Molecular Modeling in Glycoscience

Comprehensive Glycoscience: From Chemistry to Systems Biology

Volumn 2-4, Issue , 2007, Pages 347-388

  Perez S ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955714861     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-044451967-2/00031-3     Document Type: Chapter

References (176)

1. Pérez S., Gautier C., Imberty A. Oligosaccharide conformations by diffraction methods. Oligosaccharides in Chemistry and Biology: A Comprehensive Handbook 2000, 969-1001. Wiley/VCH, Weinheim. B. Ernst, G. Hart, P. Sinay (Eds.).
2. Peters T., Pinto B.M. Curr. Opin. Struct. Biol. 1996, 6:710-720.
3. Rice K.G., Wu P., Brand L., Lee Y.C. Curr. Opin. Struct. Biol. 1993, 3:669-674.
4. Lemieux R.U., Bock K., Delbaere L.T.J., Koto S., Rao V.S.R. Can. J. Chem. 1980, 58:631-653.
5. Woods R.J. The application of molecular modeling techniques to the determination of oligosaccharide solution conformations. Reviews in Computational Chemistry 1996, Vol. 9:129-165. VCH, New York. K. Lipkowitz, D.B. Boyd (Eds.).
6. Perez S., Kouwijzer M.L. Shapes and Interactions of Polysaccharide Chains 1999, 258-293. Kluwer.
7. Perez S. Oligosaccharides and Polysaccharides Conformations by Diffraction Methods 2006.
8. Laine R.A. Glycobiology 1994, 4(6):759-767.
9. Bohne A., Lang E., von der Lieth C.W. J. Mol. Model. 1998, 4:33-43.
10. Engelsen S.B., Cros S., Mackie W., Pérez S. Biopolymers 1996, 39:417-433.
11. Imberty A., Bettler E., Karababa M., Mazeau K., Petrova P., Pérez S. Building sugars: The sweet part of structural biology. Perspectives in Structural Biology 1999, 392-409. Indian Academy of Sciences and Universities Press, Hyderabad. M. Vijayan, N. Yathindra, A.S. Kolaskar (Eds.).
12. Cremer D., Pople J.A. J. Am. Chem. Soc. 1975, 97:1354-1358.
13. Carbohydr. Res. 1997, 297:1-92. IUPAC-IUB.
14. Lemieux R.U., Koto S., Voisin D. The exo-anomeric effect. Anomeric Effect: Origin and Consequence 1979, 17-29. American Chemical Society, Washington, DC, ACS Symposium Series No. 87. W.A. Szarek, D. Horton (Eds.).
15. Tvaroska I., Bleha T. Adv. Carbohydr. Chem. Biochem. 1989, 47:45-123.
16. Allinger N.L. J. Am. Chem. Soc. 1977, 99:8127-8134.
17. Allinger N.L., Rahman M., Lii J.-H. J. Am. Chem. Soc. 1990, 112:8293-8307.
18. Allinger N.L., Yuh Y.H., Lii J.-H. J. Am. Chem. Soc. 1989, 111:8551-8566.
19. Allinger N.L., Zhu Z.-Q., Chen K. J. Am. Chem. Soc. 1990, 112:6120-6133.
20. Tvaroska I., Pérez S. Carbohydr. Res. 1986, 149:389-410.
21. van Gunsteren W.F. GROMOS: Groningen Molecular Simulation Program Package 1987, University of Groningen, Groningen.
22. Ott K.-H., Meyer B. J. Comput. Chem. 1996, 17:1068-1084.
23. Brooks B., Bruccoleri R., Olafson B., States D., Swaminathan S., Karplus M. J. Comput. Chem. 1983, 4:187-217.
24. Ha S.N., Giammona A., Field M., Brady J.W. Carbohydr. Res. 1988, 180:207-221.
25. Reiling S., Schlenkrich M., Brickmann J. J. Comput. Chem. 1996, 17:450-468.
26. Grootenhuis P.D.J., Haasnoot C.A.G. Mol. Simul. 1993, 10:75-95.
27. Kouwijzer M.L.C.E., Grootenhuis P.D.J. J. Phys. Chem. 1995, 99:13426-13436.
28. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., Weiner P. J. Am. Chem. Soc. 1984, 106:765-784.
