Chemical methods for glycoprotein discovery

Current Opinion in Chemical Biology

Volumn 11, Issue 1, 2007, Pages 52-58

  Bond, Michelle R ^a   Kohler, Jennifer J ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BORON DERIVATIVE; GLYCAN; GLYCOPROTEIN; PROTEIN TAG; PROTEOME; SUGAR;

CANCER; CORRELATION ANALYSIS; DEVELOPMENTAL STAGE; ELIMINATION REACTION; HUMAN; ISOTOPE LABELING; MASS SPECTROMETRY; MICHAEL ADDITION; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN GLYCOSYLATION; PROTEIN INTERACTION; PROTEIN ISOLATION; PROTEIN MODIFICATION; QUANTITATIVE ANALYSIS; REVIEW;

BIOLOGICAL MARKERS; ENZYMES; GLYCOPROTEINS; GLYCOSYLATION; ISOTOPE LABELING; MASS SPECTROMETRY; NEOPLASMS; POLYSACCHARIDES; PROTEOMICS;

EID: 33846818820     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.11.032     Document Type: Review

References (43)

1. Varki A. Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 3 (1993) 97-130
2. Jung E., Veuthey A., Gasteiger E., and Bairoch A. Annotation of glycoproteins in the SWISS-PROT database. Proteomics 1 (2001) 262-268
3. Apweiler R., Hermjakob H., and Sharon N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim Biophys Acta 1473 (1999) 4-8
4. Hirabayashi J., and Kasai K.-i. Separation technologies for glycomics. J Chromatogr B 771 (2002) 67-87
5. Prescher J.A., and Bertozzi C.R. Chemical technologies for probing glycans. Cell 126 (2006) 851-854. This review describes the recent advances in chemical tagging techniques.
6. Vosseller K., Trinidad J.C., Chalkley R.J., Specht C.G., Thalhammer A., Lynn A.J., Snedecor J.O., Guan S.H., Medzihradszky K.F., Maltby D.A., et al. O-linked N-acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol Cell Proteomics 5 (2006) 923-934
7. Sinz A. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom Rev 25 (2006) 663-682
8. Ramachandran P., Boontheung P., Xie Y.M., Sondej M., Wong D.T., and Loo J.A. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. J Proteome Res 5 (2006) 1493-1503. To identify N-linked glycoproteins in human saliva, the authors use hydrazide capture followed by PNGase F treatment and mass spectrometry analysis to identify 45 unique N-linked glycoproteins.
9. Hirabayashi J., Arata Y., and Kasi K. Glycome project: concept, strategy and preliminary application to Caenorhabditis elegans. Proteomics 1 (2001) 295-303
10. Wells L., Vosseller K., Cole R.N., Cronshaw J.M., Matunis M.J., and Hart G.W. Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Mol Cell Proteomics 1 (2002) 791-804
11. Sparbier K., Koch S., Kessler I., Wenzel T., and Kostrzewa M. Selective isolation of glycoproteins and glycopeptides for MALDI-TOF MS detection supported by magnetic particles. J Biomol Tech 16 (2005) 407-413
12. Sparbier K., Wenzel T., and Kostrzewa M. Exploring the binding profiles of ConA, boronic acid and WGA by MALDI-TOF/TOF MS and magnetic particles. J Chromatogr B Analyt Technol Biomed Life Sci 840 (2006) 29-36. The coupling of boronic acid-functionalized beads with MALDI-TOF analysis was used to detect glycoproteins present in low abundance in human blood samples.
13. Khidekel N., Ficarro S.B., Peters E.C., and Hsieh-Wilson L.C. Exploring the O-GlcNAc proteome: Direct identification of O-GlcNAc-modified proteins from the brain. Proc Natl Acad Sci USA 101 (2004) 13132-13137. The Hsieh-Wilson laboratory used a chemoenzymatic strategy in which they probed O-GlcNAc-glycosylated proteins from rat forebrain extract with a ketone-biotin tag. By combining this isolation strategy with BEMAD, they were also able to identify the sites of glycosylation.
14. Prescher J.A., and Bertozzi C.R. Chemistry in living systems. Nat Chem Biol 1 (2005) 13-21
15. Prescher J.A., Dube D.H., and Bertozzi C.R. Chemical remodelling of cell surfaces in living animals. Nature 430 (2004) 873-877
16. Mahal L.K., Yarema K.J., and Bertozzi C.R. Engineering chemical reactivity on cell surfaces through oligosaccharide biosynthesis. Science 276 (1997) 1125-1128
17. Saxon E., and Bertozzi C.R. Cell surface engineering by a modified Staudinger reaction. Science 287 (2000) 2007-2010
18. Vocadlo D.J., Hang H.C., Kim E.J., Hanover J.A., and Bertozzi C.R. A chemical approach for identifying O-GlcNAc-modified proteins in cells. Proc Natl Acad Sci USA 100 (2003) 9116-9121
19. Hang H.C., Yu C., Kato D.L., and Bertozzi C.R. A metabolic labeling approach toward proteomic analysis of mucin-type O-linked glycosylation. Proc Natl Acad Sci USA 100 (2003) 14846-14851
20. Sawa M., Hsu T.-L., Itoh T., Sugiyama M., Hanson S.R., Vogt P.K., and Wong C.-H. Glycoproteomic probes for fluorescent imaging of fucosylated glycans in vivo. Proc Natl Acad Sci USA 103 (2006) 12371-12376. The authors took advantage of the [3+2] cycloaddition to fluorescently label proteins with incorporated 6-azidofucose.
