Structure and dynamics of oligosaccharides NMR and modeling studies

Current Opinion in Structural Biology

Volumn 6, Issue 5, 1996, Pages 710-720

  Peters, Thomas ^b   Pinto, B Mario ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE BINDING PROTEIN; GLYCOPEPTIDE; GLYCOPROTEIN; GLYCOSIDE; LIGAND; OLIGOSACCHARIDE;

CARBOHYDRATE ANALYSIS; CHEMICAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; REVIEW;

EID: 0001248255     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80039-X     Document Type: Article

References (82)

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5. 13C relaxation data at two different field strengths. In conjunction with extended molecular dynamics simulations, a motional model is obtained that allows a very satisfactory theoretical calculation of experimental NOE data.
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9. c values can be estimated from NOE buildup curves.
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18. x tetrasaccharide bound to E-selectin is derived on the basis of transfer NOESY experiments.
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20. 20. Andrews JS, Weimar T, Frandsen TP, Svensson B, Pinto BM: Novel disaccharides containing sulfur in the ring and nitrogen in the interglycosidic linkage. Conformation of methyl 5-thio4-W-α-maltoside bound to glucoamylase and its activity as a competitive inhibitor. J Am Chem Soc 1995, 117:10799-10804. Transferred NOEs are used to demonstrate that methyl 5-thio-4-N-α-malto-side is bound by glucoamylase G1. The bound conformation is in the area of the global energy minimum of the free ligand.
21. 21. Casset F, Hamelryck T, Loris R, Brisson J-R, Tellier C, Dao-Thi M-H, Wyns L, Poortmans F, Pérez S, Imberty A: NMR, molecular modeling, and crystallographic studies of lentil lectin-sucrose interaction. J Biol Chem 1995, 270:25619-25628. A crystal structure at 1.9 Å resolution of the sucrose-lentil-lectin complex is presented and compared to trNOE experiments and molecular modeling studies. A detailed model for the complex is obtained.
22. 22. Evans SV, Sigurskjold BW, Jennings HJ, Brisson J-R, To R, Tse WC, Altman E, Frosch M, Weisgerber C, Kratzin HD et al.: Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 Åresolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for α-(2-8)-polysialic acid. Biochemistry 1995, 34:6737-6744. From combined X-ray crystallographic, thermodynamic and NMR spectroscopic data it is concluded that the binding site of an antibody with specificity for α-(2-8)-linked sialic acid polymers accommodates at least eight sialic acid residues.
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24. 1H NMR study of the interaction of N,N′,N′triacetyl chitotriose with Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus. FEBS Lett 1995, 370: 245-249.
25. 25. Xu G-Y, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR, Harris-Brandts M, Carver JP, Kay LE, Harvey TS: Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy. Biochemistry 1995, 34:6993-7009.
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30. 30. Espinosa JF, Martin-Pastor M, Asensio JL, Dietrich H, Martin-Lomas M, Schmidt RR, Jimenez-Barbero J: Experimental and theoretical evidences of conformational flexibility of C-glycosides. NMR analysis and molecular mechanics calculations of C-lactose and its O-analogue. Tetrahedron Lett 1995, 36:6329-6332.
31. 31. Espinosa J-F, Dietrich H, Martin-Lomas M, Schmidt RR, Jimenez-Barbero J: Conformational flexibility of C-glycosides: experimental evidence of the existence of a gauche-gauche conformation around the glycosidic linkage for a lactose analogue. Tetrahedron Lett 1996, 37:1467-1470.
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34. 34. Stoffer B, Aleshin AE, Firsov LM, Svensson B, Honzatko RB: Refined structure for the complex of D-glucoodihydroacarbose with glucoamylase from Aspergillus awamori var.X100 to 2.2 Å resolution: dual conformations for extended inhibitors bound to the active site of glucoamylase. FEBS Lett 1995, 358:57-61.