29. Homans S.W. Biochemistry 1990, 29(39):9110-9118.
30. Glennon T.M., Zheng Y.-J., Le Grand S.M., Schutzberg B.A., Merz K.M. J. Comput. Chem. 1994, 15:1019-1040.
31. Momany F.A., Willett J.L. Carbohydr. Res. 2000, 326:194-209.
32. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., Woods R.J. J. Comput. Chem. 2005, 26(16). 1668-88.
33. Mohamadi F., Richards N.G.H., Guida W.C., Liskamp R., Lipton M., Caufield C., Chang G., Hendrickson T., Still W.C. J. Comput. Chem. 1990, 11:440-467.
34. Senderowitz H., Still W.C. J. Org. Chem. 1997, 62:1427-1438.
35. Lifson S., Warshel A. J. Chem. Phys. 1968, 49:5116.
36. Fabricius J., Engelsen S.B., Rasmussen K. J. Carbohydr. Chem. 1997, 16:751-772.
37. Kildeby K., Melberg S., Rasmussen K. Acta Chem. Scand. 1977, A31:1-13.
38. Dauchez M., Derreumaux P., Lagant P., Vergoten G. J. Comput. Chem. 1995, 16:188-199.
39. Clark M., Cramer R.D.I., van den Opdenbosch N. J. Comput. Chem. 1989, 10(8):982-1012.
40. Imberty A., Hardman K.D., Carver J.P., Pérez S. Glycobiology 1991, 1:456-484.
41. Pérez S., Meyer C., Imberty A. Practical tools for accurate modeling of complex carbohydrates and their interactions with proteins. Modeling of Biomolecular Structures and Mechanisms 1995, 425-454. Kluwer, Dordrecht. A. Pullman, J. Jortner, B. Pullman (Eds.).
42. Hwang M.-J., Ni X., Waldman M., Ewig C.S., Hagler A.T. Biopolymers 1998, 45:435-468.
43. Mayo S.L., Olafson B.D., Goddard W.A.I. J. Phys. Chem. 1990, 94:8897-8909.
44. Jorgensen W.L., Maxwell D.S., Tirado-Rives J. J. Am. Chem. Soc. 1996, 118:11225-11236.
45. Damm W., Frontera A., Tirado-Rives J., Jorgensen W.L. J. Comput. Chem. 1997, 18:1955-1970.
46. Halgren T.A. J. Comput. Chem. 1996, 17:490-641.
47. Pérez S., Imberty A., Engelsen S.B., Gruza J., Mazeau K., Jiménez-Barbero J., Poveda A., Espinosa J.F., van Eyck B.P., Jonhson G., et al. Carbohydr. Res. 1998, 314:141-155.
