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Chemistry » Organic Chemistry » "Glycosylation", book edited by Stefana Petrescu, ISBN 978-953-51-0771-2, Published: September 26, 2012 under CC BY 3.0 license. © The Author(s).

Chapter 1

The Structural Assessment of Glycosylation Sites Database - SAGS – An Overall View on N-Glycosylation

By Marius D. Surleac, Laurentiu N. Spiridon, Robi Tacutu, Adina L Milac, Stefana M. Petrescu and Andrei-J Petrescu
DOI: 10.5772/51690

  1. Y. Akune, M. Hosoda, S. Kaiya, D. Shinmachi, K. F. Aoki-Kinoshita, R. I. N. G. S. The, for. resource, informatics. glycome, analysis, mining. data, the. on, O. M. I. C. Web, OMICS.,14(4), 475 EOF486 EOF2010

  2. A. Apte, N. S. Meitei, in. Bioinformatics, glycan. glycomics, with. characterization, spectrometric. mass, using. data, Glycan. Sim, Methods Mol Biol. 600, 269 EOF81 EOF2010

  3. N. Branza-Nichita, A. Petrescu-J, G. Negroiu, R. A. Dwek, S. M. Petrescu, processing. N-glycosylation, folding-lessons. glycoprotein, the. from, proteins. tyrosinase-related, Chem, Rev., 100, 4697 EOF4712 EOF2000

  4. Calo D, Kaminski L, Eichler J, Protein glycosylation in Archaea: sweet and extreme, Glycobiology, 20(9), 1065-1076 (2010).

  5. M. P. Campbell, Struwe. W. B. Hayes, M. R. Wilkins, K. F. Aoki-Kinoshita, D. J. Harvey, P. M. Rudd, D. Kolarich, F. Lisacek, N. G. Karlsson, N. H. Packer, Carb. K. B. Uni, the. putting, together. pieces, glycomics. for, research, Proteomics4117 EOF21 EOF2011

  6. M. P. Campbell, L. Royle, C. M. Radcliffe, R. A. Dwek, P. M. Rudd, Base. Glyco, G. U. auto, for. H. P. L. tools, glycan. C-based, analysis, Bioinformatics1214 EOF1216 EOF2008

  7. A. Ceroni, K. Maass, H. Geyer, R. Geyer, A. Dell, S. M. Haslam, Workbench. a. Glyco, for. tool, computer-assisted. the, of. annotation, spectra. mass, glycans. of, J Proteome Res. 7(4):1650 EOF9 EOF2008

  8. Chandonia JM, Brenner SE.The impact of structural genomics: expectations and outcomesScience2006

  9. V. T. Chang, M. Crispin, A. R. Aricescu, D. J. Harvey, J. E. Nettleship, J. A. Fennelly, C. Yu, K. S. Boles, E. J. Evans, D. I. Stuart, R. A. Dwek, E. Y. Jones, R. J. Owens, S. J. Davis, structural. Glycoprotein, solving. genomics, glycosylation. the, problem, Structure267 EOF273 EOF2007

  10. D. Cioaca, S. Ghenea, L. N. Spiridon, M. Marin, A. J. Petrescu, S. M. Petrescu, C-terminus glycans with critical functional role in the maturation of secretory glycoproteins.PLoS Onee19979 EOF2011

  11. A. Dell, A. Galadari, F. Sastre, P. Hitchen, Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotesInt J Microbiol. 2010

  12. L. H. Greene, T. E. Lewis, S. Addou, A. Cuff, T. Dallman, M. Dibley, O. Redfern, F. Pearl, R. Nambudiry, A. Reid, I. Sillitoe, C. Yeats, J. M. Thornton, The. C. A. T. H. Orengo, structure. domain, new. database, protocols, levels. classification, a. give, comprehensive. more, for. resource, evolution. exploring, Nucleic Acids ResearchD291D297 (2007

  13. U. Güldener, M. Münsterkötter, G. Kastenmüller, N. Strack, J. van Helden, C. Lemer, J. Richelles, S. J. Wodak, J. Garcia-Martinez, J. E. Perez-Ortin, H. Michael, A. Kaps, E. Talla, B. Dujon, B. Andre, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, H. W. C. Y. G. D. Mewes, Comprehensive. the, Genome. Yeast, Database, Nucleic Acids Res, 33, D364D368 (2005

  14. K. Hashimoto, S. Goto, S. Kawano, K. F. Aoki-Kinoshita, N. Ueda, M. Hamajima, T. Kawasaki, M. K. E. G. G. Kanehisa, a. glycome, resource. informatics, GlycobiologyR-70R (2006

