Skip to main content
SpringerLink
Log in

Structural Analysis of Oligosaccharides and Glycoconjugates Using NMR

  • Chapter
  • First Online:
Book cover Glycobiology of the Nervous System

Part of the book series: Advances in Neurobiology ((NEUROBIOL,volume 9))

Abstract

Carbohydrate chains play critical roles in cellular recognition and subsequent signal transduction in the nervous system. Furthermore, gangliosides are targets for various amyloidogenic proteins associated with neurodegenerative disorders. To better understand the molecular mechanisms underlying these biological phenomena, atomic views are essential to delineate dynamic biomolecular interactions. Nuclear magnetic resonance (NMR) spectroscopy provides powerful tools for studying structures, dynamics, and interactions of biomolecules at the atomic level. This chapter describes the basics of solution NMR techniques and their applications to the analysis of 3D structures and interactions of glycoconjugates in the nervous system.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

Aβ:

Amyloid β

DIS:

Deuterium-induced isotope shift

FID:

Free induction decay

HSQC:

Heteronuclear single-quantum coherence

MD:

Molecular dynamics

NMR:

Nuclear magnetic resonance

NOE:

Nuclear Overhauser effect

NOESY:

NOE spectroscopy

PCS:

Pseudocontact shift

PRE:

Paramagnetic relaxation enhancement

REMD:

Replica exchange MD

RF:

Radio frequency

STD:

Saturation transfer difference

TRNOE:

Transferred NOE

TROSY:

Transverse relaxation optimized spectroscopy

References

  • Abragam A. The principles of nuclear magnetism. The international series of monographs on physics. Oxford: Clarendon; 1961.

    Google Scholar 

  • Acquotti D, Poppe L, Dabrowski J, von der Lieth CW, Sonnino S, Tettamanti G. Three-dimensional structure of the oligosaccharide chain of GM1 ganglioside revealed by a distance-mapping procedure: a rotating and laboratory frame nuclear overhauser enhancement investigation of native glycolipid in dimethyl sulfoxide and in water- dodecylphosphocholine solutions. J Am Chem Soc. 1990;112(21):7772–8.

    Article  CAS  Google Scholar 

  • Ariga T, McDonald MP, Yu RK. Role of ganglioside metabolism in the pathogenesis of Alzheimer’s disease – a review. J Lipid Res. 2008;49(6):1157–75.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bertini I, Luchinat C, Parigi G, Pierattelli R. NMR spectroscopy of paramagnetic metalloproteins. ChemBioChem. 2005;6(9):1536–49.

    Article  CAS  PubMed  Google Scholar 

  • Bodenhausen G, Ruben DJ. Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem Phys Lett. 1980;69(1):185–9.

    Article  CAS  Google Scholar 

  • Brocca P, Bernardi A, Raimondi L, Sonnino S. Modeling ganglioside headgroups by conformational analysis and molecular dynamics. Glycoconj J. 2000;17(5):283–99.

    Article  CAS  PubMed  Google Scholar 

  • Clore GM, Gronenborn AM. Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J Magn Reson. 1982;48(3):402–17.

    CAS  Google Scholar 

  • Clore GM, Gronenborn AM. Theory of the time-dependent transferred nuclear Overhauser effect – applications to structural-analysis of ligand protein complexes in solution. J Magn Reson. 1983;53(3):423–42.

    CAS  Google Scholar 

  • Cornilescu G, Delaglio F, Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR. 1999;13(3):289–302.

    Article  CAS  PubMed  Google Scholar 

  • Cumming DA, Carver JP. Virtual and solution conformations of oligosaccharides. Biochemistry. 1987;26(21):6664–76.

    Article  CAS  PubMed  Google Scholar 

  • Eggens I, Fenderson B, Toyokuni T, Dean B, Stroud M, Hakomori S. Specific interaction between Lex and Lex determinants. A possible basis for cell recognition in preimplantation embryos and in embryonal carcinoma cells. J Biol Chem. 1989;264(16):9476–84.

    CAS  PubMed  Google Scholar 

  • Englander SW, Mayne L. Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. Annu Rev Biophys Biomol Struct. 1992;21:243–65.

    Article  CAS  PubMed  Google Scholar 

  • Englander SW, Mayne L, Krishna MM. Protein folding and misfolding: mechanism and principles. Q Rev Biophys. 2007;40(4):287–326.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fadda E, Woods RJ. Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects. Drug Discov Today. 2010;15(15–16):596–609.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fantini J, Yahi N. Molecular insights into amyloid regulation by membrane cholesterol and sphingolipids: common mechanisms in neurodegenerative diseases. Expert Rev Mol Med. 2010;12:e27.