48. Von der Lieth C.-W., Kozar T., Hull W.E. J. Mol. Struct. (Theochem) 1997, 395-396:225-244.
49. French A.D. Biopolymers 1988, 27:1519-1525.
50. Kozár T., Petrák F., Gálová Z., Tvaroska I. Carbohydr. Res. 1990, 204:27-36.
51. Stortz C.A. Carbohydr. Res. 1999, 322(1-2):77-86.
52. Koca J. J. Mol. Struct. (Theochem) 1994, 308:13-24.
53. Koca J. Progr. Biophys. Mol. Biol. 1998, 70:137-173.
54. Engelsen S.B., Koca J., Braccini I., Hervé du Penhoat C., Pérez S. Carbohydr. Res. 1995, 276:1-29.
55. Peters T., Meyer B., Stuike-Prill R., Somorjai R., Brisson J.R. Carbohydr. Res. 1993, 238:49-73.
56. Weimar T., Meyer B., Peters T. J. Biomolec. NMR. 1993, 3:399-414.
57. Frank M., Gutbrod P., Hassayoun C., von der Lieth C.W. J. Mol. Model (Online) 2003, 9(5). 308-15.
58. Nahmany A., Strino F., Rosen J., Kemp G.J., Nyholm P.G. Carbohydr. Res. 2005, 340(5):1059-1064.
59. Lamarck J.B. Philosophie Zoologique 1809.
60. Michell T. Machine Learning 1997, 259-283. McGraw Hill, New York.
61. Rosen J., Robobi A., Nyholm P.G. Carbohydr. Res. 2002, 337(18):1633-1640.
62. Rosen J., Robobi A., Nyholm P.G. Carbohydr. Res. 2004, 339(5):961-966.
63. Strino F., Nahmany A., Rosen J., Kemp G.J., Sa-correia I., Nyholm P.G. Carbohydr. Res. 2005, 340(5):1019-1024.
64. Strino, F., Rosen, J., Nordstrom, R., Nyholm, P.G. In preparation.
65. Orozco M., Alhambra C., Barril X., Lopez J.M., Busquets M.A., Luque F.J. J. Mol. Model. 1996, 1:1-15.
66. Tvaroska I., Kozar T. J. Am. Chem. Soc. 1980, 102:6929-6936.
67. Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. J. Am. Chem. Soc. 1990, 112:6127-6129.
68. Höög C., Widmalm G. Glycoconj. J. 1998, 15:183-186.
69. Stenutz R., Widmalm G. Glycoconj. J. 1998, 15:415-418.
70. Grigera J.R. J. Chem. Soc. Perkin Trans. 1 1988, 84:2603-2608.
71. Brady J.W. J. Am. Chem. Soc. 1989, 111:5155-5165.
72. van Eijck B.P., Kroon J. J. Mol. Struct. 1989, 195:133-146.
73. Ott K.H., Meyer B. Carbohydr. Res. 1996, 281:11-34.
74. Brady J.W., Schmidt R.K. J. Phys. Chem. 1993, 97:958-966.
75. Corzana F., Motawia M.S., Herve du Penhoat C., Perez S., Tscampel S.M., Woods R.J., Engelsen S.B. J. Comput. Chem. 2004, 25:573-586.
76. Engelsen S.B., Hervé du Penhoat C., Pérez S. J. Phys. Chem. 1995, 99:13334-13351.
77. Immel S., Lichtenthaler F.W. Liebigs Ann. 1995, 1925-1937.
78. Kroon-Batenburg L.M.J., Kroon J., Leeflang B.R., Vliegenthart J.F. Carbohydr. Res. 1993, 245:1925-1937.
79. Liu Q., Schmidt R.K., Teo B., Karplus P.A., Brady J.W. J. Am. Chem. Soc. 1997, 119:7851-7862.
80. Engelsen S.B., Perez S. J. Phys. Chem. 2000, B 104:9301-9311.
81. Naidoo K.J., Brady J.W. J. Am. Chem. Soc. 1999, 121:2244-2252.
82. Ueda K., Brady J.W. Biopolymers 1996, 38(4):461-469.
83. Vishnyakov A., Widmalm G., Kowalewski J., Laaksonen A. J. Am. Chem. Soc. 1999, 121:5403-5412.
84. Spronk B.A., Rivera-Sagredo A., Kamerling J.P., Vliegenthart J.F. Carbohydr. Res. 1995, 273(1):11-26.
85. Almond A., Sheehan J.K., Brass A. Glycobiology 1997, 7:597-604.
86. Kaufmann J., Möhle K., Hofmann H.-J., Arnold K. J. Mol. Struct. (Theochem) 1998, 422:109-121.
87. Corzana F., Motawia M.S., Herve du Penhoat C., van den Berg F., Blennow A., Perez S., Engelsen S.B. J. Am. Chem. Soc. 2004, 126:13144-13155.