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36. 36. Prowse WG, Kline AD, Skelton MA, Loncharich RJ: Conformation of A82846B, a glycopeptide antibiotic, complexed with its cell wall fragment: an asymmetric homodimer determined using NMR spectroscopy. Biochemistry 1995, 34:9632-9644. For the dimer complex of A82846B with a pentapeptide cell-wall fragment a solution structure was obtained on the basis of NMR experimental restraints.
37. 37. Groves P, Searle MS, Waltho JP, Williams DH: Asymmetry in the structure of glycopeptide antibiotic dimers: NMR studies of the ristocetin A complex with a bacterial cell wall analogue. J Am Chem Soc 1995, 117:7958-7964. The solution structure of a dimer complex of the glycopeptide antibiotic ristocetin A has been determined from NOE constraints, energy minimization, and molecular dynamics simulations.
38. 38. Pérez S, Meyer C, Imberty A: Practical tools for molecular modeling of complex carbohydrates and their interactions with proteins. In Modelling of Biomolecular Structures and Mechanisms. Edited by Pullman A et al. Netherlands: Kluwer Academic Publishers; 1995:425-454. A comprehensive survey of techniques that are useful for the modeling of oligosaccharides and their complexes with proteins. A parametrization for the TRIPOS force field for the simulation of oligosaccharides is given.
39. 39. Casset F, Imberty A, Haser R, Payan F, Perez S: Molecular modelling of the interaction between the catalytic site of pig pancreatic α-amylase and amylose fragments. Eur J Biochem 1995, 232:284-293.
40. 15N abundance. Contacts within the high mannose glycan chain as well as contacts between the glycan chain and the protein backbone were observed.
41. 13C line-width measurements reflect the mobility of the branched glycan chain. It is concluded that the oligosaccharide is essential for the stabilization of the protein fold, namely by counterbalancing the effect of five positive charges centered about Lys61 of CD2.
42. 42. Lommerse JPM, Kroon-Batenburg LMJ, Kamerling JP, Vliegenhart JFG: Conformational analysis of the Xylose-containing N-glycan of pineapple stem bromelain as part of the intact glycoprotein. Biochemistry 1995, 34:8196-8206. The N-glycan attached to bromelain was investigated and compared to the same glycan chain which was previously studied as part of a small glycopeptide [9•]. On the basis of detailed NMR experiments, differences in mobility and conformation of the glycan chains in the glycoprotein and the corresponding glycopeptide fragment were unambiguously detected.
43. 43. Pieper J, Ott K-H, Meyer B: Stabilization of the T1 fragment of glycophorin AN through interactions with N-and O-linked glycans. Nat Struct Biol 1996, 3:228-232. For the first time, an NMR study of a highly glycosylated glycoprotein has been performed. It is demonstrated that the saccharide conformations are well defined, and that the peptide backbone has an extended structure.
44. 15N-enriched recombinant human chorionic gonadotropin. Biochemistry 1996, 35:8815-8823. This is the first NMR study of a uniformly isotopically 13C,15N-enriched glycoprotein. Different homonuclear and heteronuclear NMR experiments were applied to analyze the conformational properties of the glycan chain on the a subunit of recombinant human chorionic gonadotropin.
45. 45. Imberty A, Perez S: Stereochemistry of the N-glycosylation sites in glycoproteins. Protein Eng 1995, 8:699-709.
46. 46. Liang R, Andreotti AH, Kahne D: Sensivitiy of glycopeptide conformation to carbohydate chain length. J Am Chem Soc 1995, 117:10395-10396.
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48. 48. Spronk BA, Rivera-Sagredo A, Kamerling JP, Vliegenhart JFG: A reinvestigation towards the conformation of methyl α-D-mannopyranosyl-(1-6)-α-D-mannopyranoside by a combined ROE and molecular dynamics analysis. Carbohydr Res 1995, 273:11-26. In contrast to previous literature data for the 1-6 glycosidic linkage, it was found that the gg conformer is present to the extent of 96%.
