Protein Engineering, Vol. 13, No. 2, 89-98,
February 2000
© 2000 Oxford University Press
Analysis and prediction of carbohydrate binding sites
1 Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT and Department of Crystallography, Birkbeck College, Malet Street, London, WC1 7HX, UK
An analysis of the characteristic properties of sugar binding sites was performed on a set of 19 sugar binding proteins. For each site six parameters were evaluated: solvation potential, residue propensity, hydrophobicity, planarity, protrusion and relative accessible surface area. Three of the parameters were found to distinguish the observed sugar binding sites from the other surface patches. These parameters were then used to calculate the probability for a surface patch to be a carbohydrate binding site. The prediction was optimized on a set of 19 non-homologous carbohydrate binding structures and a test prediction was carried out on a set of 40 protein–carbohydrate complexes. The overall accuracy of prediction achieved was 65%. Results were in general better for carbohydrate-binding enzymes than for the lectins, with a rate of success of 87%.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. I. Lehrer, G. Jung, P. Ruchala, S. Andre, H. J. Gabius, and W. Lu Multivalent Binding of Carbohydrates by the Human {alpha}-Defensin, HD5 J. Immunol., July 1, 2009; 183(1): 480 - 490. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Voss, A. Diez-Sampedro, B. A. Hirayama, D. D. F. Loo, and E. M. Wright Imino Sugars Are Potent Agonists of the Human Glucose Sensor SGLT3 Mol. Pharmacol., February 1, 2007; 71(2): 628 - 634. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Bejar, X. Jin, M. A. Ballicora, and J. Preiss Molecular Architecture of the Glucose 1-Phosphate Site in ADP-glucose Pyrophosphorylases J. Biol. Chem., December 29, 2006; 281(52): 40473 - 40484. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Zhou, G. Zhao, J. J. Truglio, L. Wang, G. Li, W. J. Lennarz, and H. Schindelin Structural and biochemical studies of the C-terminal domain of mouse peptide-N-glycanase identify it as a mannose-binding module PNAS, November 14, 2006; 103(46): 17214 - 17219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. M. Wright, D. D. F. Loo, B. A. Hirayama, and E. Turk Surprising Versatility of Na+-Glucose Cotransporters: SLC5 Physiology, December 1, 2004; 19(6): 370 - 376. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Shionyu-Mitsuyama, T. Shirai, H. Ishida, and T. Yamane An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins Protein Eng. Des. Sel., July 1, 2003; 16(7): 467 - 478. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Connaris, T. Takimoto, R. Russell, S. Crennell, I. Moustafa, A. Portner, and G. Taylor Probing the Sialic Acid Binding Site of the Hemagglutinin-Neuraminidase of Newcastle Disease Virus: Identification of Key Amino Acids Involved in Cell Binding, Catalysis, and Fusion J. Virol., February 15, 2002; 76(4): 1816 - 1824. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Nobeli, R. A. Laskowski, W. S. J. Valdar, and J. M. Thornton On the molecular discrimination between adenine and guanine by proteins Nucleic Acids Res., November 1, 2001; 29(21): 4294 - 4309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. W. McLean, M. R. Bray, A. B. Boraston, N. R. Gilkes, C. A. Haynes, and D. G. Kilburn Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues Protein Eng. Des. Sel., November 1, 2000; 13(11): 801 - 809. [Abstract] [Full Text] [PDF]
|
|