88. Petrova P., Koca J., Imberty A. Eur. J. Biochem. 2001, 268:5365-5374.
89. Jorgensen W.L., Chandresekhar J., Madura J.D., Impey R.W., Klein M.L. J. Chem. Phys. 1983, 79:926-935.
90. Engelsen S.B., Monteiro C., Herve de Penhoat C., Perez S. Biophys. Chem. 2001, 93(2-3):103-127.
91. Engelsen S.B. Molecular Dynamics Simulations of Carbohydrate-Water Interactions 2001, 53-89.
92. Anderson C.A., Engelsen S.B. J. Mol. Graph. Model 1999, 17:101-105.
93. Goodford P.J. J. Med. Chem. 1985, 28(7):849-857.
94. Dheu-Andries M.-L., Perez S. Carbohydr. Res. 1983, 124:324-332.
95. Braccini I., Grasso R.P., Perez S. Carbohydr. Res. 1999, 317(1-4):119-130.
96. Braccini I., Perez S. Biomacromolecules 2001, 2(4):1089-1096.
97. Brant D.A. Q. Rev. Biophys. 1976, 9:527-596.
98. Kumar S., Muchmore A. Kidney Int. 1990, 37(6):1395-1401.
99. Easton R.L., Patankar M.S., Lattanzio F.A., Leaven T.H., Morris H.R., Clark G.F., Dell A. J. Biol. Chem. 2000, 275(11):7731-7742.
100. Mitoma J., Petryniak B., Hiraoka N., Yeh J.C., Lowe J.B., Fukuda M. J. Biol. Chem. 2003, 278(11):9953-9961.
101. Cioci G., Rivet A., Koca J., Perez S. Carbohydr. Res. 2004, 339(5):949-959.
102. O'Neill M.A., Warrenfeltz D., Kates K., Pellerin P., Doco T., Darvill A.G., Albersheim P. J. Biol. Chem. 1996, 271:22923-22930.
103. Pellerin P., Doco T., Vidal S., Williams P., Brillouet J.-M., O'Neill M.A. Carbohydr. Res. 1996, 299:183-197.
104. Mazeau K., Pérez S. Carbohydr. Res. 1998, 311:203-217.
105. Herve du Penhoat C., Gey C., Pellerin P., Perez S. J. Biomol. NMR 1999, 14:253-271.
106. Vidal S., Doco T., Williams P., Pellerin P., York W.S., O'Neill M.A., Glushka J., Darvill A.G., Albersheim P. Carbohydr. Res. 2000, 326:277-294.
107. Rodriguez-Carvajal M.A., Herve du Penhoat C., Mazeau K., Doco T., Perez S. Carbohydr. Res. 2003, 338:651-671.
108. Perez S., Rodriguez-Carvajal M.A., Doco T. Biochimie 2003, 85:109-121.
109. Homans S.W., Ferguson M.A., Dwek R.A., Rademacher T.W., Anand R., Williams A.F. Nature 1988, 333(6170):269-272.
110. Chevalier F., Lopez-Prados J., Perez S., Martin-Lomas M., Nieto P.M. Eur. J. Org. Chem. 2005, 15:3489-3498.
111. Chevalier F., Lopez-Prados J., Grooves P., Perez S., Martin-Lomas M., Nieto P.M. Structure and Dynamics of a GPI Anchor Moiety Inserted into a Micelle 2006, (in press).
112. Rees D.A., Morris E.R., Thom D., Madden J.K. Glycobiology 2006, 16:969-980.
113. Burton B.A., Brant D.A. Biopolymers 1983, 22:1769-1792.
114. Brant D.A., Christ M.D. Realistic Conformational Modeling of Carbohydrates 1990, 42-68. American Chemical Society, Washington, DC.
