Oligosaccharide structures: Theory versus experiment

Current Opinion in Structural Biology

Volumn 7, Issue 5, 1997, Pages 617-623

  Imberty, Anne ^a  

^a CENTRE DE RECHERCHES SUR LES MACROMOLÉCULES VÉGÉTALES CERMAV CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BLOOD GROUP A ANTIGEN; BLOOD GROUP ANTIGEN; LACTOSE; OLIGOSACCHARIDE; PROTEIN; RECEPTOR;

ACCURACY; BLOOD GROUP LEWIS SYSTEM; CARBOHYDRATE ANALYSIS; COMPUTER; COMPUTER PROGRAM; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; RECEPTOR BINDING; REVIEW; SIMULATION; THEORY;

EID: 0030834858     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80069-3     Document Type: Article

References (62)

1. Glennon TM, Zheng YJ, Le Grand SM, Shutzberg BA, Merz KM Jr. A force field for monosaccharides and (1-4) linked polysaccharides. J Comput Chem. 15:1994;1019-1040.
2. Woods RJ, Dwek RA, Edge CJ. Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM-93 parameter development. J Am Chem Soc. 99:1995;3832-3846.
3. Senderowitz H, Parish C, Still WC. Carbohydrates: united atom AMBER parametrization of pyranoses and simulations yielding anomeric free energies. J Am Chem Soc. 118:1996;2078-2086.
4. Reiling S, Schlenkrich M, Brickmann J. Force field parameters for carbohydrates. J Comput Chem. 17:1996;450-468.
5. Ott KH, Meyer B. Parametrization of GROMOS force field for oligosaccharide assessment of efficiency of molecular dynamics simulations. J Comput Chem. 17:1996;1068-1084.
6. Hardy BJ, Bystricky S, Kovac P, Wildmalm G. Conformational analysis and molecular dynamics simulation of α-(1-2) and α-(1-3) linked rhamnose oligosaccharides: reconciliation with optical rotation and NMR experiments. Biopolymers. 41:1996;83-96.
7. Ott KH, Meyer B. Molecular dynamics simulation of maltose in water. Carbohydr Res. 281:1996;11-34 Extended MD simulations allow the determination of statistics on the conformational behavior of the αGlc(1-4)Glc linkage. of special interest.
8. Engelsen SB, Pérez S. The hydration of sucrose. Carbohydr Res. 292:1996;21-38 An analysis of a 500 ps MD simulation with water molecules which allows conclusions to be drawn concerning the hydration shell, the bridging water molecules, and their residence times. of outstanding interest.
9. Peters T, Pinto BM. Structure and dynamics of oligosaccharides: NMR and modeling studies. Curr Opin Struct Biol. 6:1996;710-720 An in-depth review which includes oligosaccharides as part of glycoproteins and protein - carbohydrate complexes. of special interest.
10. Poveda A, Asensio JL, Espinosa JF, Martin-Pastor M, Canada J, Jimenez-Barbero J. Application of nuclear magnetic resonance spectroscopy and molecular modeling to the study of protein - carbohydrate interactions. J Mol Graph. 14:1997; This is an excellent review which covers all protein - carbohydrate interactions investigated by transferred NOEs. of outstanding interest.
11. Casset F, Peters T, Etzler M, Korchagina E, Nifant'ev N, Pérez S, Imberty A. Conformational analysis of blood group A trisaccharide in solution and in the binding site of Dolichos biflorus lectin using transient and transferred nuclear Overhauser enhancement (NOE) and rotating-frame NOE experiments. Eur J Biochem. 239:1996;710-719 From a transferred-NOE investigation, lectin is concluded to select one conformation of blood group A trisaccharide from the equilibrium present in water solution. of special interest.
12. Siebert HC, Gilleron M, Kaltner H, von der Lieth CW, Kozar T, Bovin N, Korchagina EY, Vliegenthart JF, Gabius HJ. NMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Galβ1-2Gal β1-R) for an animal galectin in the free and in the bound state. Biochem Biophys Res Commun. 219:1996;205-212.
