Activity-based proteomics probes for carbohydrate-processing enzymes: Current trends and future outlook

Carbohydrate Research

Volumn 390, Issue 1, 2014, Pages 9-19

  Stubbs, Keith A ^a  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Activity based proteomics probes; Carbohydrate processing enzymes; Glycobiology; Glycoside hydrolases; Glycosyl transferases

Indexed keywords

BIOLOGICAL SYSTEMS; CARBOHYDRATES; MOLECULAR BIOLOGY; PROBES; PROTEINS;

ACTIVITY-BASED; COMPLEX BIOLOGICAL SYSTEMS; FUTURE PERSPECTIVES; GLYCAN STRUCTURES; GLYCOBIOLOGY; GLYCOSIDE HYDROLASES; GLYCOSYL TRANSFERASE; PROTEOMICS;

ENZYMES;

CARBOHYDRATE; CARBOHYDRATE PROCESSING ENZYME; CYCLITOL; EPOXIDE; GLYCOSIDASE; GLYCOSYLTRANSFERASE; QUINONE DERIVATIVE; UNCLASSIFIED DRUG; FLUORESCENT DYE;

ACTIVITY BASED PROTEOMICS PROBE; COVALENT BOND; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME INHIBITION; ENZYME SUBSTRATE; HUMAN; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REVIEW; ANIMAL; ANTAGONISTS AND INHIBITORS; CHEMISTRY; ENZYME ASSAY;

ANIMALS; CYCLITOLS; ENZYME ASSAYS; FLUORESCENT DYES; GLYCOSIDE HYDROLASES; GLYCOSYLTRANSFERASES; HUMANS; PROTEOMICS; QUINONES;

EID: 84897032144     PISSN: 00086215     EISSN: 1873426X     Source Type: Journal    
DOI: 10.1016/j.carres.2014.02.023     Document Type: Review

References (108)

