Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor

J Mol Model. 2009 Feb;15(2):133-45. doi: 10.1007/s00894-008-0410-0. Epub 2008 Nov 28.


The beta-lactam-based antibiotics are among the most prescribed and effective antibacterial agents. Widespread use of these antibiotics, however, has created tremendous pressure for the emergence of resistance mechanisms in bacteria. The most common cause of antibiotic resistance is bacterial production of actamases that efficiently degrade antibiotics. The metallo-beta-lactamases are of particular clinical concern due to their transference between bacterial strains. We used molecular dynamics (MD) simulations to further study the conformational changes that occur due to binding of an inhibitor to the dicanzinc metallo-beta-lactamase from Bacteroides fragilis. Our studies confirm previous findings that the major flap is a major source of plasticity within the active site, therefore its dynamic response should be considered in drug development. However, our results also suggest the need for care in using MD simulations in evaluating loop mobility, both due to relaxation times and to the need to accurately model the zinc active site. Our study also reveals two new robust responses to ligand binding. First, there are specific localized changes in the zinc active site--a local loop flip--due to ligand intercalation that may be critical to the function of this enzyme. Second, inhibitor binding perturbs the dynamics throughout the protein, without otherwise perturbing the enzyme structure. These dynamic perturbations radiate outward from the active site and their existence suggests that long-range communication and dynamics may be important in the activity of this enzyme.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Bacteroides fragilis / enzymology*
  • Catalytic Domain
  • Enzyme Inhibitors / chemistry
  • Models, Molecular*
  • Protein Conformation / drug effects
  • Zinc / chemistry*
  • beta-Lactamase Inhibitors*
  • beta-Lactamases / chemistry*
  • beta-Lactams / chemistry


  • Anti-Bacterial Agents
  • Enzyme Inhibitors
  • beta-Lactamase Inhibitors
  • beta-Lactams
  • beta-Lactamases
  • Zinc