Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2013, Article ID 783540, 11 pages
http://dx.doi.org/10.1155/2013/783540
Research Article

Molecular Characterization and In Silico Analysis of Naturally Occurring TEM Beta-Lactamase Variants among Pathogenic Enterobacteriaceae Infecting Indian Patients

Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108 C. R. Avenue, Kolkata 700073, India

Received 24 April 2013; Accepted 9 September 2013

Academic Editor: Veeranoot Nissapatorn

Copyright © 2013 Lena Dhara et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. A. Bradford, “Extended-spectrum β-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat,” Clinical Microbiology Reviews, vol. 14, no. 4, pp. 933–951, 2001. View at Publisher · View at Google Scholar · View at Scopus
  2. M. Andre, L. B. Josette, and M. Jean, “Catalytic properties of class A β-lactamases: efficiency and diversity,” Biochemical Journal, vol. 330, no. 2, pp. 581–598, 1998. View at Google Scholar · View at Scopus
  3. C. L. Worth, R. Preissner, and T. L. Blundell, “SDM: a server for predicting effects of mutations on protein stability and malfunction,” Nucleic Acids Research, vol. 39, no. 2, pp. W215–W222, 2011. View at Publisher · View at Google Scholar · View at Scopus
  4. M. Gniadkowski, “Evolution of extended-spectrum β-lactamases by mutation,” Clinical Microbiology and Infection, vol. 14, no. 1, pp. 11–32, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. J. Sarma, P. Bhattacharya, D. Kalita, and M. Rajbangshi, “Multidrug-resistant Enterobacteriaceae including metallo-β-lactamase producers are predominant pathogens of healthcare-associated infections in an Indian teaching hospital,” Indian Journal of Medical Microbiology, vol. 29, no. 1, pp. 22–27, 2011. View at Publisher · View at Google Scholar · View at Scopus
  6. A. Jain, I. Roy, M. K. Gupta, M. Kumar, and S. K. Agarwal, “Prevalence of extended-spectrum β-lactamase-producing Gram-negative bacteria in septicaemic neonates in a tertiary care hospital,” Journal of Medical Microbiology, vol. 52, no. 5, pp. 421–425, 2003. View at Publisher · View at Google Scholar · View at Scopus
  7. A. Tripathi, S. K. Dutta, M. Majumdar, L. Dhara, D. Banerjee, and K. Roy, “High prevalence and significant association of ESBL and QNR genes in pathogenic Klebsiella pneumoniae isolates of patients from Kolkata, India,” Indian Journal of Microbiology, vol. 52, no. 4, pp. 556–564, 2012. View at Google Scholar
  8. “Performance standards for antimicrobial susceptibility testing, eighteenth informational supplement,” Tech. Rep. M100-S18, Clinical and Laboratory Standards Institute, Wayne, Pa, USA, 2008.
  9. K. T. Lim, C. C. Yeo, R. M. Yasin, G. Balan, and K. L. Thong, “Characterization of multidrug-resistant and extended-spectrum β-lactamase-producing Klebsiella pneumoniae strains from Malaysian hospitals,” Journal of Medical Microbiology, vol. 58, no. 11, pp. 1463–1469, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. J. M. Andrews, “Determination of minimum inhibitory concentrations,” Journal of Antimicrobial Chemotherapy, vol. 48, pp. 5–16, 2002. View at Google Scholar · View at Scopus
  11. J. Sambrook and D. W. Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA, 3rd edition, 2001.
  12. S. Rozen and H. J. Skaletsky, “Primer3 on the WWW for general users and for biologist programmers,” in Bioinformatics Methods and Protocols: Methods in Molecular Biology, S. Krawetz and S. Misener, Eds., 2000. View at Google Scholar
  13. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  14. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. N. Eswar, B. Webb, M. A. Marti-Renom et al., “Comparative protein structure modeling using MODELLER,” Current Protocols in Protein Science, vol. 50, pp. 2.9.1–2.9.31, 2007. View at Google Scholar · View at Scopus
  16. V. Randhawa and R. Jamwal, “Molecular modeling and virtual screening studies of NDM-1 Beta lactamase for identification of a series of potent inhibitors,” International Research Journal of Biochemistry and Bioinformatics, vol. 1, no. 4, pp. 95–102, 2011. View at Google Scholar
  17. W. L. DeLano, The PyMol Molecular Graphics System, DeLano Scientific LLC, Palo Alto, Calif, USA, 2002.
  18. V. Parthiban, M. M. Gromiha, M. Abhinandan, and D. Schomburg, “Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development,” BMC Structural Biology, vol. 7, article 54, pp. 1–9, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. M. D. S. Kumar, K. A. Bava, M. M. Gromiha et al., “ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions,” Nucleic Acids Research, vol. 34, pp. D204–D206, 2006. View at Google Scholar · View at Scopus
  20. R. Maiti, G. H. van Domselaar, H. Zhang, and D. S. Wishart, “SuperPose: a simple server for sophisticated structural superposition,” Nucleic Acids Research, vol. 32, pp. W590–W594, 2004. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Dundas, Z. Ouyang, J. Tseng, A. Binkowski, Y. Turpaz, and J. Liang, “CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues,” Nucleic Acids Research, vol. 34, pp. W116–W118, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. J. J. Irwin and B. K. Shoichet, “ZINC: a free database of commercially available compounds for virtual screening,” Journal of Chemical Information and Modeling, vol. 45, no. 1, pp. 177–182, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. Z. Zhang, Y. Li, B. Lin, M. Schroeder, and B. Huang, “Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction,” Bioinformatics, vol. 27, no. 15, Article ID btr331, pp. 2083–2088, 2011. View at Publisher · View at Google Scholar · View at Scopus
  24. G. M. Morris, D. S. Goodsell, R. S. Halliday et al., “Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function,” Journal of Computational Chemistry, vol. 19, no. 14, pp. 1639–1662, 1998. View at Google Scholar · View at Scopus
  25. A. C. Wallace, R. A. Laskowski, and J. M. Thornton, “LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions,” Protein Engineering, vol. 8, no. 2, pp. 127–134, 1996. View at Google Scholar · View at Scopus
  26. G. A. Menezes, M. A. Khan, B. N. Harish et al., “Molecular characterization of antimicrobial resistance in non-typhoidal salmonellae associated with systemic manifestations from India,” Journal of Medical Microbiology, vol. 59, no. 12, pp. 1477–1483, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. C. N. Pace and J. M. Scholtz, “A helix propensity scale based on experimental studies of peptides and proteins,” Biophysical Journal, vol. 75, no. 1, pp. 422–427, 1998. View at Google Scholar · View at Scopus
  28. M. J. Betts and R. B. Russell, “Amino acid properties and consequences of substitutions,” in Bioinformatics for Geneticists, M. R. Barnes and I. C. Gray, Eds., Wiley & Sons, New York, NY, USA, 2003. View at Google Scholar
  29. A. U. Khan, M. H. Baig, and G. Wadhwa, “Molecular docking analysis of new generation cephalosporins interactions with recently known SHV-variants,” Bioinformation, vol. 5, no. 8, pp. 331–335, 2011. View at Google Scholar
  30. A. K. Varma, R. Patil, S. Das, A. Stanley, L. Yadav, and A. Sudhakar, “Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of Drug-Designing,” PLoS ONE, vol. 5, no. 8, Article ID e12029, 2010. View at Publisher · View at Google Scholar · View at Scopus