1. I.H.G.S Consortium Nature 431 2004 931 945
2. H. Chial Nat. Educ. 1 2008 192
3. D. Simmons Nat. Educ. 1 2008 70
4. S. Girirajan, and E.E. Eichler Hum. Mol. Genet. 15 2010 176 187
5. S. Girirajan, C.D. Campbell, and E.E. Eichler Annu. Rev. Genet. 45 2011 203 226
6. T.M. Gloster, and D.J. Vocadlo Nat. Chem. Biol. 18 2012 683 694
7. A. Varki Essentials of Glycobiology 1999 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
8. G.J. Davies, and B. Henrissat Curr. Opin. Struct. Biol. 23 2013 649 651
9. B. Henrissat, and A. Bairoch Biochem. J. 293 1993 781 788
10. B. Henrissat, and A. Bairoch Biochem. J. 316 1996 695 696
11. B. Henrissat, and G. Davies Curr. Opin. Struct. Biol. 7 1997 637 644
12. V. Lombard, H. Golaconda-Ramulu, E. Drula, P.M. Coutinho, and B. Henrissat Nucleic Acids Res. 42 2014 D490 D495
13. B.F. Cravatt, A.T. Wright, and J.W. Kozarich Annu. Rev. Biochem. 77 2008 383 414
14. K.A. Stubbs, and D.J. Vocadlo Aust. J. Chem. 62 2009 521 527
15. M.D. Witte, G.A. van der Marel, J.M.F.G. Aerts, and H.S. Overkleeft Org. Biomol. Chem. 9 2011 5908 5924
16. J. Sumranjit, and S.J. Chung Molecules 18 2013 10425 10451
17. K.A. Stubbs, and D.J. Vocadlo Methods Enzymol. 415 2006 253 268
18. A. Vasella, G.J. Davies, and M. Bohm Curr. Opin. Chem. Biol. 6 2002 619 629
19. D.J. Vocadlo, and G.J. Davies Curr. Opin. Chem. Biol. 12 2008 539 555
20. D.C. Greenbaum, W.D. Arnold, F. Lu, L. Hayrapetian, A. Baruch, J. Krumrine, S. Toba, and K. Chehade Chem. Biol. 9 2002 1085 1094
21. P.F. van Swieten, R. Maehr, A.M. van den Nieuwendijk, B.M. Kessler, M. Reich, C.S. Wong, H. Kalbacher, M.A. Leeuwenburgh, C. Driessen, G.A. van der Marel, H.L. Ploegh, and H.S. Overkleeft Bioorg. Med. Chem. Lett. 14 2004 3131 3134
22. O. Hekmat, S. He, R.A. Warren, and S.G. Withers J. Proteome Res. 7 2008 3282 3292
23. N. Jessani, and B.F. Cravatt Curr. Opin. Chem. Biol. 8 2004 54 59
24. N. Jessani, S. Niessen, B.Q. Wei, M. Nicolau, M. Humphrey, Y. Ji, W. Han, D.Y. Noh, J.R.r. Yates, S.S. Jeffrey, and B.F. Cravatt Nat. Methods 2 2005 691 697
25. L.I. Willems, W.A. van der Linden, N. Li, K.Y. Li, N. Liu, S. Hoogendoorn, G.A. van der Marel, B.I. Florea, and H.S. Overkleeft Acc. Chem. Res. 44 2011 718 729
26. M.F. Debets, J.C. van Hest, and F.P. Rutjes Org. Biomol. Chem. 11 2013 6439 6455
27. E. Saxon, and C.R. Bertozzi Science 287 2000 2007 2010
28. V.V. Rostovtsev, L.G. Green, V.V. Fokin, and K.B. Sharpless Angew. Chem., Int. Ed. 41 2002 2596 2599
29. C.W. Tornoe, C. Christensen, and M. Meldal J. Org. Chem. 67 2002 3057 3064
30. N.J. Agard, J.A. Prescher, and C.R. Bertozzi J. Am. Chem. Soc. 126 2004 15046 15047
31. N.K. Devaraj, R. Weissleder, and S.A. Hilderbrand Bioconjug. Chem. 19 2008 2297 2299
32. N.K. Devaraj, R. Upadhyay, J.B. Haun, S.A. Hilderbrand, and R. Weissleder Angew. Chem., Int. Ed. 48 2009 7013 7016
33. N.K. Devaraj, S. Hilderbrand, R. Upadhyay, R. Mazitschek, and R. Weissleder Angew. Chem., Int. Ed. 49 2010 2869 2872
34. L.I. Willems, M. Verdoes, B.I. Florea, G.A. Van der Marel, and H.S. Overkleeft ChemBioChem 11 2010 1769 1781
35. T.D. Heightman, and A.T. Vasella Angew. Chem., Int. Ed. 38 1999 750 770
36. G.T.J. Vanderhorst, G.M.S. Mancini, R. Brossmer, U. Rose, and F.W. Verheijen J. Biol. Chem. 265 1990 10801 10804
37. G.T.J. Vanderhorst, U. Rose, R. Brossmer, and F.W. Verheijen FEBS Lett. 277 1990 42 44
38. J. Kopitz, K. Sinz, R. Brossmer, and M. Cantz Eur. J. Biochem. 248 1997 527 534
39. E.F.V. Scriven, and K. Turnbull Chem. Rev. 88 1988 351 368
40. A.V. Romaniouk, A. Silva, J. Feng, and I.K. Vijay Glycobiology 14 2004 301 310
41. M.N. Gandy, A.W. Debowski, and K.A. Stubbs Chem. Commun. 2011 5037 5039
