectively labeled molecule, however, is limited. In this work, we report on the chemical synthesis of residue-selectively 13C- and 2H-labeled oligosaccharides and their use in conformational analysis. 1H NMR measurements of such double isotope-labeled compounds can provide a great deal of information on the dihedral angles across glycosidic linkages. We demonstrated this method in the conformational analyses of some linear and branched β(1,3)-glucan oligosaccharides.
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Affiliation(s)
- Hiroki Hamagami
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1-H101 Ookayama, Meguro, Tokyo 152-8552, Japan
| | - Yoshiki Yamaguchi
- RIKEN-Max-Planck Joint Research Center for Systems Chemical Biology RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1-H101 Ookayama, Meguro, Tokyo 152-8552, Japan
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12
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Sensitivity enhancement of homonuclear multidimensional NMR correlations for labile sites in proteins, polysaccharides, and nucleic acids. Nat Commun 2020; 11:5317. [PMID: 33087707 PMCID: PMC7577996 DOI: 10.1038/s41467-020-19108-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/17/2020] [Indexed: 12/02/2022] Open
Abstract
Multidimensional TOCSY and NOESY are central experiments in chemical and biophysical NMR. Limited efficiencies are an intrinsic downside of these methods, particularly when targeting labile sites. This study demonstrates that the decoherence imparted on these protons through solvent exchanges can, when suitably manipulated, lead to dramatic sensitivity gains per unit time in the acquisition of these experiments. To achieve this, a priori selected frequencies are encoded according to Hadamard recipes, while concurrently subject to looped selective inversion or selective saturation procedures. Suitable processing then leads to protein, oligosaccharide and nucleic acid cross-peak enhancements of ≈200–1000% per scan, in measurements that are ≈10-fold faster than conventional counterparts. The extent of these gains will depend on the solvent exchange and relaxation rates of the targeted sites; these gains also benefit considerably from the spectral resolution provided by ultrahigh fields, as corroborated by NMR experiments at 600 MHz and 1 GHz. The mechanisms underlying these experiments’ enhanced efficiencies are analyzed on the basis of three-way polarization transfer interplays between the water, labile and non-labile protons, and the experimental results are rationalized using both analytical and numerical derivations. Limitations as well as further extensions of the proposed methods, are also discussed. Here, the authors present an approach that enhances the sensitivity of basic 2D biomolecular NMR experiments like NOESY and TOCSY, when carried out in polysaccharides, proteins and nucleic acids. This method combines principles associated to quantum Anti-Zeno Effects and advanced data acquisition methods based on Hadamard multiplexing.
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13
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Battistel MD, Freedberg DI. Dispersing the crowd: Adopting 13C direct detection for glycans. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106792. [PMID: 32759046 DOI: 10.1016/j.jmr.2020.106792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/08/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
As a direct consequence of technological advancements, the interest in direct detection of low-gamma/low-sensitivity heteronuclei for NMR experiments has been revived. Until recently, experimental development of 13C/15N detected experiments has been focused on protein NMR. In the present report, we extend the use of 13C-detected experiments to structural studies of glycans in natural abundance. The narrow 1H and wider 13C signal dispersion make glycans ideal candidates for heteronuclear detection. We show that 13C-detected HSQC offers a ten-fold increase in 13C dimension resolution compared to the analogous 1H-detected HSQC, when the experiments are acquired for the same amount of time. The enhanced resolution comes at the expense of 2 to 3-fold loss in SNR; however, the observed signal loss is a fraction of the theoretical 8-fold difference expected between experiments. Further, we show that by combining a 1H constant time element (CT), SMILE data reconstruction and 13C-direct detection, complete resonance assignments of highly degenerate glycan signals are possible. Finally, we demonstrate the potential of our strategy to aid in the assignment of complex glycans, by using a novel 13C-detected version of the CT-HSQC-TOCSY experiment performed on sialyl Lewis X pentasaccharide model system.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration (FDA), Silver Spring, MD 20993, United States.
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14
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Long M, Ní Cheallaigh A, Reihill M, Oscarson S, Lahmann M. Synthesis of type 1 Lewis b hexasaccharide antigen structures featuring flexible incorporation of l-[U- 13C 6]-fucose for NMR binding studies. Org Biomol Chem 2020; 18:4452-4458. [PMID: 32478348 DOI: 10.1039/d0ob00426j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While 13C-labelled proteins are common tools in NMR studies, lack of access to 13C-labelled carbohydrate structures has restricted their use. l-Fucose is involved in a wide range of physiological and pathophysiological processes in mammalian organisms. Here, l-[U-13C6]-Fuc labelled type I Lewis b (Leb) structures have been synthesised for use in NMR binding studies with the Blood-group Antigen Binding Adhesin (BabA), a membrane-bound protein from the bacterium Helicobacter pylori. As part of this work, an efficient synthesis of a benzylated l-[U-13C6]-Fuc thioglycoside donor from l-[U-13C6]-Gal has been developed. The design and synthesis of an orthogonally protected tetrasaccharide precursor enabled controlled introduction of one or two 13C-labelled or non-labelled fucosyl residues prior to global deprotection. NMR analysis showed that it is straightforward to assign the anomeric centres as well as the H-5 positions to the individual fucosyl residues which are relevant for NMR binding studies.
