Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted nmr spectroscopy in conjunction with molecular dynamics simulation

Advances in Experimental Medicine and Biology

Volumn 842, Issue , 2015, Pages 217-230

  Zhang, Ying ^a,b,c   Yamaguchi, Takumi ^a,b,c   Satoh, Tadashi ^c,d   Yagi Utsumi, Maho ^a,c,e   Kamiya, Yukiko ^a,f   Sakae, Yoshitake ^f   Okamoto, Yuko ^f   Kato, Koichi ^a,b,c,g,h  

^a OKAZAKI INSTITUTE FOR INTEGRATIVE BIOSCIENCE   (Japan)

^b GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^c NAGOYA CITY UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f NAGOYA UNIVERSITY   (Japan)

^g OCHANOMIZU UNIVERSITY   (Japan)

^h The Glycoscience Institute Ochanomizu University ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA SYNUCLEIN; AMYLOID BETA PROTEIN; GANGLIOSIDE GM1; GANGLIOSIDE GM2; GANGLIOSIDE GM3; GLYCOLIPID; OLIGOSACCHARIDE; GLYCOPROTEIN; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE PROTEIN;

ANALYTICAL PARAMETERS; ARTICLE; CARBOHYDRATE ANALYSIS; CELL SURFACE; CLUSTER ANALYSIS; CONFORMATION; ELECTRON SPIN RESONANCE; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CARBOHYDRATE INTERACTION; SAMPLING; SCALAR COUPLING; X RAY CRYSTALLOGRAPHY; CHEMISTRY; ENDOPLASMIC RETICULUM; GENETICS; GOLGI COMPLEX; MAGNETISM; METABOLISM; MOLECULAR GENETICS; PROCEDURES; PROTEIN TERTIARY STRUCTURE; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE;

CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; ENDOPLASMIC RETICULUM; GLYCOPROTEINS; GOLGI APPARATUS; MAGNETIC RESONANCE SPECTROSCOPY; MAGNETICS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; OLIGOSACCHARIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84912051180     PISSN: 00652598     EISSN: 22148019     Source Type: Book Series    
DOI: 10.1007/978-3-319-11280-0_14     Document Type: Article

References (35)