42. M. van Scherpenzeel, R.J.B.H.N. van den Berg, W.E. Donker-Koopman, R.M.J. Liskamp, J.M.F.G. Aerts, H.S. Overkleeft, and R.J. Pieters Bioorg. Med. Chem. 18 2010 267 273
43. C. Kuhn, J. Lehmann, G. Jung, and S. Stevanovic Carbohydr. Res. 232 1992 227 233
44. C. Kuhn, J. Lehmann, and K. Sandhoff Bioconjugate Chem. 3 1992 230 233
45. B.P. Rempel, and S.G. Withers Glycobiology 18 2008 570 586
46. D.J. Vocadlo, J. Wicki, K. Rupitz, and S.G. Withers Biochemistry 41 2002 9736 9746
47. J. Yariv, K.J. Wilson, J. Hildeshiem, and S. Blumberg FEBS Lett. 15 1971 24 26
48. S. Hagihara, A. Miyazaki, I. Matsuo, A. Tatami, T. Suzuki, and Y. Ito Glycobiology 17 2007 1070 1076
49. L.M. Chauvigné-Hines, L.N. Anderson, H.M. Weaver, J.N. Brown, P.K. Koech, C.D. Nicora, B.A. Hofstad, R.D. Smith, M.J. Wilkins, S.J. Callister, and A.T. Wright J. Am. Chem. Soc. 134 2012 20521 20532
50. M.L. Sinnott, and P.J. Smith Biochem. J. 175 1978 525 538
51. O.P. Van Diggelen, H. Galjaard, M.L. Sinnott, and P.J. Smith Biochem. J. 188 1980 337 343
52. S. Halazy, V. Berges, A. Ehrhard, and C. Danzin Bioorg. Chem. 18 1990 330 334
53. M. Kurogochi, S. Nishimura, and Y.C. Lee J. Biol. Chem. 279 2004 44704 44712
54. H. Hinou, M. Kurogochi, H. Shimizu, and S. Nishimura Biochemistry 44 2005 11669 11675
55. D.H. Kwan, H.M. Chen, K. Ratananikom, S.M. Hancock, Y. Watanabe, P.T. Kongsaeree, A.L. Samuels, and S.G. Withers Angew. Chem., Int. Ed. 50 2011 300 303
56. K.D. Janda, L.C. Lo, C.H. Lo, M.M. Sim, R. Wang, C.H. Wong, and R.A. Lerner Science 275 1997 945 948
57. M. Ichikawa, and Y. Ichikawa Bioorg. Med. Chem. Lett. 11 2001 1769 1773
58. C.S. Tsai, Y.K. Li, and L.C. Lo Org. Lett. 4 2002 3607 3610
59. C. Lu, C. Ren, Y. Lai, S. Wu, W. Wang, J. Chen, and L. Lo Angew. Chem., Int. Ed. 44 2005 6888 6892
60. G. Legler Z. Physiol. Chem. 345 1966 197 214
61. G. Legler Hoppe-Seylers Z. Physiol. Chem. 349 1968 767 774
62. G. Legler, and S.N. Hasnain Hoppe-Seyler's Z. Physiol. Chem. 351 1970 25 31
63. N. Kanfer, G. Legler, J. Sullivan, S.S. Raghavan, and R.A. Mumford Biochem. Biophys. Res. Commun. 67 1975 85 90
64. S. Atsumi, K. Umezawa, H. Iinuma, H. Naganawa, H. Nakamura, Y. Iitaka, and T. Takeuchi J. Antibiot. 43 1990 49 53
65. S.G. Withers, and K. Umezawa Biochem. Biophys. Res. Commun. 177 1991 532 537
66. H. Braun Biochim. Biophys. Acta 452 1976 452 457
67. G. Legler, and M. Herrchen FEBS Lett. 135 1981 139 144
68. K.T. Cavanagh, R.A. Fisher, G. Legler, M. Herrchen, M.Z. Jones, E. Julich, R.P. Sewell-Alger, M.L. Sinnott, and F.E. Wilkinson Enzyme 34 1985 75 82
69. W.J. White Jr., K.J. Schray, G. Legler, and J.A. Alhadeff Biochim. Biophys. Acta 873 1986 198 203
70. K. Tatsuta, Y. Niwata, K. Umezawa, K. Toshima, and M. Nakata J. Antibiot. 44 1991 456 458
71. K. Tatsuta, Y. Niwata, K. Umezawa, K. Toshima, and M. Nakata J. Antibiot. 44 1991 912 914
72. M.D. Witte, M.T. Walvoort, K.Y. Li, W.W. Kallemeijn, W.E. Donker-Koopman, R.G. Boot, J.M. Aerts, J.D. Codée, G.A. van der Marel, and H.S. Overkleeft ChemBioChem 12 2011 1263 1269
73. M.D. Witte, W.W. Kallemeijn, J. Aten, K.Y. Li, A. Strijland, W.E. Donker-Koopman, A.M. van den Nieuwendijk, B. Bleijlevens, G. Kramer, B.I. Florea, B. Hooibrink, C.E. Hollak, R. Ottenhoff, R.G. Boot, G.A. van der Marel, H.S. Overkleeft, and J.M. Aerts Nat. Chem. Biol. 6 2010 907 913
74. W.W. Kallemeijn, K.Y. Li, M.D. Witte, A.R. Marques, J. Aten, S. Scheij, J. Jiang, L.I. Willems, T.M. Voorn-Brouwer, C.P. van Roomen, R. Ottenhoff, R.G. Boot, H. van den Elst, M.T. Walvoort, B.I. Florea, J.D. Codée, G.A. van der Marel, J.M. Aerts, and H.S. Overkleeft Angew. Chem., Int. Ed. 51 2012 12529 12533