49. 49. Weimar T, Peters T, Pérez S, Imberty A: Combined NMR, grid search/MM3 and Metropolis Monte Carlo/GEGOP studies of two L-fucose containing disaccharides: α-L-Fuc-(1-4)-β-D-GIcNAc-OMe and α-L-Fuc-(1-4)-β-D-GIcNAc-OMe. Theochem 1996, in press. Accurate NOE curves for both disaccharides were acquired to analyze their conformational behaviour. Overall R-factors around 20% were obtained when experimental NOE data was compared with theoretical NOE data.
50. 50. Martin-Pastor M, Asensio JL, López R, Jiménez-Barbero J: Conformational studies of a trisaccharide epitope in solution by using NMR spectroscopy and molecular mechanics and dynamics calculations with the MM3 program. J Chem Soc Perkin Trans 2 1995, 2:713-721.
51. 51. Toma L, Colombo D, Ronchetti F, Panza L, Russo G: Oligosaccharides related to tumor-associate antigens. Modeling of the terminal tetrasaccharide of an antigen recognized by the MBr1 antibody and of overlapping di-and trisaccharide sequences. Helv Chim Acta 1995, 78:636-646.
52. 52. Bernabé M, Jiménez-Barbero J, Gil-Serrano AM, González-Jiménez I, Tejero-Mateo P, Megias M: Solution structure of the trisaccharide and hexasaccharide fragments of the O-antigen of the lipopolysaccharide of Rhizobium tropici CIAT899. Carbohydr Res 1995, 279:339-352.
53. 53. Jansson P-E, Kjellberg A, Rundlöf T, Widmalm G: Synthesis, NMR spectroscopy and conformational studies of two vicinally disubstituted trisaccharides. J Chem Soc Perkin Trans 2 1995, 5:33-37.
54. 1H NMR relaxation measurements and molecular dynamics simulations. J Chem Soc Chem Commun 1996:421-422.
55. 55. Klein RA, Hartmann R, Egge H, Behr T, Fischer W: The aqueous solution structure of a lipoteichoic acid from Streptococcus pneumoniae strain R6 containing 2,4-diamino-2,4,6-trideoxygalactose: evidence for conformation mobility of the galactopyranose ring. Carbohydr Res 1996, 281:79-98.
56. 56. Tvaroska I, Taravel FR: Carbon-proton coupling constants in the conformational analysis of sugar molecules. Adv Carbohydr Chem Biochem 1995, 51:15-61.
57. 57. Tvaroska I, Gajdos J: Angular dependence of vicinal carbon-proton coupling constants for conformation studies of the hydroxymethyl group in carbohydrates. Carbohydr Res 1995, 271:151-162.
58. 58. Andre I, Mazeau K, Taravel FR, Tvaroska I: NMR and molecular modelling of sophorose and sophorotriose in solution. New J Chem 1995, 19:331-339.
59. 59. Desai UR, Vlahov IR, Pervin A, Linhardt RJ: Conformational analysis of sucrose octasulfate by high resolution nuclear magnetic resonance spectroscopy. Carbohydr Res 1995, 275:391-401.
60. 13C scalar coupling constants, and chemical-shift temperature and ionic-strength dependence, the conformational properties of sucrose octasulfate in solution were analyzed. Free sucrose octasulfate appears to assume a conformation that is significantly different from any of the eight conformations observed bound to acidic fibroblast growth factor.
61. 1H long-range coupling constants combined with molecular modeling. Biopolymers 1996, 38:339-353.
62. 1H chemical shifts. J Am Chem Soc 1995, 117:8635-8644.
63. 13C spincoupling constants in carbohydrates: effect of structure on coupling magnitude and sign. Carbohydr Res 1996, 280:177-186.
64. 64. Dabrowski J, Kozár T, Grosskurth H, Nifantev NE: Conformational mobility of oligosaccharides: experimental evidence for the existence of an anti conformer of the Galβ1-3Glcβ1-OME disaccharide. J Am Chem Soc 1995, 117:5534-5539. A hydrogen bond between the Glc OH4 and Gal OH2 groups was detected in DMSO solution. As a nonaveraged constraint, this hydrogen bond proves the existence of the 'anti' conformer of the disaccharide in DMSO solution.
65. 65. Engelsen SB, Koca J, Braccini I, Du Penhoat CH, Pérez S: Travelling on the potential energy surfaces of carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search. Carbohydr Res 1995, 276:1-29.
