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Glycan Data Retrieval and Analysis Using GLYCOSCIENCES.de Applications

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A Practical Guide to Using Glycomics Databases

Abstract

The GLYCOSCIENCES.de web portal (www.glycosciences.de) combines various databases and applications related to glycobiology and glycomics. This chapter demonstrates the use of these resources to find a variety of information on the LewisX (LeX) epitope such as literature references, NMR data, or corresponding PDB entries. Several query options are presented that enable the users to find the information of interest from different point of views. The main focus of GLYCOSCIENCES.de is put on 3D structural data. Therefore, methods to create 3D structure models with the Sweet-II tool and to analyze conformational properties of LeX by usage of PDB data and conformational maps from GlycoMapsDB are also introduced in this chapter.

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References

  • Aoki-Kinoshita KF (2013) Using databases and web resources for glycomics research. Mol Cell Proteomics 12(4):1036–1045. doi:10.1074/mcp.R112.026252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aoki-Kinoshita KF, Kanehisa M (2006) Bioinformatics approaches in glycomics and drug discovery. Curr Opin Mol Ther 8(6):514–520

    CAS  PubMed  Google Scholar 

  • Aoki-Kinoshita KF, Bolleman J, Campbell MP, Kawano S, Kim JD, Lutteke T, Matsubara M, Okuda S, Ranzinger R, Sawaki H, Shikanai T, Shinmachi D, Suzuki Y, Toukach P, Yamada I, Packer NH, Narimatsu H (2013) Introducing glycomics data into the Semantic Web. J Biomed Semant 4(1):39. doi:10.1186/2041-1480-4-39

    Article  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berteau O, Stenutz R (2004) Web resources for the carbohydrate chemist. Carbohydr Res 339(5):929–936

    Article  CAS  PubMed  Google Scholar 

  • Bohne A, Lang E, von der Lieth CW (1999) SWEET – WWW-based rapid 3D construction of oligo- and polysaccharides. Bioinformatics 15(9):767–768

    Article  CAS  PubMed  Google Scholar 

  • Bohne-Lang A, Lang E, Forster T, von der Lieth CW (2001) LINUCS: linear notation for unique description of carbohydrate sequences. Carbohydr Res 336(1):1–11

    Article  CAS  PubMed  Google Scholar 

  • Campbell MP, Ranzinger R, Lütteke T, Mariethoz J, Hayes CA, Zhang J, Akune Y, Aoki-Kinoshita KF, Damerell D, Carta G, York WS, Haslam SM, Narimatsu H, Rudd PM, Karlsson NG, Packer NH, Lisacek F (2014) Toolboxes for a standardised and systematic study of glycans. BMC Bioinf 15(Suppl 1):S9. doi:10.1186/1471-2105-15-S1-S9

    Article  Google Scholar 

  • Ceroni A, Dell A, Haslam SM (2007) The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures. Source Code Biol Med 2:3

    Article  PubMed  PubMed Central  Google Scholar 

  • Crispin M, Stuart DI, Jones EY (2007) Building meaningful models of glycoproteins. Nat Struct Mol Biol 14(5):354

    Article  CAS  PubMed  Google Scholar 

  • Doubet S, Albersheim P (1992) CarbBank. Glycobiology 2(6):505

    Article  CAS  PubMed  Google Scholar 

  • Doubet S, Bock K, Smith D, Darvill A, Albersheim P (1989) The complex carbohydrate structure database. Trends Biochem Sci 14(12):475–477

    Article  CAS  PubMed  Google Scholar 

  • Emsley P, Brunger AT, Lütteke T (2015) Tools to assist determination and validation of carbohydrate 3D structure data. Methods Mol Biol 1273:229. doi:10.1007/978-1-4939-2343-4_17

    Article  CAS  PubMed  Google Scholar 

  • Frank M, Schloissnig S (2010) Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci 67(16):2749–2772. doi:10.1007/s00018-010-0352-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Frank M, Lütteke T, von der Lieth CW (2007) GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. Nucleic Acids Res 35(Database issue):287–290. doi:10.1093/nar/gkl907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gadhoum SZ, Sackstein R (2008) CD15 expression in human myeloid cell differentiation is regulated by sialidase activity. Nat Chem Biol 4(12):751–757. doi:10.1038/nchembio.116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hooft RW, Sander C, Vriend G (1997) Objectively judging the quality of a protein structure from a Ramachandran plot. Comput Appl Biosci 13(4):425–430

    CAS  PubMed  Google Scholar 

  • Kumar S, Lütteke T, Schwartz-Albiez R (2012) GlycoCD: a repository for carbohydrate-related CD antigens. Bioinformatics 28(19):2553–2555. doi:10.1093/bioinformatics/bts481

    Article  CAS  PubMed  Google Scholar 

  • Lohmann KK, von der Lieth CW (2004) GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates. Nucleic Acids Res 32:W261–W266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loss A, Lütteke T (2015) Using NMR data on GLYCOSCIENCES.de. Methods Mol Biol 1273:87. doi:10.1007/978-1-4939-2343-4_6

    Article  CAS  PubMed  Google Scholar 

  • Loss A, Bunsmann P, Bohne A, Schwarzer E, Lang E, von der Lieth CW (2002) SWEET-DB: an attempt to create annotated data collections for carbohydrates. Nucleic Acids Res 30(1):405–408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loss A, Stenutz R, Schwarzer E, von der Lieth CW (2006) 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(Web Server issue):W733–W737

