Conformation of glycopeptides and glycoproteins

Topics in Current Chemistry

Volumn 267, Issue , 2006, Pages 187-251

  Meyer, Bernd ^a   Möller, Heiko ^b  

^a UNIVERSITY OF HAMBURG   (Germany)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Glycopeptide; Glycoprotein; Molecular modeling; NMR spectroscopy; X ray crystallography

Indexed keywords

EID: 85014310281     PISSN: 23650869     EISSN: 23648961     Source Type: Journal    
DOI: 10.1007/128_2006_078     Document Type: Article

References (176)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235
2. Apweiler R, Hermjakob H, Sharon N (1999) Biochim Biophys Acta 1473:4
3. Dwek RA (1998) Dev Biol Stand 96:43
4. Borman S (2005) Chem Eng News 83:41–50
5. Bush CA, Martin-Pastor M, Imberty A (1999) Annu Rev Biophys Biomol Struct 28:269
6. Wyss DF, Wagner G (1996) Curr Opin Biotechnol 7:409
7. Imperiali B, O’Connor SE (1999) Curr Opin Chem Biol 3:643
8. Haase C, Seitz O (2007) Top Curr Chem (in this volume)
9. Duus J, Gotfredsen CH, Bock K (2000) Chem Rev 100:4589
10. Woods RJ (1998) Glycoconj J 15:209
11. Imberty A, Pérez S (2000) Chem Rev 100:4567
12. Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RA (2002) Chem Rev 102:371
13. Liu HL, Hsu JP (2005) Proteomics 5:2056
14. Heinemann U, Illing G, Oschkinat H (2001) Curr Opin Biotechnol 12:348
15. Sattler M, Schleucher J, Griesinger C (1999) Prog NMR Spectrosc 34:93
16. Dauter Z (2006) Acta Crystallogr D Biol Crystallogr 62:1
17. Williams SP, Kuyper LF, Pearce KH (2005) Curr Opin Chem Biol 9:371
18. Grogan MJ, Pratt MR, Marcaurelle LA, Bertozzi CR (2002) Annu Rev Biochem 71:593
19. Fletcher CM, Harrison RA, Lachmann PJ, Neuhaus D (1994) Structure 2:185
20. Imberty A, Pérez S (1995) Protein Eng 8:699
21. Rudd PM, Morgan BP, Wormald MR, Harvey DJ, van den Berg CW, Davis SJ, Ferguson MA, Dwek RA (1997) J Biol Chem 272:7229
22. Yokoyama S (2003) Curr Opin Chem Biol 7:39
23. Pickford AR, O’Leary JM (2004) Methods Mol Biol 278:17
24. Li P, Gao XG, Arellano RO, Renugopalakrishnan V (2001) Protein Expr Purif 22:369
25. Jarvis DL (2003) Virology 310:1
26. Lustbader JW, Birken S, Pollak S, Pound A, Chait BT, Mirza UA, Ramnarain S, Canfield RE, Brown JM (1996) J Biomol NMR 7:295
27. Hansen AP, Petros AM, Mazar AP, Pederson TM, Rueter A, Fesik SW (1992) Biochemistry 31:12713
28. Wyss DF, Choi JS, Li J, Knoppers MH, Willis KJ, Arulanandam AR, Smolyar A, Reinherz EL, Wagner G (1995) Science 269:1273
29. Wood MJ, Komives EA (1999) J Biomol NMR 13:149
30. Cubeddu L, Moss CX, Swarbrick JD, Gooley AA, Williams KL, Curmi PM, Slade MB, Mabbutt BC (2000) Protein Expr Purif 19:335
31. Wendeler M, Hoernschemeyer J, John M, Werth N, Schoeniger M, Lemm T, Hart-mann R, Kessler H, Sandhoff K (2004) Protein Expr Purif 34:147
32. Laroche Y, Storme V, De Meutter J, Messens J, Lauwereys M (1994) Biotechnology (NY) 12:1119
33. McAlister MS, Davis B, Pfuhl M, Driscoll PC (1998) Protein Eng 11:847
34. Weikert S, Papac D, Briggs J, Cowfer D, Tom S, Gawlitzek M, Lofgren J, Mehta S, Chisholm V, Modi N, Eppler S, Carroll K, Chamow S, Peers D, Berman P, Krummen L (1999) Nat Biotechnol 17:1116