    Article  PubMed Central  PubMed  Google Scholar 

  • Fenderson BA, Zehavi U, Hakomori S. A multivalent lacto-N-fucopentaose III-lysyllysine conjugate decompacts preimplantation mouse embryos, while the free oligosaccharide is ineffective. J Exp Med. 1984;160(5):1591–6.

    Article  CAS  PubMed  Google Scholar 

  • Forsén S, Hoffman RA. Study of moderately rapid chemical exchange reactions by means of nuclear magnetic double resonance. J Chem Phys. 1963;39(11):2892–901.

    Article  Google Scholar 

  • Forsén S, Hoffman RA. Exchange rates by nuclear magnetic multiple resonance. III. Exchange reactions in systems with several nonequivalent sites. J Chem Phys. 1964;40(5):1189–96.

    Article  Google Scholar 

  • Glaudemans CP, Lerner L, Daves Jr GD, Kováč P, Venable R, Bax A. Significant conformational changes in an antigenic carbohydrate epitope upon binding to a monoclonal antibody. Biochemistry. 1990;29(49):10906–11.

    Article  CAS  PubMed  Google Scholar 

  • Hakomori S. Carbohydrate-to-carbohydrate interaction, through glycosynapse, as a basis of cell recognition and membrane organization. Glycoconj J. 2004;21(3–4):125–37.

    Article  CAS  PubMed  Google Scholar 

  • Hanashima S, Kato K, Yamaguchi Y. 13C-NMR quantification of proton exchange at LewisX hydroxyl groups in water. Chem Commun. 2011;47(38):10800–2.

    Article  CAS  Google Scholar 

  • Hanashima S, Sato C, Tanaka H, Takahashi T, Kitajima K, Yamaguchi Y. NMR study into the mechanism of recognition of the degree of polymerization by oligo/polysialic acid antibodies. Bioorg Med Chem. 2013;21(19):6069–76.

    Article  CAS  PubMed  Google Scholar 

  • Homans SW, Dwek RA, Rademacher TW. Tertiary structure in N-linked oligosaccharides. Biochemistry. 1987;26(20):6553–60.

    Article  CAS  PubMed  Google Scholar 

  • Jain NU, Venot A, Umemoto K, Leffler H, Prestegard JH. Distance mapping of protein-binding sites using spin-labeled oligosaccharide ligands. Protein Sci. 2001;10(11):2393–400.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Jeng MF, Englander SW, Elöve GA, Wand AJ, Roder H. Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry. 1990;29(46):10433–7.

    Article  CAS  PubMed  Google Scholar 

  • Johnson PE, Brun E, MacKenzie LF, Withers SG, McIntosh LP. The cellulose-binding domains from Cellulomonas fimi β-1,4-glucanase CenC bind nitroxide spin-labeled cellooligosaccharides in multiple orientations. J Mol Biol. 1999;287(3):609–25.

    Article  CAS  PubMed  Google Scholar 

  • Kamiya Y, Yagi-Utsumi M, Yagi H, Kato K. Structural and molecular basis of carbohydrate–protein interaction systems as potential therapeutic targets. Curr Pharm Design. 2011;17(17):1672–84.

    Article  CAS  Google Scholar 

  • Kato K, Sasakawa H, Kamiya Y, Utsumi M, Nakano M, Takahashi N, et al. 920 MHz ultra-high field NMR approaches to structural glycobiology. Biochim Biophys Acta. 2008;1780(3):619–25.

    Article  CAS  PubMed  Google Scholar 

  • Kato K, Yamaguchi Y, Arata Y. Stable-isotope-assisted NMR approaches to glycoproteins using immunoglobulin G as a model system. Prog Nucl Magn Reson Spectrosc. 2010;56:346–59.

    Article  CAS  PubMed  Google Scholar 

  • Kurland RJ, McGarvey BR. Isotropic NMR shifts in transition metal complexes: the calculation of the fermi contact and pseudocontact terms. J Magn Reson. 1970;2(3):286–301.

    CAS  Google Scholar 

  • Levitt MH. Spin dynamics: basics of nuclear magnetic resonance. 2nd ed. New York: Wiley; 2008.

    Google Scholar 

  • Lian LY, Roberts GCK. Effects of chemical exchange on NMR spectra. In: Roberts GCK, editor. NMR of macromolecules. Oxford: Oxford University Press; 1993. p. 153–82.

    Google Scholar 

  • Loria JP, Rance M, Palmer AGI. A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc. 1999;121(10):2331–2.

