Application of metabolic 13C labeling in conjunction with high-field nuclear magnetic resonance spectroscopy for comparative conformational analysis of high mannose-type oligosaccharides

Biomolecules

Volumn 3, Issue 1, 2013, Pages 108-123

  Kamiya, Yukiko ^a,b,g   Yanagi, Kotaro ^a,b   Kitajima, Toshihiko ^c   Yamaguchi, Takumi ^a,b   Chiba, Yasunori ^c   Kato, Koichi ^a,b,d,e,f  

^a OKAZAKI INSTITUTE FOR INTEGRATIVE BIOSCIENCE   (Japan)

^b NAGOYA CITY UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^d OCHANOMIZU UNIVERSITY   (Japan)

^e RIKEN   (Japan)

^f GLYENCE Co Ltd   (Japan)

^g NAGOYA UNIVERSITY   (Japan)

Author keywords

High mannose type oligosaccharide; Nuclear magnetic resonance spectroscopy; Nuclear Overhauser effect; Saccharomyces cerevisiae; Stable isotope labeling

Indexed keywords

CARBON 13; GLYCAN DERIVATIVE; LECTIN; MANNOSE; OLIGOSACCHARIDE;

ARTICLE; BIOENGINEERING; COMPARATIVE STUDY; ENZYME CONFORMATION; GENE OVEREXPRESSION; HETERONUCLEAR SINGLE QUANTUM COHERENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLYMERASE CHAIN REACTION; PURIFICATION; SACCHAROMYCES CEREVISIAE;

EID: 85016338076     PISSN: None     EISSN: 2218273X     Source Type: Journal    
DOI: 10.3390/biom3010108     Document Type: Article

References (40)