35. Xu R, Hanson SR, Zhang Z, Yang YY, Schultz PG, Wong CH (2004) J Am Chem Soc 126:15654
36. Zhang Z, Gildersleeve J, Yang YY, Xu R, Loo JA, Uryu S, Wong CH, Schultz PG (2004) Science 303:371
37. Meinjohanns E, Meldal M, Paulsen H, Dwek RA, Bock K (1998) J Chem Soc Perkin Trans 1:549
38. George SK, Schwientek T, Holm B, Reis CA, Clausen H, Kihlberg J (2001) J Am Chem Soc 123:11117
39. Thayer DA, Wong CH (2007) Top Curr Chem (in this volume)
40. Warren DJ, Geng X, Danishefsky SJ (2007) Top Curr Chem (in this volume)
41. Pratt MR, Bertozzi CR (2005) Chem Soc Rev 34:58
42. Holemann A, Seeberger PH (2004) Curr Opin Biotechnol 15:615
43. Herzner H, Reipen T, Schultz M, Kunz H (2000) Chem Rev 100:4495
44. Dawson PE, Muir TW, Clark-Lewis I, Kent SB (1994) Science 266:776
45. Evans TC Jr, Benner J, Xu MQ (1998) Protein Sci 7:2256
46. Macmillan D, Bertozzi CR (2004) Angew Chem Int Ed Engl 43:1355
47. Hojo H, Watabe J, Nakahara Y, Nakahara Y, Ito Y, Nabeshima K, Toole BP (2001) Tetrahedron Lett 42:3001
48. Hackenberger CP, Friel CT, Radford SE, Imperiali B (2005) J Am Chem Soc 127:12882
49. Smith KD, Davies MJ, Hounsell EF (1994) Methods Mol Biol 32:143
50. Dell A, Morris HR (2001) Science 291:2351
51. Peter-Katalinic J (2005) Methods Enzymol 405:139
52. Rudd PM, Dwek RA (1997) Curr Opin Biotechnol 8:488
53. Gallego RG, Blanco JL, Thijssen-van Zuylen CW, Gotfredsen CH, Voshol H, Duus JO, Schachner M, Vliegenthart JF (2001) J Biol Chem 276:30834
54. Halkes KM, Gotfredsen CH, Grotli M, Miranda LP, Duus JO, Meldal M (2001) Chemistry 7:3584
55. Wüthrich K (1986) NMR of Proteins and Nucleic Acids. Wiley, New York
56. Kessler H, Seip S (1994) NMR of Peptides. In: Croasmun WR, Carlson RMK (eds) Two-Dimensional NMR Spectroscopy. VCH, New York, p 619
57. Leeflang BR, Faber EJ, Erbel P, Vliegenthart JF (2000) J Biotechnol 77:115
58. Seavey BR, Farr EA, Westler WM, Markley JL (1991) J Biomol NMR 1:217
59. Yamaguchi Y, Takizawa T, Kato K, Arata Y, Shimada I (2000) J Biomol NMR 18:357
60. Bock K, Thoegersen H (1982) Annu Rep NMR Spectrosc 13:1
61. Bock K, Pedersen C (1983) Adv Carbohydr Chem Biochem 41:27
62. Prytulla S, Lambert J, Lauterwein J, Klessinger M, Thiem J (1990) Magn Reson Chem 28:888
63. Prytulla S, Lauterwein J, Klessinger M, Thiem J (1991) Carbohydr Res 215:345
64. Haverkamp J, Spoormaker T, Dorland L, Vliegenthart JFG, Schauer R (1979) J Am Chem Soc 101:4851
65. Lommerse JP, van Rooijen JJ, Kroon-Batenburg LM, Kamerling JP, Vliegenthart JF (2002) Carbohydr Res 337:2279
66. Homans SW (1992) Glycobiology 2:153
67. Milton MJ, Harris R, Probert MA, Field RA, Homans SW (1998) Glycobiology 8:147
68. Harris R, Rutherford TJ, Milton MJ, Homans SW (1997) J Biomol NMR 9:547
69. Poppe L, van Halbeek H (1991) J Magn Reson 92:636–41
70. Poppe L, van Halbeek H (1991) J Magn Reson 93:214–17
71. Martin-Pastor M, Bush CA (1999) Biochemistry 38:8045
72. Bose B, Zhao S, Stenutz R, Cloran F, Bondo PB, Bondo G, Hertz B, Carmichael I, Serianni AS (1998) J Am Chem Soc 120:11158
73. Xu Q, Gitti R, Bush CA (1996) Glycobiology 6:281