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Affiliation(s)
- Mark Long
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Aisling Ní Cheallaigh
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, IE
| | - Mark Reihill
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, IE
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, IE
| | - Martina Lahmann
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
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15
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Turupcu A, Blaukopf M, Kosma P, Oostenbrink C. Molecular Conformations of Di-, Tri-, and Tetra- α-(2→8)-Linked Sialic Acid from NMR Spectroscopy and MD Simulations. Int J Mol Sci 2019; 21:ijms21010030. [PMID: 31861593 PMCID: PMC6981865 DOI: 10.3390/ijms21010030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 12/26/2022] Open
Abstract
By using molecular dynamics simulations with an efficient enhanced sampling technique and in combination with nuclear magnetic resonance (NMR) spectroscopy quantitative structural information on α-2,8-linked sialic acids is presented. We used a bottom-up approach to obtain a set of larger ensembles for tetra- and deca-sialic acid from model dimer and trimer systems that are in agreement with the available J-coupling constants and nuclear Overhauser effects. The molecular dynamic (MD) simulations with enhanced sampling are used to validate the force field used in this study for its further use. This empowered us to couple NMR observables in the MD framework via J-coupling and distance restraining simulations to obtain conformations that are supported by experimental data. We used these conformations in thermodynamic integration and one-step perturbation simulations to calculate the free-energy of suggested helical conformations. This study brings most of the available NMR experiments together and supplies information to resolve the conflict on the structures of poly-α-2,8-linked sialic acid.
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Affiliation(s)
- Aysegül Turupcu
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria;
| | - Markus Blaukopf
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria; (M.B.); (P.K.)
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria; (M.B.); (P.K.)
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria;
- Correspondence: ; Tel.: +43-1-47654-89411
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16
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Affiliation(s)
- Darón I. Freedberg
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
| | - Jeahoo Kwon
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
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17
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Bezerra FF, Vignovich WP, Aderibigbe AO, Liu H, Sharp JS, Doerksen RJ, Pomin VH. Conformational properties of l-fucose and the tetrasaccharide building block of the sulfated l-fucan from Lytechinus variegatus. J Struct Biol 2019; 209:107407. [PMID: 31698075 DOI: 10.1016/j.jsb.2019.107407] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 01/19/2023]
Abstract
Although the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan composed of the following structure [l-Fucp4(SO3-)-α(1-3)-l-Fucp2,4(SO3-)-α(1-3)-l-Fucp2(SO3-)-α(1-3)-l-Fucp2(SO3-)] and the composing monosaccharide unit Fucp, primarily by nuclear magnetic resonance (NMR) experiments performed at very low temperatures and using H2O as the solvent for the sugars rather than using the conventional deuterium oxide. By slowing down the fast chemical exchange rates and forcing the protonation of labile sites, we increased the number of through-space 1H-1H distances that could be measured by NMR spectroscopy. Following this strategy, additional conformational details of the tetrasaccharide and l-Fucp in solution were obtained. Computational molecular dynamics was performed to complement and validate the NMR-based measurements. A model of the NMR-restrained 3D structure is offered for the tetrasaccharide.
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Affiliation(s)
- Francisco F Bezerra
- Institute of Medical Biochemistry Leopoldo de Meis, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941, RJ, Brazil
| | - William P Vignovich
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - AyoOluwa O Aderibigbe
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Hao Liu
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Joshua S Sharp
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Robert J Doerksen
- BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA
| | - Vitor H Pomin
- Institute of Medical Biochemistry Leopoldo de Meis, University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro 21941, RJ, Brazil; BioMolecular Sciences Department, School of Pharmacy, University of Mississippi, University, 38677 MS, USA; Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, 38677 MS, USA.
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18
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
| | - Peter H. Seeberger
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
- Institute of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | - Martina Delbianco
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Potsdam Germany
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19
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Brown GD, Bauer J, Osborn HMI, Kuemmerle R. A Solution NMR Approach To Determine the Chemical Structures of Carbohydrates Using the Hydroxyl Groups as Starting Points. ACS OMEGA 2018; 3:17957-17975. [PMID: 31458388 PMCID: PMC6644132 DOI: 10.1021/acsomega.8b02136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/07/2018] [Indexed: 06/10/2023]
Abstract
An efficient NMR approach is described for determining the chemical structures of the monosaccharide glucose and four disaccharides, namely, nigerose, gentiobiose, leucrose and isomaltulose. This approach uses the 1H resonances of the -OH groups, which are observable in the NMR spectrum of a supercooled aqueous solution, as the starting point for further analysis. The 2D-NMR technique, HSQC-TOCSY, is then applied to fully define the covalent structure (i.e., the topological relationship between C-C, C-H, and O-H bonds) that must be established for a novel carbohydrate before proceeding to further conformational studies. This process also leads to complete assignment of all 1H and 13C resonances. The approach is exemplified by analyzing the monosaccharide glucose, which is treated as if it were an "unknown", and also by fully assigning all the NMR resonances for the four disaccharides that contain glucose. It is proposed that this technique should be equally applicable to the determination of chemical structures for larger carbohydrates of unknown composition, including those that are only available in limited quantities from biological studies. The advantages of commencing the structure elucidation of a carbohydrate at the -OH groups are discussed with reference to the now well-established 2D-/3D-NMR strategy for investigation of peptides/proteins, which employs the -NH resonances as the starting point.