13. Espinosa JF, Canada FJ, Asensio JL, Dietrich H, Martin-Lomas M, Schmidt RR, Jiménes-Barbero J. Conformation differences of O and C-glycosides in the protein-bound state: different conformations of C-lactose and its O-analog are recognized by ricin B, a galactose-binding lectin. Int Ed Angew Chem. 35:1996;303-306.
14. Espinosa JF, Canada FJ, Asensio JL, Martin-Pastor M, Dietrich H, Martin-Lomas M, Schmidt RR, Jiménes-Barbero J. Experimental evidence of conformational differences between C-glycosides and O-glycosides in solution and in the protein-bound state: the C-lactose/O-lactose case. J Am Chem Soc. 118:1996;10862-10871 A transferred-NOEs investigation which concludes that ricin B selects different conformers of lactose and its analog, C-lactose. The flexibility of this C-disaccharide in solution is also demonstrated. of outstanding interest.
15. Casset F, Imberty A, Pérez S, Etzler ME, Paulsen H, Peters T. Transferred nuclear Overhauser enhancement (NOE) and rotating-frame NOE experiments reflect the size of the bound segment of the Forssman pentasaccharide in the binding site of Dolichos biflorus lectin. Eur J Biochem. 244:1997;242-250 Ratio-dependent transferred NOE values are different for the buried and exposed extremities of the oligosaccharide. Within the binding site, the nature of the amino acid involved in each contact is determined by observation of ligand - protein transfer NOEs. of special interest.
16. x tetrasaccharide, free in solution and bound to E-, P-, and L-selectin. J Am Chem Soc. 119:1997;172-1736 The bound conformations of the ligand are calculated from transferred NOE data using the full relaxation matrix analysis, together with the ellipsoid model for the motion of the complex. The conformation of the ligand is predicted to be different when complexed with L-selectin than when complexed with E- and P-selectin. of special interest.
17. Naismith JH, Field RA. Structural basis of trimannoside recognition by concanavalin A. J Biol Chem. 271:1996;972-976.
18. Loris R, Maes D, Poortmans F, Wyns L, Bouckaert J. A structure of the complex between concanavalin A and methyl-3,6-di-O-(α-D-mannopyranosyl)-α-D-mannopyranoside reveals two binding modes. J Biol Chem. 271:1996;30614-30618.
19. Hester G, Wright CS. The mannose-specific bulb lectin from Galanthus nivalis (snowdrop) binds mono- and dimannosides at distinct sites. Structure analysis of refined complexes at 2.3 Å and 3.0 Å resolution. J Mol Biol. 262:1996;516-531.
20. Wright CS, Hester G. The 2.0 Å structure of a cross-linked complex between snowdrop lectin and a branched mannopentaose: evidence for two unique binding modes. Structure. 4:1996;1339-1352 The conformation and binding mode of branched 3,6-core mannopentaose at two independent binding sites is described. Different conformations are observed primarily due to the flexibility about the φ angle. of special interest.
21. Asensio JL, Jiménez-Barbero J. The use of the AMBER force field in conformational analysis of carbohydrate molecules: determination of the solution conformation of methyl α-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations. Biopolymers. 35:1995;55-73.
22. Engelsen SB, Pérez S, Braccini I, Hervédu Penhoat C. Internal motions of carbohydrates as probed by comparative molecular modeling and nuclear magnetic resonance of ethyl β-lactoside. J Comput Chem. 16:1995;1096-1119.
23. Martin-Pastor M, Espinosa JF, Asensio JL, Jiménez-Barbero J. A comparison of the geometry and of the energy results obtained by application of different molecular mechanics force fields to methyl α-lactoside and the C-analogue of lactose. Carbohydr Res. 298:1997;15-49 A comparison with clear conclusions about the force-fields that could be use for modeling carbohydrates. of special interest.