75. S.G. Withers, I.P. Street, P. Bird, and D.H. Dolphin J. Am. Chem. Soc. 109 1987 7530 7531
76. C. Braun, G.D. Brayer, and S.G. Withers J. Biol. Chem. 270 1995 26778 26781
77. J.D. McCarter, and S.G. Withers J. Am. Chem. Soc. 118 1996 241 242
78. C.P. Phenix, B.P. Rempel, K. Colobong, D.J. Doudet, M.J. Adam, L.A. Clarke, and S.G. Withers Proc. Natl. Acad. Sci. U.S.A. 107 2010 10842 10847
79. J.H. Kim, R. Resende, T. Wennekes, H.M. Chen, N. Bance, S. Buchini, A.G. Watts, P. Pilling, V.A. Streltsov, M. Petric, R. Liggins, S. Barrett, J.L. McKimm-Breschkin, M. Niikura, and S.G. Withers Science 340 2013 71 75
80. J. Wicki, D.R. Rose, and S.G. Withers Methods Enzymol. 354 2002 84 105
81. D.J. Vocadlo, and C.R. Bertozzi Angew. Chem., Int. Ed. 43 2004 5338 5342
82. M.T. Walvoort, W.W. Kallemeijn, L.I. Willems, M.D. Witte, J.M. Aerts, G.A. van der Marel, J.D. Codée, and H.S. Overkleeft Chem. Commun. 2012 10386 10388
83. B.P. Rempel, M.B. Tropak, D.J. Mahuran, and S.G. Withers Angew. Chem., Int. Ed. 50 2011 10381 10383
84. K.A. Stubbs, A. Scaffidi, A.W. Debowski, B.L. Mark, R.V. Stick, and D.J. Vocadlo J. Am. Chem. Soc. 130 2008 327 335
85. K.A. Stubbs, M. Balcewich, B.L. Mark, and D.J. Vocadlo J. Biol. Chem. 282 2007 21382 21391
86. M. Balcewich, K.A. Stubbs, Y. He, T. James, G.J. Davies, D.J. Vocadlo, and B.L. Mark Protein Sci. 18 2009 1541 1551
87. C.S. Tsai, H.Y. Yen, M.I. Lin, T.I. Tsai, S.Y. Wang, W.I. Huang, T.L. Hsu, Y.S. Cheng, J.M. Fang, and C.H. Wong Proc. Natl. Acad. Sci. U.S.A. 2013 2466 2471
88. S.J. Williams, O. Hekmat, and S.G. Withers ChemBioChem 7 2006 116 124
89. O. Hekmat, Y.W. Kim, S.J. Williams, S. He, and S.G. Withers J. Biol. Chem. 280 2005 35126 35135
90. O. Hekmat, C. Florizone, Y.W. Kim, L.D. Eltis, R.A. Warren, and S.G. Withers ChemBioChem 8 2007 2125 2132
91. L.L. Lairson, B. Henrissat, G.J. Davies, and S.G. Withers Annu. Rev. Biochem. 77 2008 521 555
92. S.S. Lee, S.Y. Hong, J.C. Errey, A. Izumi, G.J. Davies, and B.G. Davis Nat. Chem. Biol. 7 2011 631 638
93. R.R. Drake, and A.D. Elbein Glycobiology 2 1992 279 284
94. S.G. Lawson, T.L. Mason, R.D. Sabin, M.E. Sloan, R.R. Drake, B.E. Haley, and B.P. Wasserman Plant Physiol. 90 1989 101 108
95. D.J. Frost, S.M. Read, R.R. Drake, B.E. Haley, and B.P. Wasserman J. Biol. Chem. 265 1990 2162 2167
96. F.C. Lin, R.M. Brown, R.R. Drake, and B.E. Haley J. Biol. Chem. 265 1990 4782 4784
97. P.J. Meikle, K.F. Ng, E. Johnson, N.J. Hoogenraad, and B.A. Stone J. Biol. Chem. 266 1991 22569 22581
98. R.R. Drake, Y. Igari, R. Lester, A.D. Elbein, and A. Radominska J. Biol. Chem. 267 1992 11360 11365
99. A. Radominska, J. Little, J.S. Pyrek, R.R. Drake, Y. Igari, S. Fournel-Gigleux, J. Magdalou, B. Burchell, A.D. Elbein, G. Siest, and R. Lester J. Biol. Chem. 268 1993 15127 15135
100. Z.N. Kyossev, R.R. Drake, S.V. Kyosseva, and A.D. Elbein Eur. J. Biochem. 228 1995 109 112
101. M.E. Carrizo, and J.A. Curtino Biochem. Biophys. Res. Commun. 253 1998 786 789
102. J.W. Huh, H.J. Lee, M.M. Choi, S.J. Yang, S.Y. Yoon, D.W. Kim, S.Y. Kim, S.Y. Choi, and S.W. Cho Bioconjug. Chem. 16 2005 710 716
103. Y. Zeng, Y. Shabalin, T. Szumilo, I. Pastuszak, R.R. Drake, and A.D. Elbein Anal. Biochem. 239 1996 99 106
104. E.H. Holmes J. Biol. Chem. 265 1990 13150 13156
105. M. Lommel, A. Schott, T. Jank, V. Hofmann, and S. Strahl J. Biol. Chem. 286 2011 39768 39775
106. E. Bause, M. Wesemann, A. Bartoschek, and W. Breuer Biochem. J. 322 1997 95 102
107. A.K. Pathak, V. Pathak, S.S. Gurcha, G.S. Besra, and R.C. Reynolds Bioorg. Med. Chem. Lett. 12 2002 2749 2752
108. A.K. Pathak, V. Pathak, L. Seitz, S.S. Gurcha, G.S. Besra, J.M. Riordan, and R.C. Reynolds Bioorg. Med. Chem. 15 2007 5629 5650