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Affiliation(s)
- Geoffrey D. Brown
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Julia Bauer
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Helen M. I. Osborn
- Department of Chemistry and Reading School of Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, United Kingdom
| | - Rainer Kuemmerle
- Bruker
Biospin AG, NMR Division, Industriestrasse 26, CH-8117 Fallanden, Switzerland
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20
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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21
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Casadevall A, Coelho C, Cordero RJB, Dragotakes Q, Jung E, Vij R, Wear MP. The capsule of Cryptococcus neoformans. Virulence 2018; 10:822-831. [PMID: 29436899 PMCID: PMC6779390 DOI: 10.1080/21505594.2018.1431087] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The capsule of Cryptococcus neoformans is its dominant virulence factor and plays a key role in the biology of this fungus. In this essay, we focus on the capsule as a cellular structure and note the limitations inherent in the current methodologies available for its study. Given that no single method can provide the structure of the capsule, our notions of what is the cryptococcal capsule must be arrived at by synthesizing information gathered from very different methodological approaches including microscopy, polysaccharide chemistry and physical chemistry of macromolecules. The emerging picture is one of a carefully regulated dynamic structure that is constantly rearranged as a response to environmental stimulation and cellular replication. In the environment, the capsule protects the fungus against desiccation and phagocytic predators. In animal hosts the capsule functions in both offensive and defensive modes, such that it interferes with immune responses while providing the fungal cell with a defensive shield that is both antiphagocytic and capable of absorbing microbicidal oxidative bursts from phagocytic cells. Finally, we delineate a set of unsolved problems in the cryptococcal capsule field that could provide fertile ground for future investigations.
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Affiliation(s)
- Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - Carolina Coelho
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - Radames J B Cordero
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - Quigly Dragotakes
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - Eric Jung
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - Raghav Vij
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
| | - Maggie P Wear
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore , MD , USA
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22
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Ghimire S, McCarthy PC. Capture of Pb 2+ and Cu 2+ Metal Cations by Neisseria meningitidis-type Capsular Polysaccharides. Biomolecules 2018; 8:E23. [PMID: 29734757 PMCID: PMC6023028 DOI: 10.3390/biom8020023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 12/14/2022] Open
Abstract
Heavy metal pollution of water is a significant environmental and public health concern. Current biological strategies for heavy metal removal from water are performed using microbial biopolymers, including polysaccharides, that are already fully formed. This creates limitations in adapting polysaccharides to increase binding affinity for specific metals. We propose that altering the specificity of polysaccharide-producing enzymes could be beneficial to improving metal capture by modified polysaccharides. We assess binding of Cu2+ and Pb2+ metal cations to Neisseria meningitidis-type polysaccharides. All concentrations of metal cations tested were able to completely bind to colominic acid. This polymer is equivalent to the capsular polysaccharide of N. meningitidis serogroup B comprised of a homopolymer of negatively charged sialic acid. There was slightly less binding observed with N. meningitidis serogroup W, which contains repeating units of the neutral sugar galactose and sialic acid. Our work represents the first assessment of the metal-binding properties of these capsular polysaccharides. Future work will seek to optimize metal-binding with Neisseria meningitidis serogroup W polysaccharide.
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Affiliation(s)
- Sujan Ghimire
- Department of Chemistry, Morgan State University, Baltimore, MD 21251, USA.
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23
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Abstract
We present here that adenovirus type 52 (HAdV-52) attaches to target cells through a mechanism not previously observed in other human pathogenic viruses. The interaction involves unusual, transient, electrostatic interactions between the short fiber capsid protein and polysialic acid (polySia)-containing receptors on target cells. Knowledge about the binding interactions between polySia and its natural ligands is relatively limited, and our results therefore provide additional insight not only into adenovirus biology but also into the structural basis of polySia function. Since polySia can be found in high expression levels in brain and lung cancers where its presence is associated with poor prognosis, we suggest that this polySia-binding adenovirus could be useful for design of vectors for gene therapy of these cancers. Human adenovirus 52 (HAdV-52) is one of only three known HAdVs equipped with both a long and a short fiber protein. While the long fiber binds to the coxsackie and adenovirus receptor, the function of the short fiber in the virus life cycle is poorly understood. Here, we show, by glycan microarray analysis and cellular studies, that the short fiber knob (SFK) of HAdV-52 recognizes long chains of α-2,8-linked polysialic acid (polySia), a large posttranslational modification of selected carrier proteins, and that HAdV-52 can use polySia as a receptor on target cells. X-ray crystallography, NMR, molecular dynamics simulation, and structure-guided mutagenesis of the SFK reveal that the nonreducing, terminal sialic acid of polySia engages the protein with direct contacts, and that specificity for polySia is achieved through subtle, transient electrostatic interactions with additional sialic acid residues. In this study, we present a previously unrecognized role for polySia as a cellular receptor for a human viral pathogen. Our detailed analysis of the determinants of specificity for this interaction has general implications for protein–carbohydrate interactions, particularly concerning highly charged glycan structures, and provides interesting dimensions on the biology and evolution of members of Human mastadenovirus G.
