Abstract
Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix (PGA), which is a linear polymer of β(1,6)-linked N-acetylglucosamine (GlcNAc) residues. Dispersin B (DspB), a soluble glycoside hydrolase produced by the periodontal pathogen Actinobacillus actinomycetemcomitans degrades PGA. The enzyme DspB is an α/β TIM-barrel protein and belongs to family 20 glycosyl hydrolases members. The enzyme activity of DspB with regard to its substrate specificity towards β(1,6)-linked GlcNAc polymers and its endo/exo character was investigated through ligand docking and the hydrolysis of synthetic oligosaccharides. Ligand docking analysis suggested that β(1,6)-linked GlcNAc oligosaccharide bound to the active site better that β(1,4)-linked GlcNAc oligosaccharide. Our combined results indicate that DspB is an exo-acting enzyme that hydrolyzes p(1,6)-linked N-acetylglucosamine oligomers.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Aqvist, J., Marelius, J. (2001) The linear interaction energy method for predicting ligand binding free energies. Comb. Chem. High Throughput Screen 4, 613–626.
Berendsen, H. J., Postma, J. P. M. Van Gunsteren, W. F., Hermans, J. (1981) Interaction models for water in relation to protein hydration. In: Reidel, D. (ed.) Intermolecular Forces. Dordrecht, The Netherlands, pp. 331–342.
Case, D. A., Chetham, I., Darden, T., Gohlke, H., Luo, R., Merz, K. M, Onufriev, A., Simmerling, C., Wang, B., Woods, R. (2005) The amber biomolecular simulation programs. J. Comput. Chem. 26, 1668–1688.
Davies, G. J., Wilson, K. S., Henrissat, B. (1997) Nomenclature for sugar-binding subsites in glyco-syl hydrolases. Biochem. J. 321 (Pt 2) 557–559.
Ferguson, D. (1995) Parameterization and evaluation of a flexible water model. J. Comput. Chem. 16, 501–511.
Fine, D. H., Furgang, D., Kaplan, J., Charlesworth, J., Figurski, D. H. (1999) Tenacious adhesion of Actinobacillus actinomycetemcomitans strain CU1000 to salivary-coated hydroxyapatite. Arch. Oral. Biol. 44, 1063–1076.
Hess, B., Bekker, H., Berendsen, H. J. C., Fraaije, I. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations. J. Comp. Chem. 18, 1463–1472.
Itoh, Y., Wang, X., Hinnebusch, B. J., Preston, J. F. 3r., Romeo, T. (2005) Depolymerization of beta-1,6-N-acetyl-D-glucosamine disrupts the integrity of diverse bacterial biofilms. J. Bacteriol. 187, 382–387.
Kandra, L., Gyémánt, G., Remenyik, J., Ragunath, N., Ramasubbu, N. (2003) Subsite mapping of human salivary α-amylase and the mutant Y151M. FEBS Lett. 544, 194–198.
Kaplan, J. B., Meyenhofer, M. F., Fine, D. H. (2003) Biofilm growth and detachment of Actinobacillus actinomycetemcomitans. J. Bacteriol. 185, 1399–1404.
Kaplan, J. B., Ragunath, C., Ramasubbu, N., Fine, D. H. (2003) Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity. J. Bacteriol. 185, 4693–4698.
Kaplan, J. B., Ragunath, C., Velliyagounder, K., Fine, D. H., Ramasubbu, N. (2004) Enzymatic detachment of Staphylococcus epidermidis biofilms. Antimicrob. Agents Chemother. 48, 2633–2636.
Kirschner, K. N., Woods, R. J. (2001) Solvent interactions determine carbohydrate conformation. Proc. Natl. Acad. Sci. USA 98, 10541–10545.
Kuntz, I. D., Meng, E. C., Shoichet, B. K. (1994) Structure-based molecular design. Ace. Chem. Res. 27, 117–123.
Lindahl, E., Hess, B., van der Spoel, D. (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306–317.
MacGregor, E. A., Janecek, S., Svensson, B. (2001) Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. Biochim. Biophys. Acta 1546, 1–20.
Maier, T., Strater, N., Schuette, C. G., Klingenstein, R., Sandhoff, K., Saenger, W. (2003) The X-ray crystal structure of human beta-hexosaminidase B provides new insights into Sandhoff disease. J. Mol. Biol. 328, 669–681.
Mark, B. L., Vocadlo, D. I, Knapp, S., Triggs-Raine, B. L., Withers, S. G., James, M. N. (2001) Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase. J. Biol. Chem. 276, 10330–10337.
Miyamoto, S., Kollman, P. A. (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comp. Chem. 13, 952–962.
Ramasubbu, N., Ragunath, C., Mishra, P. J. (2003) Probing the role of a mobile loop in substrate binding and enzyme activity of human salivary amylase. J. Mol. Biol. 325, 1061–1076.
Ramasubbu, N., Thomas, L. M., Ragunath,., Kaplan, J. B. (2005) Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans. J. Mol. Biol. 349, 475–486.
Slots, J., Genco, R. J. (1984) Black-pigmented Bacteroides species, Capnocytophaga species, and Actinobacillus actinomycetemcomitans in human periodontal disease: virulence factors in colonization, survival, and tissue destruction. J. Dent. Res. 63, 412–421.
Van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., Vriend, G. (1996) PRO-DRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des. 10, 255–262.
Van Gunsteren, W. F., Berendsen H. J. (1987) Gromos-87 Manual. Biomos BV:AG Groningen, The Netherlands.
Wang, J., Cieplak, P., Kollman, P. A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049–1074.
Xiang, J. Z. (2002) A Protein Structure Modeling Package. Columbia University, New York, NY.
Zambon, J. J. (1985) Actinobacillus actinomycetemcomitans in human periodontal disease. J. Clin. Periodontal. 12, 1–20.
Author information
Authors and Affiliations
Corresponding authors
Rights and permissions
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
About this article
Cite this article
Kerrigan, J.E., Ragunath, C., Kandra, L. et al. Modeling and Biochemical Analysis of the Activity of Antibiofilm Agent Dispersin B. BIOLOGIA FUTURA 59, 439–451 (2008). https://doi.org/10.1556/ABiol.59.2008.4.5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1556/ABiol.59.2008.4.5