1. Ando H, Ishida H, Kiso M (2010) Renewed synthetic approach to gangliosides exploiting versatile and powerful synthetic units. Methods Enzymol 478;521–540
2. Bodner CR, Maltsev AS, Dobson CM, Bax A (2010) Differential phospholipid binding of α- synuclein variants implicated in Parkinson’s disease revealed by solution NMR spectroscopy. Biochemistry 49:862–871
3. Drickamer K, Taylor ME (1993) Biology of animal lectins. Annu Rev Cell Biol 9:237–264
4. Ernst B, Magnani JL (2009) From carbohydrate leads to glycomimetic drugs. Nat Rev Drug Discov 8:661–677
5. Fantini J, Yahi N (2010) Molecular insights into amyloid regulation by membrane cholesterol and sphingolipids: common mechanisms in neurodegenerative diseases. Expert Rev Mol Med 12:e27
6. Gayen A, Mukhopadhyay C (2008) Evidence for effect of GM1 on opioid peptide conformation: NMR study on leucine enkephalin in ganglioside-containing isotropic phospholipid bicelles. Langmuir 24:5422–5432
7. Kamiya Y, Yagi-Utsumi M, Yagi H, Kato K (2011a) Structural and molecular basis of carbohydrateprotein interaction systems as potential therapeutic targets. Curr Pharm Des 17:1672–1684
8. Kamiya Y, Yamamoto S, Chiba Y, Jigami Y, Kato K (2011b) Overexpression of a homogeneous oligosaccharide with 13C labeling by genetically engineered yeast strain. J Biomol NMR 50:397–401
9. Kamiya Y, Satoh T, Kato K (2012) Molecular and structural basis for N -glycan-dependent determination of glycoprotein fates in cells. Biochim Biophys Acta 1820:1327–1337
10. Kamiya Y, Yanagi K, Kitajima T, Yamaguchi T, Chiba Y, Kato K (2013) Application of metabolic 13C labeling in conjunction with high-fi eld nuclear magnetic resonance spectroscopy for comparative conformational analysis of high mannose-type oligosaccharides. Biomolecules 3:108–123
11. Kamiya Y, Satoh T, Kato K (2014) Recent advances in glycoprotein production for structural biology: toward tailored design of glycoforms. Curr Opin Struct Biol 26:44–53
12. Khatun UL, Mukhopadhyay C (2013) Interaction of bee venom toxin melittin with ganglioside GM1 bicelle. Biophys Chem 180–181:66–75
13. Lepenies B, Yin J, Seeberger PH (2010) Applications of synthetic carbohydrates to chemical biology. Curr Opin Chem Biol 14:404–411
14. Luchinat C, Parigi G (2007) Paramagnetic systems in biochemistry: solution NMR studies eMagRes. Wiley, New York
15. Matsuzaki K, Kato K, Yanagisawa K (2010) Abeta polymerization through interaction with membrane gangliosides. Biochim Biophys Acta 1801:868–877
16. Nakanishi-Shindo Y, Nakayama K, Tanaka A, Toda Y, Jigami Y (1993) Structure of the N-linked oligosaccharides that show the complete loss of α-1,6-polymannose outer chain from och1 , och1 mnn1 , and och1 mnn1 alg3 mutants of Saccharomyces cerevisiae . J Biol Chem 268:26338–26345
17. Peters T, Pinto BM (1996) Structure and dynamics of oligosaccharides: NMR and modeling studies. Curr Opin Struct Biol 6:710–720
18. Piccinini M, Scandroglio F, Prioni S, Buccinnà B, Loberto N, Aureli M, Chigorno V, Lupino E, Demarco G, Lomartire A, Rinaudo MT, Sonnino S, Prinetti A (2010) Deregulated sphingolipid metabolism and membrane organization in neurodegenerative disorders. Mol Neurobiol 41:314–340
19. Satoh T, Suzuki K, Yamaguchi T, Kato K (2014) Structural basis for disparate sugar-binding specifi cities in the homologous cargo receptors ERGIC-53 and VIP36. PLoS One 9:e87963
20. Sharon N, Lis H (2003) Lectins, 2nd edn. Springer, Dordrecht Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314:141–151
21. Takeda Y, Totani K, Matsuo I, Ito Y (2009) Chemical approaches toward understanding glycanmediated protein quality control. Curr Opin Chem Biol 13:582–591
22. Ulmer TS, Bax A, Cole NB, Nussbaum RL (2005) Structure and dynamics of micelle-bound human α-synuclein. J Biol Chem 280:9595–9603
23. Utsumi M, Yamaguchi Y, Sasakawa H, Yamamoto N, Yanagisawa K, Kato K (2009) Up-and-down topological mode of amyloid beta-peptide lying on hydrophilic/hydrophobic interface of ganglioside clusters. Glycoconj J 26:999–1006
24. Wang Z, Chinoy ZS, Ambre SG, Peng W, Mcbride R, De Vries RP, Glushka J, Paulson JC, Boons GJ (2013) A general strategy for the chemoenzymatic synthesis of asymmetrically branched N -glycans. Science 341:379–383
25. Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RA (2002) Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. Chem Rev 102:371–386
26. Yagi-Utsumi M, Kameda T, Yamaguchi Y, Kato K (2010) NMR characterization of the interactions between lyso-GM1 aqueous micelles and amyloid beta. FEBS Lett 584:831–836
27. Yamaguchi T, Kamiya Y, Choo YM, Yamamoto S, Kato K (2013a) Terminal spin labeling of a high-mannose-type oligosaccharide for quantitative NMR analysis of its dynamic conformation. Chem Lett 42:544–546
28. Yamaguchi T, Uno T, Uekusa Y, Yagi-Utsumi M, Kato K (2013b) Ganglioside-embedding small bicelles for probing membrane-landing processes of intrinsically disordered proteins. Chem Commun (Camb) 49:1235–1237
29. Yamaguchi T, Sakae Y, Zhang Y, Yamamoto S, Okamoto Y, Kato K (2014) Exploration of conformational spaces of high-mannose-type oligosaccharides by an NMR-validated simulation. Angew Chem Int Ed Engl in press
30. Yamamoto S, Yamaguchi T, Erdélyi M, Griesinger C, Kato K (2011) Paramagnetic lanthanide tagging for NMR conformational analyses of N -linked oligosaccharides. Chem Eur J 17:9280–9282
31. Yamamoto S, Zhang Y, Yamaguchi T, Kameda T, Kato K (2012) Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations. Chem Commun (Camb) 48:4752–4754
32. Zhang Y (2014) Paramagnetism–assisted NMR analyses of conformational dynamics of ganglioside glycans. The Graduate University for Advanced Studies
33. Zhang Y, Yamamoto S, Yamaguchi T, Kato K (2012) Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched oligosaccharide. Molecules 17:6658–6671
34. Zhang Y, Yamaguchi T, Kato K (2013) New NMR tools for characterizing the dynamic conformations and interactions of oligosaccharides. Chem Lett 42:1455–1462
35. Zhao H, Pan Q, Zhang W, Carmichael I, Serianni AS (2007) 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 72:7071–7082