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24
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Yu H, An Y, Battistel MD, Cipollo JF, Freedberg DI. Improving Analytical Characterization of Glycoconjugate Vaccines through Combined High-Resolution MS and NMR: Application to Neisseria meningitidis Serogroup B Oligosaccharide-Peptide Glycoconjugates. Anal Chem 2018; 90:5040-5047. [DOI: 10.1021/acs.analchem.7b04748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Huifeng Yu
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Yanming An
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - John F. Cipollo
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, Maryland 20993, United States
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25
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Chin-Hun Kuo J, Gandhi JG, Zia RN, Paszek MJ. Physical biology of the cancer cell glycocalyx. NATURE PHYSICS 2018; 14:658-669. [PMID: 33859716 PMCID: PMC8046174 DOI: 10.1038/s41567-018-0186-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The glycocalyx coating the outside of most cells is a polymer meshwork comprising proteins and complex sugar chains called glycans. From a physical perspective, the glycocalyx has long been considered a simple 'slime' that protects cells from mechanical disruption or against pathogen interactions, but the great complexity of the structure argues for the evolution of more advanced functionality: the glycocalyx serves as the complex physical environment within which cell-surface receptors reside and operate. Recent studies have demonstrated that the glycocalyx can exert thermodynamic and kinetic control over cell signalling by serving as the local medium within which receptors diffuse, assemble and function. The composition and structure of the glycocalyx change markedly with changes in cell state, including transformation. Notably, cancer-specific changes fuel the synthesis of monomeric building blocks and machinery for production of long-chain polymers that alter the physical and chemical structure of the glycocalyx. In this Review, we discuss these changes and their physical consequences on receptor function and emergent cell behaviours.
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Affiliation(s)
- Joe Chin-Hun Kuo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Jay G. Gandhi
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Roseanna N. Zia
- Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Matthew J. Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Field of Biophysics, Cornell University, Ithaca, NY, USA
- Correspondence should be addressed to M.J.P.
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26
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Nestor G, Anderson T, Oscarson S, Gronenborn AM. Direct Observation of Carbohydrate Hydroxyl Protons in Hydrogen Bonds with a Protein. J Am Chem Soc 2017; 140:339-345. [PMID: 29227646 DOI: 10.1021/jacs.7b10595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyl proton resonances of uniformly 13C-labeled Manα(1-2)Manα(1-2)ManαOMe (Man3) bound to cyanovirin-N (CV-N) were detected at ambient temperature in aqueous solution by NMR spectroscopy. The directions of the hydroxyl groups were determined on the basis of NOEs, and a previously unknown hydrogen-bonding network between Man3 and CV-N was discovered. This is the first report on detecting hydroxyl protons of a protein-bound carbohydrate in aqueous solution by NMR. Approaches such as those presented here may open the door for accurately determining intermolecular hydrogen bonds in carbohydrate-protein complexes.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
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27
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Azurmendi HF, Battistel MD, Zarb J, Lichaa F, Negrete Virgen A, Shiloach J, Freedberg DI. The β-reducing end in α(2-8)-polysialic acid constitutes a unique structural motif. Glycobiology 2017; 27:900-911. [PMID: 28369425 PMCID: PMC6283323 DOI: 10.1093/glycob/cwx025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/10/2017] [Accepted: 03/14/2017] [Indexed: 12/13/2022] Open
Abstract
Over the years, structural characterizations of α(2-8)-polysialic acid (polySia) in solution have produced inconclusive results. Efforts for obtaining detailed information in this important antigen have focused primarily on the α-linked residues and not on the distinctive characteristics of the terminal ones. The thermodynamically preferred anomeric configuration for the reducing end of sialic acids is β, which has the [I]CO2- group equatorial and the OH ([I]OH2) axial, while for all other residues the CO2- group is axial. We show that this purportedly minor difference has distinct consequences for the structure of α(2-8)-polySia near the reducing end, as the β configuration places the [I]OH2 in a favorable position for the formation of a hydrogen bond with the carboxylate group of the following residue ([II]CO2-). Molecular dynamics (MD) simulations predicted the hydrogen bond, which we subsequently directly detected by NMR. The combination of MD and residual dipolar couplings shows that the net result for the structure of Sia2-βOH is a stable conformation with well-defined hydration and charge patterns, and consistent with experimental NOE-based hydroxyl and aliphatic inter-proton distances. Moreover, we provide evidence that this distinct conformation is preserved on Sia oligosaccharides, thus constituting a motif that determines the structure and dynamics of α(2-8)-polySia for at least the first two residues of the polymer. We suggest the hypothesis that this structural motif sheds light on a longtime puzzling observation for the requirement of 10 residues of α(2-8)-polySia in order to bind effectively to specific antibodies, about four units more than for analogous cases.