115. Gagnaire D., Pérez S., Tran V. Carbohyd. Polym. 1982, 2:271-291.
116. Levy S., York W.S., Stuike-Prill R., Meyer B., Staehelin L.A. Plant J. 1991, 1:195-215.
117. Urbani R., Cesaro A. Polymers 1991, 32:3013-3020.
118. Robijn G.W., Imberty A., van den Berg D.J., Ledeboer A.M., Kamerling J.P., Vliegenthart J.F., Pérez S. Carbohydr. Res. 1996, 288:57-74.
119. Mazeau K., Pérez S., Rinaudo M. J. Carbohydr. Chem. 2000, 19:1269-1284.
120. Haxaire K., Braccini I., Milas M., Rinaudo M., Pérez S. Glycobiology 2000, 10:587-594.
121. Cros S., Garnier C., Axelos M.A., Imberty A., Pérez S. Biopolymers 1996, 39(3):339-352.
122. Ruggiero J.R., Urbani R., Cesaro A. Int. J. Biol. Macromol. 1995, 4:213-217.
123. Boutherin B., Mazeau K., Tvaroska I. Carbohydr. Polym. 1997, 32:255-266.
124. French A.D., Murphy V.G. Polymer 1977, 18:489-494.
125. Smith P.J.C., Arnott S. Acta Crystallogr. 1978, A34:3-11.
126. Zugenmaier P., Sarko A. Biopolymers 1976, 15:2121-2136.
127. Pérez S. Polysaccharides-Water Interactions 1993, 295-320. The Macmillan Press.
128. Jeffrey G.A., Saenger W. Hydrogen Bonding in Biological Structures 1991, Springer, Berlin.
129. Holmbeck S.M.A., Petillo P.A., Lerner L.E. Biochemistry 1994, 33:14246-14255.
130. Miertus S., Bella J., Toffanin R., Matulova M., Paoletti S. J. Mol. Struct. (Theochem) 1997, 395-396:437-449.
131. Cowman M.K., Hittner D.M., Feter-Davis J. Macromolecules 1996, 29:2894-2902.
132. Sicinska W., Lerner L.E. Carbohydr. Res. 1996, 286:151-159.
133. Pérez S., Imberty A., Scaringe R.P. Modeling of interactions of polysaccharide chains: Application to the crystalline polymorphism of starch granules. Computer Modelling of Carbohydrate Molecules 1990, Vol. 430:281-299. ACS, Washington, DC. A.D. French, J.W. Brady (Eds.).
