Presentation, presentation, presentation! Molecular-level insight into linker effects on glycan array screening data

Glycobiology

Volumn 24, Issue 1, 2014, Pages 17-25

  Grant, Oliver C ^a   Smith, Hannah M K ^a   Firsova, Daria ^a   Fadda, Elisa ^a,b   Woods, Robert J ^a,b  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

glycan array screening; glycan specificity; glycan binding protein; linker effects; molecular dynamics

Indexed keywords

CARBOHYDRATE BINDING PROTEIN; GLYCAN; GLYCAN BINDING PROTEIN; N ACETYLGALACTOSAMINE; N ACETYLGLUCOSAMINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; FALSE NEGATIVE RESULT; GLYCOBIOLOGY; HYDROPHILICITY; HYDROPHOBICITY; MICROARRAY ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MODEL; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN CARBOHYDRATE INTERACTION; SCREENING;

GLYCAN ARRAY SCREENING; GLYCAN SPECIFICITY; GLYCAN-BINDING PROTEIN; LINKER EFFECTS; MOLECULAR DYNAMICS;

AMINO ACIDS; HUMANS; LECTINS; MICROARRAY ANALYSIS; POLYSACCHARIDES;

EID: 84890350538     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwt083     Document Type: Article

References (30)

1. Alvarez RA, Blixt O. 2006. Identification of ligand specificities for glycanbinding proteins using glycan arrays. Methods Enzymol. 415:292-310.
2. Bayly CI, Cieplak P, CornellW, Kollman PA. 1993. Awell-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem. 97:10269-10280.
3. Blixt O, Head S, Mondala T, Scanlan C, Huflejt ME, Alvarez R, Bryan MC, Fazio F, Calarese D, Stevens J, et al. 2004. Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci USA. 101:17033-17038.
4. Breneman CM, Wiberg KB. 1990. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J Comput Chem. 11:361-373.
5. Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, et al. 2012. AMBER 12. San Francisco, CA: University of California
6. Dennis JW, Granovsky M, Warren CE. 1999. Glycoprotein glycosylation and cancer progression. Biochim Biophys Acta. 1473:21-34.
7. Feizi T, Stoll MS, Yuen CT, Chai W, Lawson AM. 1994. Neoglycolipids: Probes of oligosaccharide structure, antigenicity, and function. Methods Enzymol. 230:484-519.
8. Foley BL, Tessier MN, Makeneni S, Nivedha A. GLYLIB Programmers' Libraries. Complex Carbohydrate Research Center, The University of Georgia. http://glycam.ccrc.uga.edu/glylib. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, et al. Gaussian 09, Revision A.1.Wallingford, CT: Gaussian, Inc
9. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput. 8:1542-1555.
10. Heimburg J, Yan J, Morey S, Glinskii OV, Huxley VH,Wild L, Klick R, Roy R, Glinsky VV, Rittenhouse-Olson K. 2006. Inhibition of spontaneous breast cancer metastasis by anti-Thomsen-Friedenreich antigen monoclonal antibody JAA-F11. Neoplasia. 8:939-948.
11. Heimburg-Molinaro J, Lum M, Vijay G, Jain M, Almogren A, Rittenhouse-Olson K. 2011. Cancer vaccines and carbohydrate epitopes. Vaccine. 29:8802-8826.
12. Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. 2006. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65:712-725.
13. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 79:926-935.
14. Kirschner KN, Yongye AB, Tschampel SM, Gonzalez-Outeirino J, Daniels CR, Foley BL, Woods RJ. 2008. GLYCAM06: A generalizable biomolecular force field. Carbohydrates. J Comput Chem. 29:622-655.
15. Lewallen DM, Siler D, Iyer SS. 2009. Factors affecting protein-glycan specificity: Effect of spacers and incubation time. Chembiochem. 10:1486-1489.
16. Nishikawa I, Nakajima Y, Ito M, Fukuchi S, Homma K, Nishikawa K. 2010. Computational prediction of O-linked glycosylation sites that preferentially map on intrinsically disordered regions of extracellular proteins. Int J Mol Sci. 11:4991-5008.
17. Oyelaran O, Gildersleeve JC. 2009. Glycan arrays: Recent advances and future challenges. Curr Opin Chem Biol. 13:406-413.
18. Padler-Karavani V, Song X, Yu H, Hurtado-Ziola N, Huang S, Muthana S, Chokhawala HA, Cheng J, Verhagen A, Langereis MA, et al. 2012. Cross-comparison of protein recognition of sialic acid diversity on two novel sialoglycan microarrays. J Biol Chem. 287:22593-22608.
19. Pai SS, Hammouda B, Hong K, Pozzo DC, Przybycien TM, Tilton RD. 2011. The conformation of the poly(ethylene glycol) chain in mono-PEGylated lysozyme and mono-PEGylated human growth hormone. Bioconjug Chem. 22:2317-2323.
20. Paulson JC, Blixt O, Collins BE. 2006. Sweet spots in functional glycomics. Nat Chem Biol. 2:238-248.
21. Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MR. 2004. Statistical analysis of the protein environment of N-glycosylation sites: Implications for occupancy, structure, and folding. Glycobiology. 14:103-114.
22. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 25:1605-1612.
23. Rittenhouse-Diakun K, Xia Z, Pickhardt D, Morey S, Baek MG, Roy R. 1998. Development and characterization of monoclonal antibody to T-antigen: (gal beta1-3GalNAc-alpha-O). Hybridoma. 17:165-173.
24. Rudd PM, Elliott T, Cresswell P, Wilson IA, Dwek RA. 2001. Glycosylation and the immune system. Science. 291:2370-2376.
25. Suite. 2011. Maestro, version 9.2. New York, NY: Schrödinger, LLC. Tessier MB, Grant OC, Heimburg-Molinaro J, Smith D, Jadey S, Gulick AM, Glushka J, Deutscher SL, Rittenhouse-Olson K, Woods RJ. 2013. Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PLoS One. 8: E54874.
26. Thompson MA. ArgusLab 4.0.1. Seattle,WA: Planaria Software LLC
27. Varki A, Cummings RD, Esko JD, H.H. F, Stanley P, Bertozzi CR, Hart GW, Etzler ME. 2009a. Glycans in Acquired Human Diseases. Essentials of Glycobiology. 2nd ed. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press, Available from http://www.ncbi.nlm.nih.gov/books/NBK1908
28. ang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. 2004. Development and testing of a general amber force field. J Comput Chem. 25:1157-1174.
29. Woods Group. (2005-2013). GLYCAM Web. Athens, GA: Complex Carbohydrate Research Center, University of Georgia (http://www.glycam.com).
30. Yu LG. 2007. The oncofetal Thomsen-Friedenreich carbohydrate antigen in cancer progression. Glycoconj J. 24:411-420.