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lütteke T (2009) Analysis and validation of carbohydrate three-dimensional structures. Acta Crystallogr D Biol Crystallogr 65(2):156–168

    Article  PubMed  PubMed Central  Google Scholar 

  • Lütteke T (2012) The use of glycoinformatics in glycochemistry. Beilstein J Org Chem 8:915–929. doi:10.3762/bjoc.8.104

    Article  PubMed  PubMed Central  Google Scholar 

  • Lütteke T, von der Lieth C-W (2004) pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinf 5:69

    Article  Google Scholar 

  • Lütteke T, von der Lieth CW (2009) Data mining the PDB for glyco-related data. Methods Mol Biol 534:293–310. doi:10.1007/978-1-59745-022-5_21

    PubMed  Google Scholar 

  • Lütteke T, Frank M, von der Lieth CW (2004) Data mining the protein data bank: automatic detection and assignment of carbohydrate structures. Carbohydr Res 339(5):1015–1020. doi:10.1016/j.carres.2003.09.038

    Article  PubMed  Google Scholar 

  • Lütteke T, Frank M, von der Lieth CW (2005) Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the Protein Data Bank. Nucleic Acids Res 33(Database Issue):D242–D246

    Article  PubMed  Google Scholar 

  • Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth CW (2006) GLYCOSCIENCES.de: an internet portal to support glycomics and glycobiology research. Glycobiology 16(5):71R–81R

    Article  PubMed  Google Scholar 

  • McNaught AD (1997) Nomenclature of carbohydrates (recommendations 1996). Adv Carbohydr Chem Biochem 52:43–177

    Article  CAS  PubMed  Google Scholar 

  • Moran AP (2009) Molecular mimicry of host glycosylated structures by bacteria. In: Moran AP, Holst O, Brennan PJ, von Itzstein M (eds) Microbial glycobiology. Academic, London, pp 847–870

    Google Scholar 

  • Nakahara T, Hashimoto R, Nakagawa H, Monde K, Miura N, Nishimura S-I (2008) Glycoconjugate Data Bank: structures – an annotated glycan structure database and N-glycan primary structure verification service. Nucleic Acids Res 36(Database issue):D368–D371

    CAS  PubMed  Google Scholar 

  • Pederson K, Mitchell DA, Prestegard JH (2014) Structural characterization of the DC-SIGN-Lewis(X) complex. Biochemistry 53(35):5700–5709. doi:10.1021/bi5005014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ponder JW, Richards FM (1987) An efficient newton-like method for molecular mechanics energy minimization of large molecules. J Comput Chem 8:1016–1024

    Article  CAS  Google Scholar 

  • Powlesland AS, Barrio MM, Mordoh J, Hitchen PG, Dell A, Drickamer K, Taylor ME (2011) Glycoproteomic characterization of carriers of the CD15/Lewisx epitope on Hodgkin’s Reed-Sternberg cells. BMC Biochem 12:13. doi:10.1186/1471-2091-12-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95–99

    Article  CAS  PubMed  Google Scholar 

  • Ranzinger R, Aoki-Kinoshita KF, Campbell MP, Kawano S, Lutteke T, Okuda S, Shinmachi~D, Shikanai T, Sawaki H, Toukach P, Matsubara M, Yamada I, Narimatsu H (2014) GlycoRDF: an ontology to standardize glycomics data in RDF. Bioinformatics, in press. doi:10.1093/bioinformatics/btu732

  • Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH (2011) A new generation of crystallographic validation tools for the protein data bank. Structure 19(10):1395–1412. doi:10.1016/j.str.2011.08.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rojas-Macias MA, Loss A, Bohne-Lang A, Frank M, Lütteke T (2014) Databases and tools of GLYCOSCIENCES.de web server. In: Taniguchi N, Endo T, Hart GW, Seeberger P, Wong CH (eds) Glycoscience: biology and medicine. Springer, Tokyo, pp 233–239

    Google Scholar 

  • Schwartz-Albiez R (2009) Inflammation and glycoscience. In: Gabius HJ (ed) The sugar code. Wiley-VCH, Weinheim, pp 447–467

    Google Scholar 

  • Toukach P, Joshi HJ, Ranzinger R, Knirel Y, von der Lieth CW (2007) Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the bacterial carbohydrate structure DataBase and GLYCOSCIENCES.de. Nucleic Acids Res 35(Database issue):D280–D286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Kuik JA, Hard K, Vliegenthart JFG (1992) A 1H NMR database computer program for the analysis of the primary structure of complex carbohydrates. Carbohydr Res 235:53–68

    Article  PubMed  Google Scholar 

  • Zola H, Swart B, Boumsell L, Mason DY (2003) Human leucocyte differentiation antigen nomenclature: update on CD nomenclature. Report of IUIS/WHO subcommittee. J Immunol Methods 275(1–2):1–8

    CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Justus-Liebig-University Giessen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392, Giessen, Germany

    Thomas Lütteke

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  1. Thomas Lütteke
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Correspondence to Thomas Lütteke .

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Editors and Affiliations

  1. Faculty of Science and Engineering, Soka University, Hachioji, Tokyo, Japan

    Kiyoko F. Aoki-Kinoshita

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Lütteke, T. (2017). Glycan Data Retrieval and Analysis Using GLYCOSCIENCES.de Applications. In: Aoki-Kinoshita, K. (eds) A Practical Guide to Using Glycomics Databases. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56454-6_16

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