Computational carbohydrate chemistry: What theoretical methods can tell us

Glycoconjugate Journal

Volumn 15, Issue 3, 1998, Pages 209-216

  Woods, Robert J ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

Conformational analysis; Free energy; GLYCAM; Molecular dynamics; NMR; Oligosaccharide; Perturbation; Polysaccharide

Indexed keywords

CARBOHYDRATE; GLYCAN; OLIGOSACCHARIDE; POLYSACCHARIDE; RECEPTOR PROTEIN;

BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; CRYSTAL STRUCTURE; ENERGY; MACROMOLECULE; METHODOLOGY; MODEL; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; REVIEW; TECHNIQUE; THEORY;

CARBOHYDRATE CONFORMATION; CARBOHYDRATE METABOLISM; CARBOHYDRATES; CHEMISTRY, ORGANIC; ELECTROSTATICS; HISTORY, 20TH CENTURY; MACROMOLECULAR SUBSTANCES; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; OLIGOSACCHARIDES; POLYSACCHARIDES; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 0031935175     PISSN: 02820080     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1006984709892     Document Type: Review

References (94)

1. McIntire TM, Penner RM, Brant DA (1995) Macromolecules 28: 6375-7.
2. Riee KG, Wu P, Brand L, Lee YC (1991) Biochemistry 30: 6646-55.
3. Stevens ES (1994) Biopolymers 34: 1395-401.
4. Fernández P, Jiménez-Barbero J (1994) J Carbohydr Chem 13: 207-33.
5. Fernández P, Jiménez-Barbero J (1993) Carbohydr Res 248: 15-36.
6. Cumming DA, Carver JP (1987) Biochemistry 26: 6664-76.
7. Woolen EW, Edge CJ, Bazzo R, Dwek RA, Rademacher TW (1990) Carbohydr Res 203: 13-17.
8. Woods RJ (1996) In Reviews in Computational Chemistry (Lipkowitz KB, Boyd DB, eds) pp 129-65. New York: VCH Publishers Inc.
9. Melberg S, Rasmussen K (1980) Carbohydr Res 78: 215-24.
10. Bock K, Lemicux RU (1982) Carbohydr Res 100: 63-74.
11. Bock K, Josephson S, Bundle DR (1982) J Chem Soc Perkin Trans 11: 59-70.
12. Lemieux RU, Bock K, Delbaere LTJ, Koto S, Rao VS (1980) Can J Chem 58: 631-53.
13. Lemieux RU, Bock K (1983) Arch Biochem Biophys 221: 125-34.
14. Paulsen H, Peters T, Sinnwell V, Lebhun R, Meyer B (1984) Liebigs Ann Chem 951-76.
15. Peters T, Meyer B, Stuike-Prill R, Somorjai R, Brisson J-R (1993) Carbohydr Res 238: 49-73.
16. Levery SB (1991) Glycoconjugate J 8: 484-92.
17. Poppe L, Stuike-Prill R, Meyer B, van Halbeek H (1992) J Biomol NMR 2: 109-36.
18. Weimar T, Meyer B, Peters T (1993) J Biomol NMR 3: 399-414.
19. Engelsen SB, Rasmussen K (1993) Int J Biol Macromol 15: 56 62.
20. Stuike-Prill R, Meyer B (1990) Eur J Biochem 194: 903-19.
21. Woods RJ, Dwek RA, Edge CJ, Fraser-Reid B (1995) J Phys Chem 99: 3832-46.
22. Imberty A, Pérez S (1994) Glycobiology 4: 351-66.
23. Glennon TM, Zheng Y-J, LcGrand SM, Shutzberg BA, Merz KM Jr (1994) J Comput Chem 15: 1019-40.
24. Grootenhuis PDJ, Haasnoot CAG (1993) Molec Simulation 10: 75-95.