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67. 67. Dowd MK, French AD: Molecular mechanics modelling of α-(1-2)-, α-(1-3)-, and α-(1-6)-linked mannosyl disaccarides with MM3(92). J Carbohydr Chem 1995, 14:589-600.
68. 68. Kouwijzer MLCE, Grootenhuis PDJ: Parametrization and application of CHEAT95, an extended atom force field for hydrated (oligo)saccharides. J Phys Chem 1995, 99:13426-13436.
69. 69. Schmidt RK, Teo B, Brady JW: Use of umbrella sampling in the calculation of the potential of mean force for maltose in vacuum from molecular dynamics simulations. J Phys Chem 1995, 99:11339-11343.
70. 70. Kreis UC, Varma V, Pinto BM: Application of two-dimensional NMR spectroscopy and molecular dynamics simulations to the conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of Streptococcus Group A. Int J Biol Macromol 1995, 17:117-130.
71. 71. Hardy BJ, Gutierrez A, Lesiak K, Seidl E, Widmalm G: Structural analysis of the solution conformation of methyl-4-O-β-D-glucopyranosyl-α-D-glucopyranoside by molecular mechanics and ab initio calculation, stochastic dynamics simulation and NMR spectroscopy. J Phys Chem 1996, 100:9187-9192.
72. 72. Stuike-Prill R, Pinto BM: Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus Group A by Metropolis Monte Carlo simulations. Carbohydr Res 1995, 279:59-73.
73. 73. Sheng S, Van Halbeek H: Evidence for a transient interresidue hydrogen bond in sucrose in aqueous solution obtained by rotating-frame exchange NMR spectroscopy under supercooled conditions. Biochem Biophys Res Commun 1995, 215:504-510.
74. 74. Rutherford TJ, Neville DCA, Homans SW: Influence of the extent of branching on solution conformations of complex oligosaccharides: a molecular dynamics and NMR study of a penta-antennary, bisected N-glycan. Biochemistry 1995, 34:14131-14137.
75. 75. Taguchi T, Kitajima K, Muto Y, Yokoyama S, Inoue S, Inoue Y: Proton NMR study of the trimannosyl unit in a penta-antennary N-linked decasaccharide structure. Eur J Biochem 1995, 228:822-829. Using chemical shifts and homonuclear vicinal coupling constants the conformation of the C5-C6 bond in the α-D-Man-(1→6)-β-D-Man linkage was unambiguously shown to be predominantly confined to a gg orientation. Before, this was only observed for N-glycans containing a bisecting GlcNAc residue.
76. 76. Coterón JM, Singh K, Asensio JL, Dominguez-Dalda M, Fernández-Mayoralas A, Jiménez-Barbero J, Martin-Lomas M: Oligosaccharides structurally related to E-selectin ligands are inhibitors of neural cell division: synthesis, conformational analysis, and biological activity. J Org Chem 1995, 60:1502-1519.
77. 77. Bernardi A, Raimondi L: Conformational analysis of GM1 oligosaccharide in water solution with a new set of parameters for the Neu5Ac moiety. J Org Chem 1995, 60:3370-3377.
78. a pentasaccharide lacto-N-fucopentaose II and both sulfated and sialylated analogs have been studied using NMR spectroscopic techniques, mainly laboratory and rotating frame NOEs.
79. 79. Stubbs HJ, Lih JJ, Gustafson TL, Rice KG: Influence of core fucosylation on the flexibility of a biantennary N-linked oligosaccharide. Biochemistry 1996, 35:937-947. Using fluorescence energy transfer, core fucosylation is shown to have a strong influence on the overall conformation of the glycan chain.
80. 4J correlations across glycosidic linkages occur in several linear and branched oligosaccharides.
81. HH value. Examples are provided for COSY and TOCSY spectra.
82. 15N abundance (see also [44••]). The secondary structure of the peptide backbone is partially similar to that of the crystal structure, but large structural differences are found in an intersubunit region that is stabilized in the crystal through interactions with the β subunit, but disordered in free α-hCG in solution. Both glycan chains at Asn52 and Asn78 are largely extended into solution, but the GlcNAc residue directly attached to Asn78 is tightly packed against the protein, as inferred from numerous NOEs.