74. Mulloy B, Frenkiel TA, Davies DB (1988) Carbohydr Res 184:39
75. Tvaroska I, Hricovini H, Perakova E (1989) Carbohydr Res 189:359
76. Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1995) Proc Natl Acad Sci USA 92:9279
77. Tjandra N, Bax A (1997) Science 278:1111
78. Prestegard JH, Bougault CM, Kishore AI (2004) Chem Rev 104:3519
79. de Alba E, Tjandra N (2002) Prog Nucl Magn Reson 40:175
80. Griesinger C, Peti W, Meiler J, Bruschweiler R (2004) Methods Mol Biol 278:107
81. Deschamps M, Campbell ID, Boyd J (2005) J Magn Reson 172:118
82. Meiler J, Prompers JJ, Peti W, Griesinger C, Bruschweiler R (2001) J Am Chem Soc 123:6098
83. Peti W, Meiler J, Bruschweiler R, Griesinger C (2002) J Am Chem Soc 124:5822
84. Azurmendi HF, Bush CA (2002) Carbohydr Res 337:905
85. Almond A, Duus JO (2001) J Biomol NMR 20:351
86. Almond A, Petersen BO, Duus JO (2004) Biochemistry 43:5853
87. Reif B, Hennig M, Griesinger C (1997) Science 276:1230
88. Reif B, Diener A, Hennig M, Maurer M, Griesinger C (2000) J Magn Reson 143:45
89. Scheurer C, Skrynnikov NR, Lienin SF, Straus SK, Bruschweiler R, Ernst RR (1999) J Am Chem Soc 121:4242
90. Markwick PR, Sprangers R, Sattler M (2005) Angew Chem Int Ed Engl 44:3232
91. Kover KE, Batta G, Kowalewski J, Ghalebani L, Kruk D (2004) J Magn Reson 167:273
92. Larsson EA, Urbina F, Yang Z, Weintraub A, Widmalm G (2004) Carbohydr Res 339:1491
93. Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC (2005) Structure (Camb) 13:197
94. Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, Harrison SC (2005) Nature 433:834
95. Case DA, Cheatham TE III, Darden T, Gohlke H, Luo R, Merz KM Jr., Onufriev A, Simmerling C, Wang B, Woods RJ (2005) J Comput Chem 26:1668
96. Homans SW (1990) Biochemistry 29:9110
97. Woods RJ, Dwek RA, Edge CJ, Fraser-Reid B (1995) J Phys Chem 99:3832
98. Glennon TM, Merz KMJ (1997) Theochem 395–396:157
99. Momany FA, Willett JL (2000) Carbohydr Res 326:194
100. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comp Chem 4:187
101. Ha SN, Giammona A, Field M, Brady JW (1988) Carbohydr Res 180:207
102. Reiling S, Schlenkrich M, Brickmann J (1996) J Comp Chem 17:450
103. Christen M, Hunenberger PH, Bakowies D, Baron R, Burgi R, Geerke DP, Heinz TN, Kastenholz MA, Krautler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF (2005) J Comput Chem 26:1719
104. Ott K-H, Meyer B (1996) J Comp Chem 17:1068
105. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 118:11225
106. Damm W, Frontera A, Tirado-Rives J, Jorgensen WL (1997) J Comp Chem 18:1955
107. Clark M, Cramer RDI, Van Opdenbosch N (1989) J Comp Chem 10:982
108. Imberty A, Hardman KD, Carver JP, Pérez S (1991) Glycobiology 1:631
109. Pérez S, Imberty A, Engelsen SB, Gruza J, Mazeau K, Jimenez-Barbero J, Poveda A, Espinosa J-F, Van Eyck BP, Johnson G, French AD, Kouwijzer MLCE, Grootenuis PDJ, Bernardi A, Raimondi L, Senderowitz H, Durier V, Vergoten G, Rasmussen K (1998) Carbohydr Res 314:141
110. van Gunsteren WF, Brunne RM, Gros P, van Schaik RC, Schiffer CA, Torda AE (1994) Methods Enzymol 239:619
111. Weis WI, Brunger AT, Skehel JJ, Wiley DC (1990) J Mol Biol 212:737