25. Imberty A, Hardman KD, Carver JP, Pérez S (1991) Glycobiology 1:631-42.
26. Homans SW (1990) Biochemistry 29: 9110-18.
27. Ha SN, Giammona A, Field M, Brady JW (1988) Carbohydr Res 180: 207-21.
28. Rutherford TJ, Partridge J, Weller CT, Homans SW (1993) Biochemistry 32: 12715-24.
29. Bock K (1983) Pure Appl Chem 55: 605-22.
30. Thogersen H, Lemieux RU, Bock K, Meyer B (1982) Can J Chem 60: 44-57.
31. Momany FA, McGuire RF, Burgess AW, Scheraga HA (1975) J Phys Chem 79: 2361-81.
32. Lemieux RU, Koto S (1974) Tetrahedron 30: 1933-44.
33. Rasmussen K (1982) Acta Chem Scand A36: 323-7.
34. Koehler JEH, Saenger W, van Gunsteren WF (1987) Eur Biophys J 15: 197-210.
35. Prabhakaran M, Harvey SC (1987) Biopolymers 26: 1087-96.
36. Clark M, Cramer III R D, Van Opdenbosch N (1989) J Comput Chem 10 982-1012.
37. Hagler AT, Lifson S, Dauber P (1979) J Am Chem Soc 101: 5122-30.
38. Casset F, Hamelryck T, Loris R, Brisson J-R, Tellier C, Dao-Thi M-H, Wyns L, Poortmans F, Pérez S, Imberty A (1995) J Biol Chem 270: 25619-28.
39. Dauchez M, Mazurier J, Montreuil J, Vergoten G (1992) Biochemie 74: 63-74
40. Balaji PV, Qasba PK, Rao VSR (1993) Biochemistry 32: 12599-611.
41. Asensio JL, Lôpez R, Fernândez-Mayoralas A. Jiménez-Barbero J (1994) Tetrahedron 50: 6417-32.
42. Allinger NL (1977) J Am Chem Soc 99: 8127-34.
43. Allinger NL, Yuh YH, Lii J-H (1989) J Am Chem Soc 111: 8551-66.
44. Asensio JL, Jimenez-Barbero J (1995) Biopolymers 35: 55-73.
45. Widmalm G, Venable RM (1994) Biopolymers 34: 1079-88.
46. French AD, Miller DP, Aabloo A (1993) Im J Biol Macromol 15: 30-6.
47. Kouwijzer MLCE, van Eijck BP, Kroes SJ, Kroon J (1993) J Comput Chem 14: 1281-9.
48. Koehler JEH, Saenger W, van Gunsteren WF (1988) J Biomolec Struct Dynam 6: 181-97.
49. Kouwijzer MLCE, van Eijck BP, Kooijman H, Kroon J (1995) Acta Cryst Sect B 51: 209-20.
50. Woods RJ, Edge CJ, Wormald MR, Dwek RA (1993) In Complex Carbohydrates in Drug Research (Bock K, Clausen H, Krogsgaard-Larsen P, Kofod H, eds) pp 15-36. Copenhagen: Munksgaard.
51. Woods RJ, Pathiaseril A, Wormald MR, Edge CJ, Dwek RA (1996) Eur J Biochem (submitted).
52. Stokke BT, Talashek TA, Brant DA (1994) Macromolecules 27: 1124-35.
53. Heiner AP, Sugiyama J, Teleman O (1995) Carbohydr Res 273: 207-23.
54. Ramachandran G, Schlick T (1996) DIMACS Series in Discrete Methematics and Theoretical Computer Science 23: 215-31.
55. Widmalm G, Pastor RW (1992) J Chem Soc 88: 1747-54.
56. Andrew SM, Thomasson KA, Northrup SA (1993) J Am Chem Soc 115: 5516-21.
57. Northrup SH, Thomasson KA, Miller CM (1993) Biochemistry 32: 6613-23.
58. Dwek RA (1995) Science 269: 1234-5.
59. Hart GW (1992) Curr Opin Cell Biol 4: 1017-23.
60. Sharon N, Lis H (1989) Science 246: 227-46.