134. Vietor R.J., Mazeau K., Lakin M., Perez S. Biopolymers 2000, 54:342-354.
135. Kouwijzer M., Perez S. Biopolymers 1998, 46:11-29.
136. Braccini I., Rodriguez-Carvajal M.A., Perez S. Biomacromolecules 2005, 6:1322-1328.
137. Bourne Y., Roussel A., Frey M., Rougé P., Fontecilla-Camps J.C., Cambillau C. Proteins 1990, 8(4):365-376.
138. Bourne Y., Mazurier J., Legrand D., Rougé P., Montreuil J., Spik G., Cambillau C. Structure 1994, 2(3):209-219.
139. Imberty A., Pérez S. Chem. Rev. 2000, 100:4567-4588.
140. Imberty A., Gautier C., Lescar J., Pérez S., Wyns L., Loris R. J. Biol. Chem. 2000, 275:17541-17548.
141. Kjellen L., Lindahl U. Annu. Rev. Biochem. 1991, 60:443-475.
142. Lane D.A., Lindhal U. Heparin 1989, Edward Arnold, London.
143. Conrad H.E. Heparin-Binding Proteins 1998, Academic Press, San Diego.
144. Choay J., Petitou M., Lormeau J.-C., Sinay P., Casu B., Gatti G. Biochem. Biophys. Res. Commun. 1983, 116:492-499.
145. Thunberg L., Bäckström G., Lindahl U. Carbohydr. Res. 1982, 100:393-410.
146. Ragazzi M., Ferro D.R., Perly B., Sinay P., Petitou M., Choay J. Carbohydr. Res. 1990, 195:169-185.
147. Cros S., Petitou M., Sizun P., Pérez S., Imberty A. Bioorg. Med. Chem. 1997, 5(7):1301-1309.
148. Hricovini M., Torri G. Carbohydr. Res. 1995, 268:159-175.
149. Hricovini M., Guerrini M., Bisio A. Eur. J. Biochem. 1999, 261:789-801.
150. Skinner R., Abrahams J.P., Whisstock J.C., Lesk A.M., Carrell R.W., Wardell M.R. J. Mol. Biol. 1997, 266:601-609.
151. Grootenhuis P.D.J., van Boeckel C.A.A. J. Am. Chem. Soc. 1991, 113:2743-2747.
152. Bitomsky W., Wade R.C. J. Am. Chem. Soc. 1999, 121. 3004-301.
153. Jin L., Abrahams J.P., Skinner R., Petitou M., Pike R.N., Carrell R.W. Proc. Natl. Acad. Sci. USA 1997, 23:14683-14688.
154. Lam K., Rao V.S.R., Qasba P.K. J. Biomol. Struct. Dyn. 1998, 15:1009-1027.
155. Huhtala M.T., Pentikainen O.T., Johnson M.S. Structure 1999, 7:699-709.
156. Stuckey J.A., St. Charles R., Edwards B.F. Proteins 1992, 14:277-287.
157. Lortat-Jacob H., Grosdidier A., Imberty A. Proc. Nat. Acad. Sci. USA 2002, 99:1229-1234.
158. Eur. J. Biochem. 1982, 126:433-437. IUPAC-IUB.
159. J. Biol. Chem. 1982, 257:3347-3351. JCBN.
160. Eur. J. Biochem. 1982, 126:439-441. JCBN.
161. Sharon N. Eur. J. Biochem. 1986, 159:1-6.
162. Doubet S.B.K., Smith D., Darvill A., Albersheim P. Trends Biochem. Sci. 1989, 14:475-477.
163. Cooper C.A., Joshi H.J., Harrison M.J., Wilkins M.R., Packer N.H. Nucleic Acids Res. 2003, 31:511-513.
164. Bohne-Lang A., Lang E., Forster T., der Lieth C.W. Carbohydr. Res. 2001, 336:1-11.
165. Banin E., Neuberger Y., Althuser Y., Halevi A., Inbar O., Dotan N., Avinoam D. Trends Glycosci. Glycotech. 2002, 14:127-137.
166. French A.D., Tran V. Biopolymers 1990, 29:1599-1611.
167. Marchessault R.H., Perez S. Biopolymers 1979, 18:2369-2374.
168. Rosen, J. PhD Dissertation, 2005, University of Goteborg, Sweden.
169. Koca J., Pérez S., Imberty A. J. Comp. Chem. 1995, 16:296-310.
170. Darvill A.G., McNeil M., Albersheim P. Plant Physiol. 1978, 62:418-422.
171. Blundell T., Carney D., Gardner S., Hayes F., Howlin B., Hubbard T., Overington J., Singh D.A., Sibanda B.L., Sutcliffe M. Eur. J. Biochem. 1988, 172:513-520.
172. SYBYL Tripos Associates, S. H. R., Suite 303, St. Louis, MO 63144, USA.
173. Loris R., Stas P.P., Wyns L. J. Biol. Chem. 1994, 269:26722-26733.
174. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. J. Appl. Crystall. 1993, 26:283-291.
175. Lortat-Jacob H., Grosdidier A., Imberty A. Proc. Natl. Acad. Sci. USA 2002, 99:1229-1234.
176. Pérez S., Mulloy B. Curr. Opin. Struct. Biol. 2005, 15:517-524.