  15. C. C. Huang, S. N. Lam, P. Acharya, M. Tang, S. H. Xiang, S. S. Hussan, R. L. Stanfield, J. Robinson, J. Sodroski, I. A. Wilson, R. Wyatt, Kwong. P. D. Bewley, Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4Science1930 EOF1934 EOF2007

  16. W. Kabsch, C. Sander, of. Dictionary, secondary. protein, pattern. structure, of. recognition, hydrogen-bonded, features. geometrical, Biopolymers2577 EOF637 EOF1983

  17. H. Kaji, J. Kamiie, H. Kawakami, K. Kido, Y. Yamauchi, T. Shinkawa, M. Taoka, N. Takahashi, T. Isobe, Proteomics reveals N-linked glycoprotein diversity in Caenorhabditis elegans and suggests an atypical translocation mechanism for integral membrane proteins.Mol Cell Proteomics. 6(12), 2100 EOF9 EOF2007

  18. L. Liu, J. E. Telford, A. Knezevic, P. M. Rudd, High-throughput glycoanalytical technology for systems glycobiologyBiochem Soc Trans. 38(5), 1374 EOF1377 EOF2010

  19. A. Loss, R. Stenutz, E. Schwarzer, Lieth. C. W. von der, Gly, GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface. Nucleic Acids Res. 34:W733W737 (2006

  20. T. Lütteke, A. Bohne-Lang, A. Loss, T. Goetz, M. Frank, Lieth. C. W. G. L. Y. C. O. S. C. I. E. N. C. E. von der, an Internet portal to support glycomics and glycobiology research. Glycobiology. 16(5):, 71R-81R (2006

  21. C. Lizak, S. Gerber, S. Numao, M. Aebi, K. P. Locher, X-ray structure of a bacterial oligosaccharyl-transferase. Nature 474(7351), 350-355 (2011

  22. N. Maita, J. Nyirenda, M. Igura, J. Kamishikiryo, D. Kohda, Comparative structural biology of eubacterial and archaeal oligosaccharyltransferasesJ Biol Chem. 285(7), 4941 EOF4950 EOF2010

  23. S. Mittermayr, J. Bones, M. Doherty, A. Guttman, P. M. Rudd, analytical. Multiplexed, rapid. glycomics, Ig. G. confident, structural. N-glycan, elucidation, J, Doherty M, Guttman A, Rudd PM. Multiplexed analytical glycomics: rapid and confident IgG N-glycan structural elucidationJ Proteome Res. 10(8), 3820 EOF3829 EOF2011

  24. E. Mohorko, R. Glockshuber, M. Aebi, the. Oligosaccharyltransferase, enzyme. central, N-linked. of, glycosylation. protein, J Inherit Metab Dis. 34(4), 869 EOF878 EOF2011

  25. T. Nakahara, R. Hashimoto, H. Nakagawa, K. Monde, N. Miura, S. Nishimura, Data. Glycoconjugate, Structures--an. Bank, glycan. annotated, database. structure, primary. N-glycan, verification. structure, service, Nucleic Acids Res. 36, D368 EOFD371 EOF2008

  26. S. J. North, P. G. Hitchen, S. M. Haslam, A. Dell, Mass spectrometry in the analysis of N-linked and O-linked glycansCurr Opin Struct Biol. 19(5), 498 EOF506 EOF2009

  27. I. Pagani, K. Liolios, J. Jansson, I. M. Chen, T. Smirnova, B. Nosrat, V. M. Markowitz, N. C. Kyrpides, The Genomes OnLine Database (GOLD) 4 status of genomic and metagenomic projects and their associated metadataNucleic Acids Res., 40, D571 EOFD579 EOF2012

  28. C. Paduraru, L. Spiridon, W. Yuan, G. Bricard, X. Valencia, S. Porcelli, G. Besra, S. M. Petrescu, A. Petrescu-J, P. . Cresswell, An N-linked glycan modulates the interaction between the CD1d heavy chain and beta 2 -microglobulin.J Biol Chem., 281(52), 40369-78 (2006

  29. A. Petrescu-J, T. D. Butters, S. M. Petrescu, F. M. Platt, R. A. Dwek, M. R. Wormald, solution. N. M. R. The, of. structure, Man. Glc, in. unit, Man. Glc, N. Glc, Ac, J. 1. Embo, 1997

  30. Petrescu A-J, Wormald MR, Dwek RA."Structural aspects of glycomes with a focus on N-glycosylation and glycoprotein folding.", Curr Opin Struct Biol.600 EOF607 EOF2006