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Affiliation(s)
- Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Jasmin Zarb
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Flora Lichaa
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Alejandro Negrete Virgen
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
| | - Joseph Shiloach
- Biotechnology Unit, MSC 5522, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20903, USA
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28
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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29
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Nestor G, Anderson T, Oscarson S, Gronenborn AM. Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy. J Am Chem Soc 2017; 139:6210-6216. [PMID: 28406013 DOI: 10.1021/jacs.7b01929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
NMR of a uniformly 13C-labeled carbohydrate was used to elucidate the atomic details of a sugar-protein complex. The structure of the 13C-labeled Manα(1-2)Manα(1-2)ManαOMe trisaccharide ligand, when bound to cyanovirin-N (CV-N), was characterized and revealed that in the complex the glycosidic linkage torsion angles between the two reducing-end mannoses are different from the free trisaccharide. Distances within the carbohydrate were employed for conformational analysis, and NOE-based distance mapping between sugar and protein revealed that Manα(1-2)Manα(1-2)ManαOMe is bound more intimately with its two reducing-end mannoses into the domain A binding site of CV-N than with the nonreducing end unit. Taking advantage of the 13C spectral dispersion of 13C-labeled carbohydrates in isotope-filtered experiments is a versatile means for a simultaneous mapping of the binding interactions on both, the carbohydrate and the protein.
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Affiliation(s)
- Gustav Nestor
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
| | - Taigh Anderson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin , Belfield, Dublin 4, Ireland
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15261, United States
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30
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Battistel MD, Azurmendi HF, Freedberg DI. Glycan OH Exchange Rate Determination in Aqueous Solution: Seeking Evidence for Transient Hydrogen Bonds. J Phys Chem B 2017; 121:683-695. [PMID: 27995788 DOI: 10.1021/acs.jpcb.6b10594] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bonds (Hbonds) are important stabilizing forces in biomolecules. However, for glycans in aqueous solution, direct NMR detection of Hbonds is elusive because of their transient nature. Here, we present Isotope-based Natural-abundance TOtal correlation eXchange SpectroscopY (INTOXSY), a new 1H-13C heteronuclear single quantum coherence-total correlation spectroscopy based method, to extract OH groups' exchange rate constants (kex) for molecules in natural 13C abundance and show that OH Hbonds can be inferred from "slower" H/D kex. We evaluate kex measured with INTOXSY in light of those extracted with line-shape analysis. Subsequently, we use a set of common glycans to establish a kex reference basis set and to infer the existence of transient Hbonds involving OH donor groups. Then, we report kex values for a series of mono- and disaccharides, as well as for oligosaccharides sialyl Lewis X and β-cyclodextrin, and compare the results with those from the reference set to extract Hbond information. Finally, we utilize NMR experimental data in conjunction with molecular dynamics simulations to establish donor and acceptor Hbond pairs. Our exchange rate measurements indicate that OH/OD exchange rates, kHD, values <10 s-1 are consistent with transient Hbond OH groups and potential acceptor groups can be uncovered through MD simulations.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
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31
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Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
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32
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Zhu Y, Zhu R, Wang M, Wu B, He X, Qian Y, Wang S. Anti-Metastatic and Anti-Angiogenic Activities of Core-Shell SiO 2@LDH Loaded with Etoposide in Non-Small Cell Lung Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2016; 3:1600229. [PMID: 27980999 PMCID: PMC5102674 DOI: 10.1002/advs.201600229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/13/2016] [Indexed: 05/29/2023]
Abstract
Currently, nanoparticles have gained a great attention in the anti-tumor research area. However, to date, studies on the anti-metastasis action of core-shell SiO2@LDH (LDH: layered double hydroxide) nanoparticles remain untouched. Two emerging aspects considered are establishing research on the controlling delivery effect of SiO2@LDH combined with anti-cancer medicine from a new perspective. The fine properties synthetic SiO2@LDH-VP16 (VP16: etoposide) are practiced to exhibit the nanoparticle's suppression on migration and invasion of non-small cell lung cancer (NSCLC). Both in vitro and in vivo inspection shows that SiO2@LDH can help VP16 better function as an anti-metastasis agent. On the other hand, anti-angiogenic efficiency, co-localization, as well as western blot are investigated to explain the possible mechanism. A clear mergence of SiO2@LDH-VP16 and cytomembrane/microtubule may be observed from co-location images. Results offer evidence that SiO2@LDH-VP16 plays positions on cytomembrane and microtubules. It efficiently inhibits metastasis on NSCLC by reducing vascularization, and eliciting depression of the PI3K-AKT and FAK-Paxillin signaling pathways. SiO2@LDH-VP16, the overall particle morphology, and function on anti-metastasis and anti-angiogenic may be tuned to give new opportunities for novel strategies for cancer therapy.