112. Erbel PJ, Karimi-Nejad Y, van Kuik JA, Boelens R, Kamerling JP, Vliegenthart JF (2000) Biochemistry 39:6012
113. Petrescu AJ, Petrescu SM, Dwek RA, Wormald MR (1999) Glycobiology 9:343
114. Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MR (2004) Glycobiology 14:103
115. Wormald MR, Wooten EW, Bazzo R, Edge CJ, Feinstein A, Rademacher TW, Dwek RA (1991) Eur J Biochem 198:131
116. Davis JT, Hirani S, Bartlett C, Reid BR (1994) J Biol Chem 269:3331
117. Kessler H, Matter H, Gemmecker G, Kling A, Kottenhahn M (1991) J Am Chem Soc 113:7550
118. Christlet TH, Biswas M, Veluraja K (1999) Acta Crystallogr D Biol Crystallogr 55(Pt8):1414
119. Bause E, Legler G (1981) Biochem J 195:639
120. Marshall RD (1972) Annu Rev Biochem 41:673
121. Berman H, Henrick K, Nakamura H (2003) Nat Struct Biol 10:980
122. Loss A, Bunsmann P, Bohne A, Loss A, Schwarzer E, Lang E, von der Lieth CW (2002) Nucleic Acids Res 30:405
123. Raman R, Venkataraman M, Ramakrishnan S, Lang W, Raguram S, Sasisekharan R (2006) Glycobiology 16:82R
124. Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M (2006) Glycobiology 16:63R
125. Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE (1999) Nucleic Acids Res 27:370
126. Julenius K, Molgaard A, Gupta R, Brunak S (2005) Glycobiology 15:153
127. Cooper CA, Joshi HJ, Harrison MJ, Wilkins MR, Packer NH (2003) Nucleic Acids Res 31:511
128. Doubet S, Bock K, Smith D, Darvill A, Albersheim P (1989) Trends Biochem Sci 14:475
129. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA (1998) Nature 393:648
130. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA, Sodroski JG (1998) Nature 393:705
131. Kwong PD, Wyatt R, Sattentau QJ, Sodroski J, Hendrickson WA (2000) J Virol 74:1961
132. Huang CC, Tang M, Zhang MY, Majeed S, Montabana E, Stanfield RL, Dimitrov DS, Korber B, Sodroski J, Wilson IA, Wyatt R, Kwong PD (2005) Science 310:1025
133. Lin PF, Blair W, Wang T, Spicer T, Guo Q, Zhou N, Gong YF, Wang HG, Rose R, Ya-manaka G, Robinson B, Li CB, Fridell R, Deminie C, Demers G, Yang Z, Zadjura L, Meanwell N, Colonno R (2003) Proc Natl Acad Sci USA 100:11013
134. Withka JM, Wyss DF, Wagner G, Arulanandam AR, Reinherz EL, Recny MA (1993) Structure 1:69
135. Wyss DF, Dayie KT, Wagner G (1997) Protein Sci 6:534
136. Kitao A, Wagner G (2000) Proc Natl Acad Sci USA 97:2064
137. Sun ZY, Dotsch V, Kim M, Li J, Reinherz EL, Wagner G (1999) EMBO J 18:2941
138. Wang JH, Smolyar A, Tan K, Liu JH, Kim M, Sun ZY, Wagner G, Reinherz EL (1999) Cell 97:791
139. Vliegenthart JFG, Dorland L, Van Halbeek H (1983) Adv Carbohydr Chem Biochem 41:209
140. Wu H, Lustbader JW, Liu Y, Canfield RE, Hendrickson WA (1994) Structure 2:545
141. Lapthorn AJ, Harris DC, Littlejohn A, Lustbader JW, Canfield RE, Machin KJ, Morgan FJ, Isaacs NW (1994) Nature 369:455
142. Lustbader JW, Pollak S, Lobel L, Trakht I, Homans S, Brown JM, Canfield RE (1996) Mol Cell Endocrinol 125:21
143. Weller CT, Lustbader J, Seshadri K, Brown JM, Chadwick CA, Kolthoff CE, Ramnarain S, Pollak S, Canfield R, Homans SW (1996) Biochemistry 35:8815