  31. Petrescu A-J, Milac A-L, Petrescu SM, Dwek RA, Wormald M.R."Statistical analysis of the protein core around N-glycosylation sites.Implications on occupancy, folding and function", Glycobiology, 14: 103-114 (2004

  32. Petrescu A-J, Petrescu S.M., Dwek R.A., Wormald M.R., "A Statistical Analysis of N- and O-glycan linkages from crystallographyc data" Glycobiology, 9, 343-352 (1999)

  33. Petrescu SM, Branza-Nichita N, Negroiu G, Petrescu A-J, Dwek RA, Tyrosinase and glycoprotein folding: roles of chaperones that recognize glycans, Biochemistry, 39, 5229-5237 (2000)

  34. R. Raman, M. Venkataraman, S. Ramakrishnan, W. Lang, S. Raguram, R. Sasisekharan, glycomics. Advancing, strategies. Implementation, the. at, for. consortium, glycomics. functional, Glycobiology 16, 82R-90R (2006

  35. Sastre L., New DNA sequencing technologies open a promising era for cancer research and treatment.Clin Transl Oncol. 3(5):301 EOF306 EOF2011

  36. F. Schwarz, M. Aebi, Mechanisms and principles of N-linked protein glycosylationCurr Opin Struct Biol. 21(5), 576 EOF582 EOF2011

  37. F. Schwarz, C. Lizak, Y. Y. Fan, S. Fleurkens, M. Kowarik, M. Aebi, Relaxed acceptor site specificity of bacterial oligosaccharyltransferase in vivoGlycobiology45 EOF54 EOF2011

  38. S. Shokralla, J. L. Spall, J. F. Gibson, M. Hajibabaei, Next-generation sequencing technologies for environmental DNA research.Mol Ecol. 21(8):1794 EOF805 EOF2012

  39. W. Song, M. G. Henquet, R. A. Mentink, A. J. van Dijk, J. H. Cordewener, D. Bosch, A. H. America, A. R. van der Krol, N-glycoproteomics in plants: perspectives and challenges. J Proteomics. 74(8), 1463-1474 (2011

  40. J. Sprenger, Fink. J. Lynn, S. Karunaratne, K. Hanson, N. A. Hamilton, R. D. L. O. C. A. T. E. a. Teasdale, protein. mammalian, localization. subcellular, database, Nucleic Acids Res. 36, D230D233 (2008

  41. T. J. Stevens, R. H. Fogh, W. Boucher, V. A. Higman, F. Eisenmenger, B. Bardiaux, B. J. van Rossum, H. Oschkinat, E. D. A. Laue, framework. software, analysing. for, M. A. S. N. M. R. solid-state, data, J, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue ED. A software framework for analysing solid-state MAS NMR dataJ Biomol NMR. 51(4), 437 EOF447 EOF2011

  42. Stuart DI, Jones EY, Wilson KS, Daenke S "SPINE: Structural Proteomics IN Europe- the best of both worlds", Acta Cryst, D62, 10 (2006).

  43. S. Y. Vakhrushev, D. Dadimov, Software. Peter-Katalinić, for. platform, glycomics. J. high-throughput, J.Anal Chem. 81(9), 3252-3260 (2009

  44. M. Wacker, D. Linton, P. G. Hitchen, M. Nita-Lazar, S. M. Haslam, S. J. North, M. Panico, H. R. Morris, A. Dell, B. W. Wren, M. Aebi, N-linked glycosylation in Campylobacter jejuni and its functional transfer into E. coliScience1790 EOF1793 EOF2002

  45. Woods RJ, Tessier MB. Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes.Curr Opin Struct Biol. 20(5), 575 EOF583 EOF2010

  46. Wormald M, Petrescu A-J, Pao Y-L, Glythero A, Elliot T, Dwek RA, "Conformational Studies of Oligosacharides and Glycopeptides: Complementarity of NMR, X-Ray Crystallogrphy and Molecular Modelling", Chem.Rev., 102, 371-387 (2002)

  47. J. Zaia, Mass spectrometry and glycomicsOMICS 14(4), 401 EOF418 EOF2010

  48. Zapun A, Petrescu SM, Rudd PM, Dwek RA, Thomas DY, Bergeron JJM, Conformation- independent binding of monoglucosylated ribonuclease B to calnexin, Cell, 88, 29-38 (1997)

  49. G. Zauner, A. M. Deelder, M. Wuhrer, Recent advances in hydrophilic interaction liquid chromatography (HILIC) for structural glycomics.Electrophoresis3456 EOF66 EOF2011

  50. Zielinska DF, Gnad F, Wisniewski JR, Mann M, Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints, Cell 141, 897-907 (2010).