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Affiliation(s)
- Yanjing Zhu
- Research Center for Translational Medicine at East HospitalSchool of Life Science and TechnologyTongji UniversityShanghai200092China
| | - Rongrong Zhu
- Research Center for Translational Medicine at East HospitalSchool of Life Science and TechnologyTongji UniversityShanghai200092China
| | - Mei Wang
- Research Center for Translational Medicine at East HospitalSchool of Life Science and TechnologyTongji UniversityShanghai200092China
| | - Bin Wu
- Research Center for Translational Medicine at East HospitalSchool of Life Science and TechnologyTongji UniversityShanghai200092China
| | - Xiaolie He
- Research Center for Translational Medicine at East HospitalSchool of Life Science and TechnologyTongji UniversityShanghai200092China
| | - Yechang Qian
- Department of Respiratory DiseaseBaoshan District Hospital of Integrated Traditional Chinese and Western MedicineShanghai201900China
| | - Shilong Wang
- Research Center for Translational Medicine at East HospitalSchool of Life Science and TechnologyTongji UniversityShanghai200092China
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33
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Zhang R, Loers G, Schachner M, Boelens R, Wienk H, Siebert S, Eckert T, Kraan S, Rojas-Macias MA, Lütteke T, Galuska SP, Scheidig A, Petridis AK, Liang S, Billeter M, Schauer R, Steinmeyer J, Schröder JM, Siebert HC. Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides. ChemMedChem 2016; 11:990-1002. [PMID: 27136597 DOI: 10.1002/cmdc.201500609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/01/2016] [Indexed: 02/05/2023]
Abstract
Polysialic acid (polySia) and polySia glycomimetic molecules support nerve cell regeneration, differentiation, and neuronal plasticity. With a combination of biophysical and biochemical methods, as well as data mining and molecular modeling techniques, it is possible to correlate specific ligand-receptor interactions with biochemical processes and in vivo studies that focus on the potential therapeutic impact of polySia, polySia glycomimetics, and sulfated polysaccharides in neuronal diseases. With this strategy, the receptor interactions of polySia and polySia mimetics can be understood on a submolecular level. As the HNK-1 glycan also enhances neuronal functions, we tested whether similar sulfated oligo- and polysaccharides from seaweed could be suitable, in addition to polySia, for finding potential new routes into patient care focusing on an improved cure for various neuronal diseases. The knowledge obtained here on the structural interplay between polySia or sulfated polysaccharides and their receptors can be exploited to develop new drugs and application routes for the treatment of neurological diseases and dysfunctions.
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Affiliation(s)
- Ruiyan Zhang
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Gabriele Loers
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Melitta Schachner
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251, Hamburg, Germany
- Center for Neuroscience, Shantou University Medical College, 22 Xin Ling Road, Shantou, Guangdong, 515041, China
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Simone Siebert
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany
| | - Thomas Eckert
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals, Justus-Liebig-Universität Gießen, Frankfurter Str. 106, 35392, Gießen, Germany
| | - Stefan Kraan
- Ocean Harvest Technology Ltd., N17 Business Park, Milltown, County Galway, Ireland
| | - Miguel A Rojas-Macias
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Sebastian P Galuska
- Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-Universität Gießen, Friedrichstr. 24, 35392, Gießen, Germany
| | - Axel Scheidig
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Athanasios K Petridis
- Neurosurgery Clinic, University Düsseldorf, Moorenstraße 5, 40255, Düsseldorf, Germany
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, 410081, Changsha, China
| | - Martin Billeter
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 100, 40530, Gothenburg, Sweden
| | - Roland Schauer
- Institute of Biochemistry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany
| | - Jürgen Steinmeyer
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University Hospital Giessen and Marburg GmbH, Paul-Meimberg-Str. 3, 35392, Gießen, Germany
| | - Jens-Michael Schröder
- Department of Dermatology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Hans-Christian Siebert
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany.
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34
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Kang Y, Gohlke U, Engström O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions. J Am Chem Soc 2016; 138:9109-18. [DOI: 10.1021/jacs.6b00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yu Kang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Olof Engström
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Christoffer Hamark
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Tom Scheidt
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Sonja Kunstmann
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut
für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106
91 Stockholm, Sweden
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische
Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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35
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Battistel MD, Azurmendi HF, Frank M, Freedberg DI. Uncovering Nonconventional and Conventional Hydrogen Bonds in Oligosaccharides through NMR Experiments and Molecular Modeling: Application to Sialyl Lewis-X. J Am Chem Soc 2015; 137:13444-7. [PMID: 26426963 DOI: 10.1021/jacs.5b03824] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe the direct NMR detection of a C-H···O nonconventional hydrogen bond (Hbond) and provide experimental and theoretical evidence for conventional Hbonds in the pentasaccharide sialyl Lewis-X (sLe(X)-5) between 5 and 37 °C in water. Extensive NMR structural studies together with molecular dynamics simulations offer strong evidence for significant local dynamics in the Le(X) core and for previously undetected conventional Hbonds in rapid equilibrium that modulate structure. These NMR studies also showed temperature-dependent (1)H and (13)C line broadening. The resulting model emerging from this study is more complex than a simple rigid core description of Le(X)-like molecules and improves our understanding of stabilizing interactions in glycans.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration ,10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration ,10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
| | - Martin Frank
- Biognos AB , Generatorsgatan 1, 41705 Gothenburg, Sweden
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Food and Drug Administration ,10903 New Hampshire Avenue, Silver Spring, Maryland 20903, United States
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36
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Abstract
Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds, providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.
