Probing glycomics

Current Opinion in Chemical Biology

Volumn 11, Issue 1, 2007, Pages 59-65

  Timmer, Mattie SM ^a   Stocker, Bridget L ^a   Seeberger, Peter H ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; PROTEIN; RESIN;

BINDING AFFINITY; ENZYME ACTIVITY; ENZYME MODIFICATION; GENE; GLYCOBIOLOGY; MICROARRAY ANALYSIS; MOLECULAR PROBE; PROTEIN BINDING; PROTEIN FUNCTION; REVIEW;

CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; GLYCOSYLATION; HEPARIN; LACTOSE; MICROARRAY ANALYSIS; MOLECULAR PROBES; MOLECULAR SEQUENCE DATA; POLYSACCHARIDES; PROTEIN BINDING; PROTEINS;

EID: 33846813769     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.11.040     Document Type: Review

References (36)

1. Raman R., Raguram S., Venkataraman G., Paulson J.C., and Sasisekharan R. Glycomics: an integrated systems approach to structure-function relationships of glycans. Nat Methods 2 (2005) 817-824
2. Seeberger P.H. Exploring life's sweet spot. Nature 437 (2005) 1239
3. Lamari F.N., Militsopoulou M., Mitropoulou T.N., Hjerpe A., and Karamanos N.K. Analysis of glycosaminoglycan-derived disaccharides in biologic samples by capillary electrophoresis and protocol for sequencing glycosaminoglycans. Biomed Chromatogr 16 (2002) 95-102
4. Hirabayashi J., and Kasai K. Separation technologies for glycomics. J Chromatogr B Analyt Technol Biomed Life Sci 771 (2002) 67-87
5. Harvey D.J. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update covering the period 1999-2000. Mass Spectrom Rev 25 (2006) 595-662
6. Campa C., Coslovi A., Flamigni A., and Rossi M. Overview on advances in capillary electrophoresis-mass spectrometry of carbohydrates: A tabulated review. Electrophoresis 27 (2006) 2027-2050
7. Morelle W., and Michalski J.C. Glycomics and mass spectrometry. Curr Pharm Des 11 (2005) 2615-2645
8. Zaia J. Mass spectrometry of oligosaccharides. Mass Spectrom Rev 23 (2004) 161-227
9. Paulson J.C., Blixt O., and Collins B.E. Sweet spots in functional glycomics. Nat Chem Biol 2 (2006) 238-248
10. Campbell C.T., and Yarema K.J. Large-scale approaches for glycobiology. Genome Biol 6 (2005) 236
11. Pohl N.L. Functional proteomics for the discovery of carbohydrate-related enzyme activities. Curr Opin Chem Biol 9 (2005) 76-81
12. Dube D.H., and Bertozzi C.R. Metabolic oligosaccharide engineering as a tool for glycobiology. Curr Opin Chem Biol 7 (2003) 616-625
13. Ratner D.M., Adams E.W., Disney M.D., and Seeberger P.H. Tools for glycomics: mapping interactions of carbohydrates in biological systems. ChemBioChem 5 (2004) 1375-1383
14. Van Swieten P.F., Leeuwenburgh M.A., Kessler B.M., and Overkleeft H.S. Bioorthogonal organic chemistry in living cells: novel strategies for labeling biomolecules. Org Biomol Chem 3 (2005) 20-27
15. Hagenstein M.C., and Sewald N. Chemical tools for activity-based proteomics. J Biotechnol 124 (2006) 56-73
16. Schmidinger H., Hermetter A., and Birner-Gruenberger R. Activity-based proteomics: enzymatic activity profiling in complex proteomes. Amino Acids 30 (2006) 333-350
17. Buskas T., Ingale S., and Boons G.-J. Glycopeptides as versatile tools for glycobiology. Glycobiology 16 (2006) 113-136
18. Seeberger P.H., and Werz D.B. Automated synthesis of oligosaccharides as a basis for drug discovery. Nat Rev Drug Discov 4 (2005) 751-763