24. Espinosa JF, Martin-Pastor M, Asensio JL, Dietrich H, Martin-Lomas M, Schmidt RR, Jiménes-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. 36:1995;6329-6332.
25. Rubinstenn G, Sinaÿ P, Berthault P. Evidence of conformational heterogeneity for carbohydrate mimetics. NMR study of methyl β-C-lactoside in aqueous solution. J Chem Phys A. 101:1997;2536-2540 The geometrical and dynamic parameters of 19 protons pairs are measured by off-resonance rotating-frame nuclear Overhauser enhancement spectroscopy. Direct determination of the conformation is not possible, however, because of structure flexibility. Combination of the NMR data with conformational analysis demonstrates the presence of two conformational families. of special interest.
26. Bevilacqua VL, Thomson DS, Prestegard JH. Conformation of methyl β-lactoside bound to the ricin B-chain: interpretation of transferred nuclear Overhauser effects facilitated by spin simulation and selective deuteration. Biochemistry. 29:1990;5529-5537.
27. Asensio JL, Canada FJ, Jiménez-Barbero J. Studies of the bound conformations of methyl α-lactoside and methyl β-gallactoside to ricin B chain using transferred NOE experiments in the laboratory and rotating frames, assisted by molecular mechanics and dynamics calculations. Eur J Biochem. 233:1995;618-630.
28. Lemieux RU, Bock K, Delbaere LTJ, Koto S, Rao VS. The conformations of oligosaccharides related to the ABH and Lewis human blood group determinants. Can J Chem. 58:1980;63-65.
29. Rao VSR, Biswas M. Conformations and interactions of oligosaccharides related to the ABH and Lewis blood groups. Top Mol Struct Biol. 8:1985;185-218.
30. Imberty A, Mikros E, Koca J, Mollicone R, Oriol R, Perez S. Computer simulation of histo-blood group oligosaccharides: energy maps of all constituting disaccharides and potential energy surfaces of 14 ABH and Lewis carbohydrate antigens. Glycoconj J. 12:1995;331-349.
31. Bizik F, Tvaroska I. Conformational analysis of disaccharides fragments of blood group determinants in solution by molecular modelling. Chem Papers. 49:1995;202-214.
32. Longchambon F, Ohanessian J, Gillier-Pandraud H, Duchet D, Jacquinet JC, Sinaÿ P. Structure de la N-acétyl-lactosamine (acétamido-2-désoxy-2-O-β-D-galactopyrannosyl-4-α-D- glucopyrannose). Acta Crystallogr B. 37:1981;601-607.
33. Watt DK, Brasch DJ, Larsen DS, Melton LD, Simpson J. Oligosaccharides related to xyloglucan: synthesis and X-ray crystal structure of methyl 2-0-(α-l-fucopyranosyl)-β-D-galactopyranoside. Carbohydr Res. 285:1996;1-15.
34. a oligosaccharides. Conformational analysis in solution by molecular modelling. Chem Papers. 50:1996;84-86.
35. Duus JO, Nifant'ev N, Shashkov AS, Khatuntseva EA, Bock K. Synthesis and structural studies of branched 2-linked trisaccharides related to blood group determinants. Carbohydr Res. 288:1996;25-44.
36. Mollicone R, Cailleau A, Imberty A, Gane P, Perez S, Oriol R. Recognition of the blood group H type 2 trisaccharide epitope by 28 monoclonal antibodies and three lectins. Glycoconj J. 13:1996;263-271.
37. Imberty A, Mollicone R, Mikros E, Carrupt PA, Perez S, Oriol R. How do antibodies and lectins recognize histo-blood group antigens? A 3D-QSAR study by comparative molecular field analysis (CoMFA). Bioorg Med Chem. 4:1996;1979-1988 An extension of molecular modeling that demonstrates that quantitative structure/activity relationship (QSAR) methods can be used in the carbohydrate field. of special interest.
38. x and derivatives. J Am Chem Soc. 114:1992;9283-9288.
39. x oligosaccharide determined by NMR spectroscopy and molecular dynamics simulations. Biochemistry. 31:1992;6703-6709.