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Affiliation(s)
- Consuelo N Beecher
- Department of Chemistry, University of California, Riverside, Riverside, CA, 92521, USA,
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37
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Fontana C, Kovacs H, Widmalm G. NMR structure analysis of uniformly 13C-labeled carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2014; 59:95-110. [PMID: 24771296 DOI: 10.1007/s10858-014-9830-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 04/16/2014] [Indexed: 05/26/2023]
Abstract
In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The (13)C resonances are traced using (13)C-(13)C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the (13)C resonances, the (1)H chemical shifts are derived in a straightforward manner using one-bond (1)H-(13)C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J CC splitting of the (13)C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either (13)C or (1)H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the (1)H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the (13)C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with (15)N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and (13)C-detected (H)CACO spectra.
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Affiliation(s)
- Carolina Fontana
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 106 91, Stockholm, Sweden
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38
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Schnaar RL, Gerardy-Schahn R, Hildebrandt H. Sialic acids in the brain: gangliosides and polysialic acid in nervous system development, stability, disease, and regeneration. Physiol Rev 2014; 94:461-518. [PMID: 24692354 DOI: 10.1152/physrev.00033.2013] [Citation(s) in RCA: 497] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Every cell in nature carries a rich surface coat of glycans, its glycocalyx, which constitutes the cell's interface with its environment. In eukaryotes, the glycocalyx is composed of glycolipids, glycoproteins, and proteoglycans, the compositions of which vary among different tissues and cell types. Many of the linear and branched glycans on cell surface glycoproteins and glycolipids of vertebrates are terminated with sialic acids, nine-carbon sugars with a carboxylic acid, a glycerol side-chain, and an N-acyl group that, along with their display at the outmost end of cell surface glycans, provide for varied molecular interactions. Among their functions, sialic acids regulate cell-cell interactions, modulate the activities of their glycoprotein and glycolipid scaffolds as well as other cell surface molecules, and are receptors for pathogens and toxins. In the brain, two families of sialoglycans are of particular interest: gangliosides and polysialic acid. Gangliosides, sialylated glycosphingolipids, are the most abundant sialoglycans of nerve cells. Mouse genetic studies and human disorders of ganglioside metabolism implicate gangliosides in axon-myelin interactions, axon stability, axon regeneration, and the modulation of nerve cell excitability. Polysialic acid is a unique homopolymer that reaches >90 sialic acid residues attached to select glycoproteins, especially the neural cell adhesion molecule in the brain. Molecular, cellular, and genetic studies implicate polysialic acid in the control of cell-cell and cell-matrix interactions, intermolecular interactions at cell surfaces, and interactions with other molecules in the cellular environment. Polysialic acid is essential for appropriate brain development, and polymorphisms in the human genes responsible for polysialic acid biosynthesis are associated with psychiatric disorders including schizophrenia, autism, and bipolar disorder. Polysialic acid also appears to play a role in adult brain plasticity, including regeneration. Together, vertebrate brain sialoglycans are key regulatory components that contribute to proper development, maintenance, and health of the nervous system.
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Battistel MD, Azurmendi HF, Yu B, Freedberg DI. NMR of glycans: shedding new light on old problems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 79:48-68. [PMID: 24815364 DOI: 10.1016/j.pnmrs.2014.01.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/10/2014] [Indexed: 06/03/2023]
Abstract
The diversity in molecular arrangements and dynamics displayed by glycans renders traditional NMR strategies, employed for proteins and nucleic acids, insufficient. Because of the unique properties of glycans, structural studies often require the adoption of a different repertoire of tailor-made experiments and protocols. We present an account of recent developments in NMR techniques that will deepen our understanding of structure-function relations in glycans. We open with a survey and comparison of methods utilized to determine the structure of proteins, nucleic acids and carbohydrates. Next, we discuss the structural information obtained from traditional NMR techniques like chemical shifts, NOEs/ROEs, and coupling-constants, along with the limitations imposed by the unique intrinsic characteristics of glycan structure on these approaches: flexibility, range of conformers, signal overlap, and non-first-order scalar (strong) coupling. Novel experiments taking advantage of isotopic labeling are presented as an option for overcoming spectral overlap and raising sensitivity. Computational tools used to explore conformational averaging in conjunction with NMR parameters are described. In addition, recent developments in hydroxyl detection and hydrogen bond detection in protonated solvents, in contrast to traditional sample preparations in D2O for carbohydrates, further increase the tools available for both structure information and chemical shift assignments. We also include previously unpublished data in this context. Accurate determination of couplings in carbohydrates has been historically challenging due to the common presence of strong-couplings. We present new strategies proposed for dealing with their influence on NMR signals. We close with a discussion of residual dipolar couplings (RDCs) and the advantages of using (13)C isotope labeling that allows gathering one-bond (13)C-(13)C couplings with a recently improved constant-time COSY technique, in addition to the commonly measured (1)H-(13)C RDCs.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Bingwu Yu
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States.
