Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands

Bioinformatics

Volumn 24, Issue 23, 2008, Pages 2740-2747

  Liu, Gang ^a   Marathe, Dhananjay D ^a   Matta, Khushi L ^b   Neelamegham, Sriram ^a,c  

^a the State University of New York   (United States)

^b ROSWELL PARK CANCER INSTITUTE   (United States)

^c UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SURFACE PROTEIN; GLYCAN; GLYCOSYLTRANSFERASE; P SELECTIN GLYCOPROTEIN LIGAND 1; SELECTIN;

ARTICLE; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PROGRAM; EPITOPE MAPPING; GENETIC ALGORITHM; GLYCOSYLATION; HUMAN; HUMAN CELL; MATHEMATICAL COMPUTING; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; SENSITIVITY ANALYSIS; SYSTEMS BIOLOGY; VALIDATION PROCESS;

COMPUTER SIMULATION; GENE REGULATORY NETWORKS; GLYCOMICS; GLYCOSYLATION; LIGANDS; OLIGOSACCHARIDES; POLYSACCHARIDES; SELECTINS; SYSTEMS BIOLOGY;

EID: 56649094580     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn515     Document Type: Article

References (26)

1. Aeed,P.A. et al. (1998) Characterization of the O-linked oligosaccharide structures on P-selectin glycoprotein ligand-1 (PSGL-1). Glycoconj. J., 15, 975-985.
2. Amano,K. et al. (2008) Engineering of mucin-type human glycoproteins in yeast cells. Proc. Natl Acad. Sci. USA, 105 3232-3237.
3. Cao,Y. et al. (2003) Adjoint sensitivity analysis or differential-algebraic equations: The adjoint DAE system and its numerical solution. Siam J. Sci. Comput., 24, 1076-1089.
4. Fukuda,M. et al. (1986) Structures of O-linked oligosaccharides isolated from normal granulocytes, chronic myelogenous leukemia cells, and acute myelogenous leukemia cells. J. Biol. Chem., 261, 12796-12806.
5. Gerken,T.A. et al. (2002) Mucin core O-glycosylation is modulated by neighboring residue glycosylation status. Kinetic modeling of the site-specific glycosylation of the apo-porcine submaxillary mucin tandem repeat by UDP-GalNAc:pOlypeptide N-acetylgalactosaminyltransferases T1 and T2. J. Biol. Chem., 277, 49850-49862.
6. Hakomori,S. (2001) Tumor-associated carbohydrate antigens defining tumor malignancy: Basis for development of anti-cancer vaccines. Adv. Exp. Med. Biol., 491, 369-402.
7. Jaeken,J. and Matthijs,G. (2007) Congenital disorders of glycosylation: a rapidly expanding disease family. Annu. Rev. Genomics Hum. Genet. 8, 261-278.
8. Karsan,A. et al. (1998) Leukocyte Adhesion Deficiency Type II is a generalized defect of de novo GDP-fucose biosynthesis. Endothelial cell fucosylation is not required for neutrophil rolling on human nonlymphoid endothelium. J. Clin. Invest., 101, 2438-2445.
9. Kikuchi,N. et al. (2005) The carbohydrate sequence markup language (CabosML): An XML description of carbohydrate structures. Bioinformatics, 21, 1717-1718.
10. Krambeck,F.J. and Betenbaugh,M.J. (2005) A mathematical model of N-linked glycosylation. Biotechnol. Bioeng., 92, 711-728.
11. Liu,G. and Neelamegham,S. (2008) In silico Biochemical Reaction Network Analysis (IBRENA): A package for simulation and analysis of reaction networks. Bioinformatics, 24, 1109-1111.
12. Liu,G. et al. (2005) Sensitivity, principal component and flux analysis applied to signal transduction: The case of epidermal growth factor mediated signaling. Bioinformatics, 21, 1194-1202.
13. Lowe,J.B. (2003) Glycan-dependent leukocyte adhesion and recruitment in inflammation. Curr. Opin. Cell. Biol., 15, 531-538.
14. Maemura,K. and Fukuda,M. (1992) Poly-N-acetyllactosaminyl O-glycans attached to leukosialin. The presence of sialyl Le(x) structures in O-glycans. J. Biol. Chem., 267, 24379-24386.
15. Marathe,D.D. et al. (2008) Systems-level studies of glycosyltransferase gene expression and enzyme activity that are associated with the selectin binding function of human leukocytes. FASEB J. [Epub ahead of print; August 26, 2008], doi: 10.1096/ fj.07-104257.
16. Monica,T.J. et al. (1997) A mathematical model of sialylation of N-linked oligosaccharides in the trans-Golgi network. Glycobiology 7, 515-521.
17. Muller,S. and Hanisch,F.G. (2002) Recombinant MUC1 probe authentically reflects cell-specific O-glycosylation profiles of endogenous breast cancer mucin. High density and prevalent core 2-based glycosylation. J. Biol. Chem., 277, 26103-26112.
18. Neelamegham,S. (2004) Transport features, reaction kinetics and receptor biomechanics controlling selectin and integrin mediated cell adhesion. Cell Commun. Adhes., 11, 35-50.
19. Packer,N.H. et al. (2008) Frontiers in glycomics: Bioinformatics and biomarkers in disease. An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006). Proteomics, 8, 8-20.
20. Royle,L. et al. (2002) An analytical and structural database provides a strategy for sequencing O-glycans from microgram quantities of glycoproteins. Anal. Biochem., 304, 70-90.
21. Sahoo,S.S. et al. (2005) GLYDE-an expressive XML standard for the representation of glycan structure. Carbohydr. Res., 340, 2802-2807.
22. Satomaa,T. et al. (2002) O-glycans on human high endothelial CD34 putatively participating in L-selectin recognition. Blood, 99 2609-2611.
23. Shelikoff,M. et al. (1996) A modeling framework for the study of protein glycosylation. Biotechnol. Bioeng., 50, 73-90.
24. Tomiya,N. et al. (2001) Determination of nucleotides and sugar nucleotides involved in protein glycosylation by high-performance anion-exchange chromatography: Sugar nucleotide contents in cultured insect cells and mammalian cells. Anal. Biochem., 293, 129-137.
25. Umana,P. and Bailey,J.E. (1997) A mathematical model of N-linked glycoform biosynthesis. Biotechnol. Bioeng., 55, 890-908.
26. Wilkins,P.P. et al. (1996) Structures of the O-glycans on P-selectin glycoprotein ligand-1 from HL-60 cells. J. Biol. Chem., 271, 18732-18742.