19. Ichikawa M., and Ichikawa Y. A mechanism-based affinity-labeling agent for possible use in isolating n-acetylglucosaminidase. Bioorg Med Chem Lett 11 (2001) 1769-1773
20. Vocadlo D.J., and Bertozzi C.R. A strategy for functional proteomic analysis of glycosidase activity from cell lysates. Angew Chem Int Ed Engl 43 (2004) 5338-5342
21. Mizanur R.M., Jaipuri F.A., and Pohl N.L. One-step synthesis of labeled sugar nucleotides for protein O-GlcNAc modification studies by chemical function analysis of an archaeal protein. J Am Chem Soc 127 (2005) 836-837
22. Guo J., Asong J., and Boons G.-J. Selective inhibition of glycosidases by feedback prodrugs. Angew Chem Int Ed Engl 45 (2006) 5345-5348. A chemical probe was designed to control very specifically the action of a glycosidase.
23. Hekmat O., Kim Y.-W., Williams S.J., He S., and Withers S.G. Active-site peptide 'fingerprinting' of glycosidases in complex mixtures by mass spectrometry. J Biol Chem 280 (2005) 35126-35135. Development of a chemical probe to be used in proteomics studies. This article is of fundamental importance.
24. Williams S.J., Hekmat O., and Withers S.G. Synthesis and testing of mechanism-based protein-profiling probes for retaining endoglycosidases. ChemBioChem 7 (2006) 116-124
25. Ballell L., Alink K.J., Slijper M., Versluis C., Liskamp R.M.J., and Pieters R.J. A new chemical probe for proteomics of carbohydrate-binding proteins. ChemBioChem 6 (2005) 291-295
26. Lee M.-r., Jung D.-W., Williams D., and Shin I. Synthesis and applications of end-labeled neoglycopolymers. Org Lett 7 (2005) 5477-5480
27. Owen R.M., Gestwicki J.E., Young T., and Kiessling L.L. Synthesis and applications of end-labeled neoglycopolymers. Org Lett 4 (2002) 2293-2296
28. Renaudet O., and Dumy P. Synthesis of multitopic neoglycopeptides displaying recognition and detection motifs. Bioorg Med Chem Lett 15 (2005) 3619-3622
29. Renaudet O., and Dumy P. On-bead synthesis and binding assay of chemoselectively template-assembled multivalent neoglycopeptides. Org Biomol Chem 4 (2006) 2628-2636
30. Larsen K., Thygesen M.B., Guillaumie F., Willats W.G.T., and Jensen K.J. Solid-phase chemical tools for glycobiology. Carbohydr Res 341 (2006) 1209-1234
31. Disney M.D., and Seeberger P.H. The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens. Chem Biol 11 (2004) 1701-1707
32. Stevens J., Blixt O., Glaser L., Taubenberger J.K., Palese P., Paulson J.C., and Wilson I.A. Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. J Mol Biol 355 (2006) 1143-1155
33. Noti C., and Seeberger P.H. Chemical approaches to define the structure-activity relationship of heparin-like glycosaminoglycans. Chem Biol 12 (2005) 731-756
34. De Paz J.L., Noti C., and Seeberger P.H. Microarrays of synthetic heparin oligosaccharides. J Am Chem Soc 128 (2006) 2766-2767. First report on heparin arrays that will be useful in assessing the specificity of heparin-protein interactions.
35. De Paz J.L., Spillmann D., and Seeberger P.H. Microarrays of heparin oligosaccharides obtained by nitrous acid depolymerization of isolated heparin. Chem Commun (Camb) (2006) 3116-3118
36. Xia B., Kawar Z.S., Ju T.Z., Alvarez R.A., Sachdev G.P., and Cummings R.D. Versatile fluorescent derivatization of glycans for glycomic analysis. Nat Methods 2 (2005) 845-850