    Article  CAS  Google Scholar 

  • Matsuzaki K, Kato K, Yanagisawa K. Aβ polymerization through interaction with membrane gangliosides. Biochim Biophys Acta. 2010;1801(8):868–77.

    Article  CAS  PubMed  Google Scholar 

  • Mayer M, Meyer B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed. 1999;38(12):1784–8.

    Article  CAS  Google Scholar 

  • Mayer M, Meyer B. Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc. 2001;123(25):6108–17.

    Article  CAS  PubMed  Google Scholar 

  • McConnell HM, Robertson RE. Isotropic nuclear resonance shifts. J Chem Phys. 1958;29(6):1361–5.

    Article  CAS  Google Scholar 

  • Mittermaier A, Kay LE. New tools provide new insights in NMR studies of protein dynamics. Science. 2006;312(5771):224–8.

    Article  CAS  PubMed  Google Scholar 

  • Ni F, Scheraga HA. Use of the transferred nuclear Overhauser effect to determine the conformations of ligands bound to proteins. Acc Chem Res. 1994;27(9):257–64.

    Article  CAS  Google Scholar 

  • Nishima W, Miyashita N, Yamaguchi Y, Sugita Y, Re S. Effect of bisecting GlcNAc and core fucosylation on conformational properties of biantennary complex-type N-Glycans in solution. J Phys Chem B. 2012;116(29):8504–12.

    Article  CAS  PubMed  Google Scholar 

  • Ohki SY, Kainosho M. Stable isotope labeling methods for protein NMR spectroscopy. Prog Nucl Magn Reson Spectrosc. 2008;53(4):208–26.

    Article  CAS  Google Scholar 

  • Otting G. Protein NMR using paramagnetic ions. Annu Rev Biophys. 2010;39:387–405.

    Article  CAS  PubMed  Google Scholar 

  • Paterson Y, Englander SW, Roder H. An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR. Science. 1990;249(4970):755–9.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Pervushin K, Riek R, Wider G, Wüthrich K. Attenuated T 2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci U S A. 1997;94(23):12366–71.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Prestegard JH, Koerner TAW, Demou PC, Yu RK. Complete analysis of oligosaccharide primary structure using two-dimensional high-field proton NMR. J Am Chem Soc. 1982;104(18):4993–5.

    Article  CAS  Google Scholar 

  • Re S, Miyashita N, Yamaguchi Y, Sugita Y. Structural diversity and changes in conformational equilibria of biantennary complex-type N-glycans in water revealed by replica-exchange molecular dynamics simulation. Biophys J. 2011;101(10):L44–6.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Satoh T, Chen Y, Hu D, Hanashima S, Yamamoto K, Yamaguchi Y. Structural basis for oligosaccharide recognition of misfolded glycoproteins by OS-9 in ER-associated degradation. Mol Cell. 2010;40(6):905–16.

    Article  CAS  PubMed  Google Scholar 

  • Solomon I. Relaxation processes in a system of two spins. Phys Rev. 1955;99(2):559–65.

    Article  CAS  Google Scholar 

  • Spera S, Ikura M, Bax A. Measurement of the exchange rates of rapidly exchanging amide protons: application to the study of calmodulin and its complex with a myosin light chain kinase fragment. J Biomol NMR. 1991;1(2):155–65.

    Article  CAS  PubMed  Google Scholar 

  • Sugase K, Dyson HJ, Wright PE. Mechanism of coupled folding and binding of an intrinsically disordered protein. Nature. 2007;447(7147):1021–5.

    Article  CAS  PubMed  Google Scholar 

  • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314(1–2):141–51.

    Article  CAS  Google Scholar 

  • Taylor DR, Hooper NM. The prion protein and lipid rafts. Mol Membr Biol. 2006;23(1):89–99.

    Article  CAS  PubMed  Google Scholar 

  • Utsumi M, Yamaguchi Y, Sasakawa H, Yamamoto N, Yanagisawa K, Kato K. Up-and-down topological mode of amyloid β-peptide lying on hydrophilic/hydrophobic interface of ganglioside clusters. Glycoconj J. 2009;26(8):999–1006.

    Article  CAS  PubMed  Google Scholar 

  • Vliegenthart JF. High resolution 1H-NMR spectroscopy of carbohydrate structures. Adv Exp Med Biol. 1980;125:77–91.

    Article  CAS  PubMed  Google Scholar 

  • Voisin S, Houliston RS, Kelly J, Brisson JR, Watson D, Bardy SL, et al. Identification and characterization of the unique N-linked glycan common to the flagellins and S-layer glycoprotein of Methanococcus voltae. J Biol Chem. 2005;280(17):16586–93.