21. Rabuka D., Hubbard S.C., Laughlin S.T., Argade S.P., and Bertozzi C.R. A chemical reporter strategy to probe glycoprotein fucosylation. J Am Chem Soc 128 (2006) 12078-12079. Azidofucose was metabolically incorporated, giving a profile of proteins that are fucosylated in Jurkat cells.
22. Sampathkumar S.-G., Li A.V., Jones M.B., Sun Z., and Yarema K.J. Metabolic installation of thiols into sialic acid modulates adhesion and stem cell biology. Nat Chem Biol 2 (2006) 149-152
23. Dube D.H., Prescher J.A., Quang C.N., and Bertozzi C.R. Probing mucin-type O-linked glycosylation in living animals. Proc Natl Acad Sci USA 103 (2006) 4819-4824. Metabolically incorporated GalNAz was observed on a variety of O-linked glycoproteins in several tissue types. Interestingly, B cell and T cell glycoproteins were labeled with different efficiencies.
24. Speers A.E., and Cravatt B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem Biol 11 (2004) 535-546
25. Agard N.J., Prescher J.A., and Bertozzi C.R. A strain-promoted [3+2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. J Am Chem Soc 126 (2004) 15046-15047
26. Sprung R., Nandi A., Chen Y., Kim S.C., Barma D., Falck J.R., and Zhao Y.M. Tagging-via-substrate strategy for probing O-GlcNAc modified proteins. J Proteome Res 4 (2005) 950-957
27. Nandi A., Sprung R., Barma D.K., Zhao Y.X., Kim S.C., Falck J.R., and Zhao Y.M. Global identification of O-GlcNAc-modified proteins. Anal Biochem 78 (2006) 452-458
28. Domon B., and Aebersold R. Mass spectrometry and protein analysis. Science 312 (2006) 212-217
29. Zhang H., Li X.J., Martin D.B., and Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 21 (2003) 660-666
30. Vosseller K., Hansen K.C., Chalkley R.J., Trinidad J.C., Wells L., Hart G.W., and Burlingame A.L. Quantitative analysis of both protein expression and serine/threonine post-translational modifications through stable isotope labeling with dithiothreitol. Proteomics 5 (2005) 388-398
31. Kaji H., Saito H., Yamauchi Y., Shinkawa T., Taoka M., Hirabayashi J., Kasai K-i, Takahashi N., and Isobe T. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol 21 (2003) 667-672
32. Lewandrowski U., Moebius J., Walter U., and Sickmann A. Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach. Mol Cell Proteomics 5 (2006) 226-233
33. Han S., Collins B.E., Bengtson P., and Paulson J.C. Homomultimeric complexes of CD22 in B cells revealed by protein-glycan cross-linking. Nat Chem Biol 1 (2005) 93-97. Sugar analogs containing photo-activatable crosslinkers were metabolically incorporated into glycoproteins. These molecules offer a powerful way to probe interactions among glycoproteins.
34. Hennet T. The galactosyltransferase family. Cell Mol Life Sci 59 (2002) 1081-1095
35. Fritz T.A., Raman J., and Tabak L.A. Dynamic association between the catalytic and lectin domains of human UDP-GalNAc:polypeptide α-N-acetylgalactosaminyltransferase-2. J Biol Chem 281 (2006) 8613-8619
36. Shah K., Liu Y., Deirmengian C., and Shokat K.M. Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc Natl Acad Sci USA 94 (1997) 3565-3570
37. Ulrich S.M., Kenski D.M., and Shokat K.M. Engineering a 'methionine clamp' into Src family kinases enhances specificity toward unnatural ATP analogues. Biochemistry 42 (2003) 7915-7921
38. Bishop A., Buzko O., Heyeck-Dumas S., Jung I., Kraybill B., Liu Y., Shah K., Ulrich S., Witucki L., Yang F., et al. Unnatural ligands for engineered proteins: new tools for chemical genetics. Annu Rev Biophys Biomol Struct 29 (2000) 577-606
39. Hang H.C., and Bertozzi C.R. Ketone isosteres of 2-N-acetamidosugars as substrates for metabolic cell surface engineering. J Am Chem Soc 123 (2001) 1242-1243
40. Luchansky S.J., Hang H.C., Saxon E., Grunwell J.R., Yu C., Dube D.H., Bertozzi C.R., Yuan C.L., and Lee R.T. Constructing azide-labeled cell surfaces using polysaccharide biosynthetic pathways. Methods Enzymol 362 (2003) 249-272
41. Luchansky S.J., and Bertozzi C.R. Azido sialic acids can modulate cell-surface interactions. Chem Bio Chem 5 (2004) 1706-1709
42. Laughlin S.T., Agard N.J., Baskin J.M., Carrico I.S., Chang P.V., Ganguli A.S., Hangauer M.J., Lo A., Prescher J.A., and Bertozzi C.R. Metabolic labeling of glycans with azido sugars for visualization and glycoproteomics. Methods in Enzymology 415 (2006) 230-250
43. Sun B, Ranish JA, Utleg AG, White JT, Yan X, Lin B, Hood L: Shotgun glycopeptide-capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics (in press).