Abstract
Carbohydrate molecules have highly complex structures and the constituent monosaccharides and substituents are linked to each other in a large number of ways. NMR spectroscopy can be used to unravel these structures, but the process may be tedious and time-consuming. The computerized approach based on the CASPER program can facilitate rapid structural determination of glycans with little user intervention, which results in the most probable primary structure of the investigated carbohydrate material. Additionally, 1H and 13C NMR chemical shifts of a user-defined structure can be predicted, and this tool may thus be employed in many aspects where NMR spectroscopy plays an important part of a study.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bubb WA (2003) NMR spectroscopy in the study of carbohydrates: characterizing the structural complexity. Concepts Magn Reson 19A:1–19
Jiménez-Barbero J, Peters T (eds) (2003) NMR spectroscopy of glycoconjugates. Wiley-VCH, Weinheim
Meiler J, Köck M (2004) Novel methods of automated structure elucidation based on 13C NMR spectroscopy. Magn Reson Chem 42:1042–1045
Satoh H, Koshino H, Uno T et al (2005) Effective consideration of ring structures in CAST/CNMR for highly accurate 13C NMR chemical shift prediction. Tetrahedron 61:7431–7437
Lam SL (2007) DSHIFT: a web server for predicting DNA chemical shifts. Nucleic Acids Res 35:W713–W717
Elyashberg ME, Williams AJ, Martin GE (2008) Computer-assisted structure verification and elucidation tools in NMR-based structure elucidation. Prog Nucl Magn Reson Spectr 53:1–104
Blinov KA, Smurnyy YD, Churanova TS et al (2009) Development of a fast and accurate method of 13C NMR chemical shift prediction. Chemometr Intell Lab Syst 97:91–97
Spanton SG, Whittern D (2009) The development of an NMR chemical shift prediction application with the accuracy necessary to grade proton NMR spectra for identity. Magn Reson Chem 47:1055–1061
Kohlhoff KJ, Robustelli P, Cavalli A et al (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131:13894–13895
Jakovkin I, Sternberg U, Ulrich AS (2010) Rapid computation of protein NMR properties – an optimal way to chemical shift driven protein structure refinement. Biochem Med Chem (Biomedch'10), Cambridge, Great Britain, February 23–25, pp 273-276
Jansson P-E, Kenne L, Widmalm G (1987) CASPER – a computerized approach to structure determination of polysaccharides using information from N.M.R. spectroscopy and simple chemical analyses. Carbohydr Res 168:67–77
McIntyre MK, Small GW (1987) Carbon-13 nuclear magnetic resonance spectrum simulation methodology for the structure elucidation of carbohydrates. Anal Chem 59:1805–1811
Lipkind GM, Shashkov AS, Knirel YA et al (1988) A computer-assisted structural analysis of regular polysaccharides on the basis of 13C-N.M.R. data. Carbohydr Res 175:59–75
Cumming DA, Hellerqvist C, Touster O (1988) On the utility of 13C-N.M.R. spectroscopy in the identification of the primary structures of manno-oligosaccharides and glycopeptides. Carbohydr Res 179:369–380
Toukash FV, Shashkov AS (2001) Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data. Carbohydr Res 335:101–114
Toukash FV (2011) Bacterial carbohydrate structure database 3: principles and realization. J Chem Inf Model 51:159–170
Pereira F (2011) Prediction of the anomeric configuration, type of linkage, and residues in disaccharides from 1D 13C NMR data. Carbohydr Res 346:960–972
Loß A, Stenutz R, Schwarzer E et al (2006) GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface. Nucleic Acids Res 34:W733–W737
Maes E, Bonachera F, Strecker G et al (2009) SOACS index: an easy NMR-based query for glycan retrieval. Carbohydr Res 344:322–330
Jansson P-E, Kenne L, Widmalm G (1991) CASPER: a computer program used for structural analysis of carbohydrates. J Chem Inf Comput Sci 31:508–516
Aires-de-Sousa J, Hemmer MC, Gasteiger J (2002) Prediction of 1H NMR chemical shifts using neural networks. Anal Chem 74:80–90
Meiler J (2003) PROSHIFT: protein chemical shift prediction using artificial neural networks. J Biomol NMR 26:25–37
Shen Y, Bax A (2010) SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48:13–22
Meyer B, Hansen T, Nute D et al (1991) Identification of the 1H-NMR spectra of complex oligosaccharides with artificial neural networks. Science 251:542–544
Ball JW, Jurs PC (1993) Simulation of polysaccharide 13C nuclear magnetic resonance spectra using regression analysis and neural networks. Anal Chem 65:3615–3621
Gerbst AG, Grachev AA, Ustuzhanina NE et al (2010) Application of artificial neural networks for analysis of 13C NMR spectra of fucoidans. J Carbohydr Chem 29:92–102
Jansson P-E, Stenutz R, Widmalm G (2006) Sequence determination of oligosaccharides and regular polysaccharides using NMR spectroscopy and a novel Web-based version of the computer program CASPER. Carbohydr Res 341:1003–1010
Lundborg M, Widmalm G (2011) Structural analysis of glycans by NMR chemical shift prediction. Anal Chem 83:1514–1517
Lundborg M, Fontana C, Widmalm G (2011) Automatic structure determination of regular polysaccharides based solely on NMR spectroscopy. Biomacromolecules 12:3851–3855
Kuttel M, Widmalm G, Mao Y et al (2011) CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation. Proceedings of the 7th IEEE International Conference eScience, 5–8 Dec, Stockholm, pp 395–402
Vranken WV, Boucher W, Stevens TJ et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins Struct Funct Bioinf 59:687–696
Pluschke G, Moll A, Kusecek B et al (1986) Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and monoclonal antibodies as tools for the subgrouping of Escherichia coli lipopolysaccharides O18 and O23 antigens. Infect Immun 51:286–293
Jansson P-E, Kenne L, Widmalm G (1989) Structure of the O-antigen polysaccharide of Escherichia coli O18ac; a revision using computer-assisted structural analysis with the program CASPER. Carbohydr Res 193:322–325
Jann B, Shashkov AS, Gupta DS et al (1992) The O18 antigens (lipopolysaccharides) of Escherichia coli. Structural characterization of the O18A, O18A1, O18B and O18B1-specific polysaccharides. Eur J Biochem 210:241–248
Acknowledgements
This work was funded by the sixth Research Framework Program of the European Union (Contract: RIDS Contract number 011952) as part of the EUROCarbDB project. It was furthermore supported by grants from the Swedish Research Council and The Knut and Alice Wallenberg Foundation. We thank Dr. Ralfh Wollin, SMI, Stockholm, Sweden, and Dr. Daniel Spencer, Ludger Ltd, Abingdon, UK, for kindly providing carbohydrate material used for spectral presentation in this study.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Lundborg, M., Widmalm, G. (2015). NMR Chemical Shift Prediction of Glycans: Application of the Computer Program CASPER in Structural Analysis. In: Lütteke, T., Frank, M. (eds) Glycoinformatics. Methods in Molecular Biology, vol 1273. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2343-4_3
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2343-4_3
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2342-7
Online ISBN: 978-1-4939-2343-4
eBook Packages: Springer Protocols