    Article  CAS  PubMed  Google Scholar 

  • Wüthrich K. NMR of proteins and nucleic acids. New York: Wiley; 1986.

    Google Scholar 

  • Wishart DS, Sykes BD. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR. 1994;4(2):171–80.

    CAS  PubMed  Google Scholar 

  • Woods RJ, Tessier MB. Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes. Curr Opin Struct Biol. 2010;20(5):575–83.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Yagi-Utsumi M, Kameda T, Yamaguchi Y, Kato K. NMR characterization of the interactions between lyso-GM1 aqueous micelles and amyloid β. FEBS Lett. 2010;584(4):831–6.

    Article  CAS  PubMed  Google Scholar 

  • Yamaguchi T, Kamiya Y, Choo YM, Yamamoto S, Kato K. Terminal spin labeling of a high-mannose-type oligosaccharide for quantitative NMR analysis of its dynamic conformation. Chem Lett. 2013a;42(5):544–6.

    Article  CAS  Google Scholar 

  • Yamaguchi T, Uno T, Uekusa Y, Yagi-Utsumi M, Kato K. Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins. Chem Commun. 2013b;49(12):1235–7.

    Article  CAS  Google Scholar 

  • Yamaguchi Y, Kato K. NMR analyses of the carbohydrate–protein interactions. Exp Med. 2007a;25(7):231–8.

    Google Scholar 

  • Yamaguchi Y, Kato K. Structural glycobiology by stable-isotope-assisted NMR spectroscopy. In: Webb GA, editor. Modern Magnetic Resonance. The Netherlands: Springer; 2007b. p. 219–25.

    Google Scholar 

  • Yamaguchi Y, Kato K. Analysis of sugar–protein interactions by NMR, Experimental Glycoscience Glycochemistry. Berlin: Springer; 2008. p. 121–3.

    Google Scholar 

  • Yamaguchi Y, Nishima W, Re SY, Sugita Y. Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography. Rapid Commun Mass Spect. 2012;26(24):2877–84.

    Article  CAS  Google Scholar 

  • Yamamoto S, Zhang Y, Yamaguchi T, Kameda T, Kato K. Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations. Chem Commun. 2012;48(39):4752–4.

    Article  CAS  Google Scholar 

  • Yu RK, Koerner TA, Scarsdale JN, Prestegard JH. Elucidation of glycolipid structure by proton nuclear magnetic resonance spectroscopy. Chem Phys Lipids. 1986;42(1–3):27–48.

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Yamaguchi T, Kato K. New NMR tools for characterizing the dynamic conformations and interactions of oligosaccharides. Chem Lett. 2013;42(12):1455–62.

    Google Scholar 

  • Zhang Y, Yamamoto S, Yamaguchi T, Kato K. Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched oligosaccharide. Molecules. 2012;17(6):6658–71.

    Article  CAS  PubMed  Google Scholar 

  • Zhao H, Pan Q, Zhang W, Carmichael I, Serianni AS. DFT and NMR studies of 2 J COH, 3 J HCOH, and 3 J CCOH spin-couplings in saccharides: C-O torsional bias and H-bonding in aqueous solution. J Org Chem. 2007;72(19):7071–82.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This study was partly supported by JSPS/MEXT KAKENHI Grant-in-Aid for Scientific Research on Innovation Areas (20107004 and 25102008), Scientific Research (A) (24249002), Scientific Research (C) (25460054), Challenging Exploratory, Research (26560451), and Young Scientists (B) (24750170).

Compliance with Ethics Requirements The authors declare that they have no conflict of interest and that they have used no human subjects in work cited that was done in their laboratory.

Author information

Authors and Affiliations

  1. Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako-City, Saitama, 351-0198, Japan

    Yoshiki Yamaguchi

  2. Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan

    Takumi Yamaguchi & Koichi Kato

  3. Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan

    Takumi Yamaguchi & Koichi Kato

  4. The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan

    Koichi Kato

Authors
  1. Yoshiki Yamaguchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Takumi Yamaguchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Koichi Kato
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yoshiki Yamaguchi or Koichi Kato .

Editor information

Editors and Affiliations

  1. Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, Georgia, USA

    Robert K. Yu

  2. Department of Biochemistry and Molecular Biology, The Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, USA

    Cara-Lynne Schengrund

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this chapter

Cite this chapter

Yamaguchi, Y., Yamaguchi, T., Kato, K. (2014). Structural Analysis of Oligosaccharides and Glycoconjugates Using NMR. In: Yu, R., Schengrund, CL. (eds) Glycobiology of the Nervous System. Advances in Neurobiology, vol 9. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-1154-7_8

Download citation

Publish with us

Policies and ethics

Search

Navigation