144. De Beer T, Van Zuylen CW, Leeflang BR, Hard K, Boelens R, Kaptein R, Kamerling JP, Vliegenthart JF (1996) Eur J Biochem 241:229
145. van Zuylen CW, Kamerling JP, Vliegenthart JF (1997) Biochem Biophys Res Commun 232:117
146. van Zuylen CW, de Beer T, Leeflang BR, Boelens R, Kaptein R, Kamerling JP, Vliegenthart JF (1998) Biochemistry 37:1933
147. Erbel PJ, Haseley SR, Kamerling JP, Vliegenthart JF (2002) Biochem J 364:485
148. Kobata A, Takeuchi M (1999) Biochim Biophys Acta 1455:315
149. O’Connor SE, Imperiali B (1997) J Am Chem Soc 119:2295
150. O’Conner SE, Imperiali B (1998) Chem Biol 5:427
151. Bosques CJ, Tschampel SM, Woods RJ, Imperiali B (2004) J Am Chem Soc 126: 8421
152. Coltart DM, Royyuru AK, Williams LJ, Glunz PW, Sames D, Kuduk SD, Schwarz JB, Chen XT, Danishefsky SJ, Live DH (2002) J Am Chem Soc 124:9833
153. Live DH, Williams LJ, Kuduk SD, Schwarz JB, Glunz PW, Chen XT, Sames D, Ku-mar RA, Danishefsky SJ (1999) Proc Natl Acad Sci USA 96:3489
154. Schuster O, Klich G, Sinnwell V, Kranz H, Paulsen H, Meyer B (1999) J Biomol NMR 14:33
155. Seitz O, Wong CH (1997) J Am Chem Soc 119:8766
156. Wu W, Pasternack L, Huang D-H, Koeller KM, Lin C-C, Seitz O, Wong C-H (1999) J Am Chem Soc 121:2409
157. Naganagowda GA, Gururaja TL, Satyanarayana J, Levine MJ (1999) J Pept Res 54:290
158. Kirnarsky L, Prakash O, Vogen SM, Nomoto M, Hollingsworth MA, Sherman S (2000) Biochemistry 39:12076
159. Dziadek S, Griesinger C, Kunz H, Reinscheid UM (2006) Chem Eur J 12:4981
160. Grinstead JS, Koganty RR, Krantz MJ, Longenecker BM, Campbell AP (2002) Biochemistry 41:9946
161. Kinarsky L, Suryanarayanan G, Prakash O, Paulsen H, Clausen H, Hanisch FG, Hollingsworth MA, Sherman S (2003) Glycobiology 13:929
162. von Mensdorff-Pouilly S, Kinarsky L, Engelmann K, Baldus SE, Verheijen RH, Hollingsworth MA, Pisarev V, Sherman S, Hanisch FG (2005) Glycobiology 15:735
163. Fontenot JD, Mariappan SV, Catasti P, Domenech N, Finn OJ, Gupta G (1995) J Biomol Struct Dyn 13:245
164. Dokurno P, Bates PA, Band HA, Stewart LM, Lally JM, Burchell JM, Taylor-Papadimitriou J, Snary D, Sternberg MJ, Freemont PS (1998) J Mol Biol 284:713
165. Möller H, Serttas N, Paulsen H, Burchell JM, Taylor-Papadimitriou J, Meyer B (2002) Eur J Biochem 269:1444
166. Bouvet V, Ben RN (2003) Cell Biochem Biophys 39:133
167. Harding MM, Anderberg PI, Haymet AD (2003) Eur J Biochem 270:1381
168. Tachibana Y, Fletcher GL, Fujitani N, Tsuda S, Monde K, Nishimura S (2004) Angew Chem Int Ed Engl 43:856
169. Sicheri F, Yang DS (1995) Nature 375:427
170. Bush CA, Feeney RE, Osuga DT, Ralapati S, Yeh Y (1981) Int J Pept Protein Res 17:125
171. Rao BN, Bush CA (1987) Biopolymers 26:1227
172. Filira F, Biondi L, Scolaro B, Foffani MT, Mammi S, Peggion E, Rocchi R (1990) Int J Biol Macromol 12:41
173. Dill K, Huang L, Bearden DW, Feeney RE (1992) J Carbohydr Chem 11:499
174. Mimura Y, Yamamoto Y, Inoue Y, Chujo R (1992) Int J Biol Macromol 14:242
175. Lane AN, Hays LM, Feeney RE, Crowe LM, Crowe JH (1998) Protein Sci 7:1555
176. Nguyen DH, Colvin ME, Yeh Y, Feeney RE, Fink WH (2002) Biophys J 82:2892