61. Rademacher TW, Parekh RB, Dwek RA (1988) Ann Rev Biochem 57: 785-838.
62. Varki A (1993) Glycobiology 3: 97-130.
63. Springer TA, Lasky LA (1991) Nature 349: 196-7.
64. Quiocho FA (1986) Ann Rev Biochem 55: 287-315.
65. Lemieux RU (1989) Chem Soc Rev 18: 347-74.
66. Chervenak MC, Toone EJ (1994) J Am Chem Soc 116: 10533-9.
67. Chervenak MC, Toone EJ (1995) Biochemistry 34: 5685-95.
68. Mandai DK, Bhattacharyya L, Koenig SH, Brown RD III, Oscarson S, Brewer CF (1994) Biochemistry 33: 1157-62.
69. Mandai DK, Kishore N, Brewer CF (1994) Biochemistry 33: 1149-56.
70. Schwarz FP, Puri KD, Bhat RG, Surolia A (1993). J Biol Chem 268: 7668-77.
71. Ramkumar R, Surolia A, Podder SK (1995) Biochem J 308: 237-41.
72. Evans SV, Sigurskjold BW, Jennings HJ, Brisson J-R, To R, Tse WC, Altman E, Frosch M, Weisgerber C, Kratzin HD, Klebert S, Vaesen M, Bitter-Suermann D, Rose DR, Young NM, Bundle DR (1995) Biochemistry 34: 6737-44.
73. Bundle DR, Eichler E, Gidney MA, Meldal M, Ragauskas A, Sigurskjold BW, Sinnot B, Watson DC, Yaguchi M, Young NM (1994) Biochemistry 33: 5172-82.
74. Ito W, Kurosawa Y (1993) J Biol Chem 268: 16639-47.
75. Varki A (1992) Curr Opin Cell Biol 4: 257-66.
76. Butcher EC (1991) Cell 67: 1033-6.
77. Weis WI, Driekamer K, Hendrickson WA (1992) Nature 360: 12-34.
78. Bourne Y, Rougé P, Cambillau C (1992) J Biol Chem 267: 197-203.
79. Williams BA, Chervenak MC, Toone FJ (1992) J Biol Chem 267: 22907-11.
80. Sigurskjold BW, Bundle DR (1992) J Biol Chem 267: 8371-6.
81. Jiménez-Barbero J, Junquera E, Martin-Pastor M, Sharma S, Vicent C, Penadés S (1995) J Am Chem Soc 117: 11198-204.
82. Lemieux RU (1992) Carbohydrate Antigens ACS Symposium Series # 519 6-18.
83. Pearlman DA, Kollman PA (1989) In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (van Gunsteren WF, Weiner PK, eds) pp 101-19. The Netherlands: ESCOM.
84. Singh UC, Brown FK, Bash PA, Kollman PA (1987) J Am Chem Soc 109: 1607-14.
85. van Gunsteren F (1989) In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (van Gunsteren WF, Weiner PK, eds) pp 27-59 The Netherlands: ESCOM.
86. Straatsma TP (1996) In Reviews in Computational Chemistry (Boyd DB. Lipkowitz K, eds) New York: VCH, pp 81-127.
87. Mizushima N, Spellmeycr D, Hirono S, Pearlman D, Kollman P (1991) J Biol Chem 266: 11801-9.
88. Miyamoto S, Kollman P (1993) Proteins 16: 226-45.
89. Woods RJ, Pathiaseril A (1996) (unpublished data).
90. Wessels MR, Pozsgay V, Kasper DL, Jennings HJ (1987) J Biol Chem 262: 8262-7.
91. Peters T, Pinto BM (1996) Curr Opin Struct Biol 6: 710-20.
92. Woods RJ (1995) Curr Opin Struct Biol 5: 591-8.
93. Pérez S, Imberty A, Carver JP (1994) Advan Comput Biol 1: 147-202.
94. Krench AD, Brady JW (1990) Computer Modeling of Carbohydrate Molecules (American Chemical Society Washington DC).