1. Varki, A. Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 1993, 3, 97-130.
2. von der Lieth, C.W.; Siebert, H.C.; Kožár, T.; Burchert, M.; Frank, M.; Gilleron, M.; Kaltner, H.; Kayser, G.; Tajkhorshid, E.; Bovin, N.V.; Vliegenthart, J.F.G.; Gabius, H.J. Lectin ligands: new insights into their conformations and their dynamic behavior and the discovery of conformer selection by lectins. Acta anatomica 1998, 161, 91-109.
3. Fadda, E.; Woods, R.J. Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects. Drug. Discov. Today 2010, 15, 596-609.
4. Gabius, H.J.; André, S.; Jiménez-Barbero, J.; Romero, A.; Solís, D. From lectin structure to functional glycomics: principles of sugar code. Trends. Biochem. Sci. 2011, 36, 298-313.
5. Kamiya, Y.; Yagi-Utsumi, M.; Yagi, H.; Kato, K. Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets. Curr. Pharm. Des. 2011, 17, 1672-1684.
6. Lederkremer, G.Z. Glycoprotein folding, quality control and ER-associated degradation. Curr. Opin. Struct. Biol. 2009, 19, 515-523.
7. Aebi, M.; Bernasconi, R.; Clerc, S.; Molinari, M. N-glycan structures: recognition and processing in the ER. Trends. Biochem. Sci. 2010, 35, 74-82.
8. Kamiya, Y.; Satoh, T.; Kato, K. Molecular and structural basis for N-glycan-dependent determination of glycoprotein fates in cells. Biochim. Biophys. Acta 2012, 1820, 1327-1337.
9. Wormald, M.R.; Petrescu, A.J.; Pao, Y.L.; Glithero, A.; Elliott, T.; Dwek, R.A. Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. Chem. Rev. 2002, 102, 371-386.
10. Kato, K.; Sasakawa, H.; Kamiya, Y.; Utsumi, M.; Nakano, M.; Takahashi, N.; Yamaguchi, Y. 920 MHz ultra-high field NMR approaches to structural glycobiology. Biochim. Biophys. Acta 2008, 1780, 619-625.
11. 13C labeling by genetically engineered yeast strain. J. Biomol. NMR 2011, 50, 397-401.
12. Herscovics, A.; Orlean, P. Glycoprotein biosynthesis in yeast. FASEB J. 1993, 7, 540-550.
13. Nakanishi-Shindo, Y.; Nakayama, K.; Tanaka, A.; Toda, Y.; Jigami, Y. Structure of the N-linked oligosaccharides that show the complete loss of 1,6-polymannose outer chain from och1, och1 mnn1, and och1 mnn1 alg3 mutants of Saccharomyces cerevisiae. J. Biol. Chem. 1993, 268, 26338-26345.
14. 2) sugar chains in Saccharomyces cerevisiae. J. Biol. Chem. 1998, 273, 26298-26304.
15. Tvaroska, I.; Taravel, F.R. One-bond carbon-proton coupling constants: angular dependence in α-linked oligosaccharides. Carbohydr. Res. 1991, 221, 83-94.
16. 1H spin-coupling constants in aldofuranosyl rings: Effect of conformation on coupling magnitude. J. Am. Chem. Soc. 1995, 117, 8645-8650.
17. 1H NMR study of urinary oligosaccharides from patients with mannosidosis. FEBS Lett. 1980, 121, 71-77.
18. 1H-nuclear magnetic resonance spectroscopy as a tool in the structural analysis of carbohydrates related to glycoproteins. Adv. Carbohydr. Chem. Biochem. 1983, 41, 209-374.
19. 2 as an essential intermediate in oligosaccharide processing. J. Biol. Chem. 1982, 257, 14657-14666.
20. González, L.; Bruix, M.; Díaz-Mauriño, T.; Feizi, T.; Rico, M.; Solís, D.; Jiménez-Barbero, J. Conformational studies of the Man8 oligosaccharide on native ribonuclease B and on the reduced and denatured protein. Arch. Biochem. Biophys. 2000, 383, 17-27.
21. Wyss, D.F.; Choi, J.S.; Wagner, G. Composition and sequence specific resonance assignments of the heterogeneous N-linked glycan in the 13.6 kDa adhesion domain of human CD2 as determined by NMR on the intact glycoprotein. Biochemistry 1995, 34, 1622-1634.
22. Wyss, D.F.; Choi, J.S.; Li, J.; Knoppers, M.H.; Willis, K.J.; Arulanandam, A.R.; Smolyar, A.; Reinherz, E.L.; Wagner, G. Conformation and function of the N-linked glycan in the adhesion domain of human CD2. Science 1995, 269, 1273-1278.
23. Homans, S.W.; Pastore, A.; Dwek, R.A.; Rademacher, T.W. Structure and dynamics in oligomannose-type oligosaccharides. Biochemistry 1987, 26, 6649-6655.
24. Wooten, E.W.; Bazzo, R.; Edge, C.J.; Zamze, S.; Dwek, R.A.; Rademacher, T.W. Primary sequence dependence of conformation in oligomannose oligosaccharides. Eur. Biophys. J. 1990, 18, 139-148.
25. Woods, R.J.; Pathiaseril, A.; Wormald, M.R.; Edge, C.J.; Dwek, R.A. The high degree of internal flexibility observed for an oligomannose oligosaccharide does not alter the overall topology of the molecule. Eur. J. Biochem. 1998, 258, 372-386.
26. Balaji, P.V.; Qasba, P.K.; Rao, V.S. Molecular dynamics simulations of high-mannose oligosaccharides. Glycobiology 1994, 4, 497-515.
27. Abe, H.; Takaoka, Y.; Chiba, Y.; Sato, N.; Ohgiya, S.; Itadani, A.; Hirashima, M.; Shimoda, C.; Jigami, Y.; Nakayama, K. Development of valuable yeast strains using a novel mutagenesis technique for the effective production of therapeutic glycoproteins. Glycobiology 2009, 19, 428-436.
28. Longtine, M.S.; McKenzie, A., 3rd; Demarini, D.J.; Shah, N.G.; Wach, A.; Brachat, A.; Philippsen, P.; Pringle, J.R. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 1998, 14, 953-961.
29. Gietz, R.D.; Schiestl, R.H. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2007, 2, 31-34.
30. Peat, S.; Whelan, W.J.; Edwards, T.E. Polysaccharides of Baker's Yeast. Part IV. Mannan. J. Chem Soc. 1961, 29-34.
31. Tanabe, K.; Ikenaka, K. In-column removal of hydrazine and N-acetylation of oligosaccharides released by hydrazionolysis. Anal. Biochem. 2006, 348, 324-326.
32. Takahashi, N.; Kato, K. GALAXY (Glycoanalysis by the Three Axes of MS and Chromatography): a web application that assists structural analyses of N-glycans. Trends. Glycosci. Glycotech. 2003, 14, 235-251.
33. Kamiya, Y.; Yamaguchi, Y.; Takahashi, N.; Arata, Y.; Kasai, K.I.; Ihara, Y.; Matsuo, I.; Ito, Y.; Yamamoto, K.; Kato, K. Sugar-binding properties of VIP36, an intracellular animal lectin operating as a cargo receptor. J. Biol. Chem. 2005, 280, 37178-37182.
34. Kato, K.; Takahashi, N. GALAXY database and pyridilaminated oligosaccharide library. In Experimental Glycoscience: Glycobiology; Taniguchi, N., Suzuki, A., Narimatsu, H., Kawasaki, T., Hase, S., Eds.; Springer: The Netherlands, 2008; pp. 413-416.
35. Kamiya, Y.; Kamiya, D.; Yamamoto, K.; Nyfeler, B.; Hauri, H.P.; Kato, K. Molecular basis of sugar recognition by the human L-type lectins ERGIC-53, VIPL, and VIP36. J. Biol. Chem. 2008, 283, 1857-1861.
36. Delaglio, F.; Grzesiek, S.; Vuister, G.W.; Zhu, G.; Pfeifer, J.; Bax, A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 1995, 6, 277-293.
37. 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, 4752-4754.
38. 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, 6658-6671.
39. Demarco, M.L.; Woods, R.J.; Prestegard, J.H.; Tian, F. Presentation of membrane-anchored glycosphingolipids determined from molecular dynamics simulations and NMR paramagnetic relaxation rate enhancement. J. Am. Chem. Soc. 2010, 132, 1334-1338.
40. Erdélyi, M.; d'Auvergne, E.; Navarro-Vázquez, A.; Leonov, A.; Griesinger, C. Dynamics of the glycosidic bond: conformational space of lactose. Chemistry 2011, 17, 9368-9376.