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40
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Shinar H, Battistel MD, Mandler M, Lichaa F, Freedberg DI, Navon G. Sialo-CEST: chemical exchange saturation transfer NMR of oligo- and poly-sialic acids and the assignment of their hydroxyl groups using selective- and HSQC-TOCSY. Carbohydr Res 2014; 389:165-73. [DOI: 10.1016/j.carres.2014.02.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 11/28/2022]
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41
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Ray GJ, Ravenscroft N, Siekmann J, Zhang Z, Sanders P, Shaligram U, Szabo CM, Kosma P. Complete structural elucidation of an oxidized polysialic acid drug intermediate by nuclear magnetic resonance spectroscopy. Bioconjug Chem 2014; 25:665-76. [PMID: 24679150 DOI: 10.1021/bc400456g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polysialic acid (PSA) is a high molecular weight glycan composed of repeat units of α(2→8) linked 5-N-acetyl-neuraminic acid. Mild periodate oxidation of PSA selectively targets the end sialic acid ring containing three adjacent alcohols generating a putative aldehyde, which can be used for terminal attachment of PSA to therapeutic proteins. The work presented here permitted complete NMR peak assignments of not only the repeat units, but also the two terminal units at each end of oxidized PSA, an intermediate, which can be used to improve drug performance. The assignments were made using a variety of NMR techniques on oligomers of sialic acid as well as oxidized PSA with molecular masses of 4 and 20 kDa. This enabled structure elucidation that showed the actual moiety formed was not the expected aldehyde or its hydrate, but is a hemiacetal between the oxidation site on the terminal sialic acid ring and the penultimate ring. The existence of a hemiacetal structure has major implications on stability, reactivity, and conjugation chemistry of oxidized PSA. The assignment process also revealed deuterium exchange of the axial hydrogen at the 3- (methylene) position of the ring, which was in agreement with the literature.
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Affiliation(s)
- G Joseph Ray
- Baxter Healthcare Corporation , Round Lake, 60073, Illinois, United States
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42
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Beecher CN, Young RP, Langeslay DJ, Mueller LJ, Larive CK. Hydroxyl-proton hydrogen bonding in the heparin oligosaccharide Arixtra in aqueous solution. J Phys Chem B 2014; 118:482-91. [PMID: 24354321 DOI: 10.1021/jp410540d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heparin is best known for its anticoagulant activity, which is mediated by the binding of a specific pentasaccharide sequence to the protease inhibitor antithrombin-III (AT-III). Although heparin oligosaccharides are thought to be flexible in aqueous solution, the recent discovery of a hydrogen bond between the sulfamate (NHSO3(-)) proton and the adjacent 3-O-sulfo group of the 3,6-O-sulfated N-sulfoglucosamine residue of the Arixtra (fondaparinux sodium) pentasaccharide demonstrates that definable elements of local structure are accessed. Molecular dynamics simulations of Arixtra suggest the presence of additional hydrogen bonds involving the C3-OH groups of the glucuronic acid and 2-O-sulfo-iduronic acid residues. NMR measurements of temperature coefficients, chemical shift differences, and solvent exchange rate constants provide experimental confirmation of these hydrogen bonds. We note that the extraction of rate constants from cross-peak buildup curves in 2D exchange spectroscopy is complicated by the presence of radiation damping in aqueous solution. A straightforward model is presented that explicitly takes into account the effects of radiation damping on the water proton relaxation and is sufficiently robust to provide an accurate measure of the proton exchange rate between the analyte hydroxyl protons and water.
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Affiliation(s)
- Consuelo N Beecher
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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NMR study into the mechanism of recognition of the degree of polymerization by oligo/polysialic acid antibodies. Bioorg Med Chem 2013; 21:6069-76. [DOI: 10.1016/j.bmc.2013.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 11/22/2022]
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44
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A compendium of cyclic sugar amino acids and their carbocyclic and heterocyclic nitrogen analogues. Amino Acids 2013; 45:613-89. [DOI: 10.1007/s00726-013-1521-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022]
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45
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Battistel MD, Pendrill R, Widmalm G, Freedberg DI. Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study. J Phys Chem B 2013; 117:4860-9. [DOI: 10.1021/jp400402b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marcos D. Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, Maryland 20852-1448, United States
| | - Robert Pendrill
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Darón I. Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, Maryland 20852-1448, United States
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