Abstract
Protein–carbohydrate interactions are involved in various essential biological events. 3D structural data from the Protein Data Bank (PDB) can help to understand the molecular basis of the specificity of carbohydrate recognition by proteins. Such interactions can be analyzed statistically using GlyVicinity. This chapter exemplifies the usage of this tool to find information on the frequency of the occurrence of specific amino acids in the vicinity of individual carbohydrate residues and to analyze the type of interacting atoms and their spatial distribution around the glycans.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Varki A (2006) Nothing in glycobiology makes sense, except in the light of evolution. Cell 126:841–845
Yarema KJ, Bertozzi CR (2001) Characterizing glycosylation pathways. Genome Biol 2:REVIEWS0004
Lee YC, Lee RT (1995) Carbohydrate-protein interactions: basis of glycobiology. Acc Chem Res 28:321–327
Etzler ME, Esko JD (2009) Free glycans as signaling molecules. In: Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzler ME (eds) Essentials of glycobiology, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, pp 523–529
Schwartz-Albiez R (2009) Inflammation and Glycosciences. In: Gabius HJ (ed) The sugar code. Wiley-VCH, Weinheim, Germany, pp 447–463
Lowe JB (2003) Glycan-dependent leukocyte adhesion and recruitment in inflammation. Curr Opin Cell Biol 15:531–538
Karlsson KA (2001) Pathogen-host protein-carbohydrate interactions as the basis of important infections. Adv Exp Med Biol 491:431–443
Smith AE, Helenius A (2004) How viruses enter animal cells. Science 304:237–242
Gabius HJ et al (2004) Chemical biology of the sugar code. Chembiochem 5:740–764
Ip WK et al (2009) Mannose-binding lectin and innate immunity. Immunol Rev 230:9–21
Heitzeneder S et al (2012) Mannan-binding lectin deficiency – good news, bad news, doesn’t matter? Clin Immunol 143:22–38
Lütteke T et al (2006) GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology 16:71R–81R
Berman HM et al (2000) The protein data bank. Nucleic Acids Res 28:235–242
Lütteke T (2009) Analysis and validation of carbohydrate three-dimensional structures. Acta Crystallogr D Biol Crystallogr 65:156–168
Lütteke T et al (2004) Data mining the protein data bank: automatic detection and assignment of carbohydrate structures. Carbohydr Res 339:1015–1020
Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
Spiro RG (2002) Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12:43R–56R
Lehmann WD et al (2000) The information encrypted in accurate peptide masses-improved protein identification and assistance in glycopeptide identification and characterization. J Mass Spectrom 35:1335–1341
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Rojas-Macias, M.A., Lütteke, T. (2015). Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity. In: Lütteke, T., Frank, M. (eds) Glycoinformatics. Methods in Molecular Biology, vol 1273. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2343-4_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2343-4_16
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2342-7
Online ISBN: 978-1-4939-2343-4
eBook Packages: Springer Protocols