40. 1H NMR relaxation measurements and molecular dynamics simulations. Chem Commun. 1996;421-422.
41. 13C relaxation data obtained at two different fields and a variety of temperatures permit the determination of local dynamical parameters. A comparison of these with MD simulation yields a fair agreement. of special interest.
42. 1H NMR spectroscopy without use of an internal distance reference. J Biomol NMR. 8:1996;23-35 The use of off-resonance rotative frame nuclear Overhauser enhancement spectroscopy allows the determination of geometrical and dynamical parameters of 30 proton pairs. of special interest.
43. x trisaccharide. Glycobiology. 6:1996;537-542 The first description of the crystal structure of a histo-blood group carbohydrate determinant. Some interactions observed between adjacent trisaccharides can provide clues for carbohydrate - carbohydrate interactions in cell adhesion. of outstanding interest.
44. x trisaccharide. Carbohydr Lett. 1:1996;475-482.
45. x expression. Glycoconj J. 11:1994;238-248.
46. Ni F. Complete relaxation analysis matrix of transferred nuclear Overhauser effects. J Magn Reson. 96:1992;651-656.
47. Imberty A, Pérez S. Traveling through the potential energy surface of sialyl Lewis x. Chapleur Y. Carbohydrate Mimics. Concepts and Methods. 1997;349-364 Wiley, Weinheim.
48. Mukhopadhyay C, Miller KE, Bush CA. Conformation of the oligosaccharide receptor for E-selectin. Biopolymers. 34:1994;21-29.
49. x antigen. Glycobiology. 4:1994;59-68.
50. a-containing oligosaccharides. of special interest.
51. x ligand changes upon binding to E-selectin. Biochemistry. 33:1994;1059-10596.
52. x complex. Int Ed Angew Chem. 34:1995;184-1844.
53. Graves BJ, Crowther RL, Chandran C, Rumberger JM, Li S, Huang KS, Presky DH, Familletti PC, Wolitzky BA, Burns DK. Insight into E-selectin - ligand interaction from the crystal structure and mutagenesis of the lec/EGF domains. Nature. 367:1994;532-538.
54. x in the crystalline complex is in good agreement with the bound conformation in solution [16,51,52]. The lack of observed interaction between NeuNAc and the protein is surprising and opens a wide range of issues. of special interest of outstanding interest.
55. Weis WI, Drickamer K, Hendrickson WA. Structure of a C-type mannose-binding protein complexed with an oligosaccharide. Nature. 360:1992;127-134.
56. Kogan TP, Revelle BM, Tapp S, Scott D, Beck PJ. A single amino acid residue can determine the ligand specificity of E-selectin. J Biol Chem. 270:1995;14047-14055.
57. Hiramatsu Y, Tsujishita H, Kondo H. Studies on selectin blockers. 3. Investigation of the carbohydrate ligand sialyl Lewis x recognition site of P-selectin. J Med Chem. 39:1996;4547-4553.
58. Tsujishita H, Hiramatsu Y, Kondo N, Ohmoto H, Kondo H, Kiso M, Hasegawa A. Selectin - ligand interactions revealed by molecular dynamics simulation in solution. J Med Chem. 40:1997;362-369.
59. Sokolowski T, Peters T, Pérez S, Imberty A. Conformational analysis of biantennary glycans and molecular modeling of their complexes with lentil lectin. J Mol Graph. 15:1997;. in press.
60. Bourne Y, Mazurier J, Legrand D, Rougé P, Montreuil J, Spik G, Cambillau C. Structures of a legume lectin complexed with the human lactotransferrin N2 fragment, and with an isolated biantennary glycopeptide: role of the fucose moiety. Structure. 2:1994;209-219.
61. Bourne Y, Rougé P, Cambillau C. X-ray structure of a biantennary octasaccharide - lectin complex refined at 2.3 Å resolution. J Biol Chem. 267:1992;197-203.
62. Bourne Y, Bolgiano B, Liao DI, Strecker G, Cantau P, Herzberg O, Feizi T, Cambillau C. Crosslinking of mammalian lectin (galectin-1) by complex biantennary saccharides. Nat Struct Biol. 1:1994;863-870.