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Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments.

Alexey Aleksandrov1, Juliane Proft, Winfried Hinrichs

  • 1Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.

Chembiochem : a European Journal of Chemical Biology
|March 17, 2007
PubMed
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Antibiotic resistance to tetracycline (Tc) involves its binding to the Tet Repressor protein (TetR). Simulations reveal Tc is preorganized for binding, with TetR using a combination of lock-and-key and induced-fit mechanisms.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Antibiotic resistance is a major global health threat.
  • Tetracycline (Tc) resistance is mediated by the Tet Repressor (TetR) protein.
  • Understanding Tc:TetR interactions is crucial for combating resistance.

Purpose of the Study:

  • To investigate the electrostatic interactions between tetracycline and the Tet Repressor protein.
  • To elucidate the role of induced fit in tetracycline binding to TetR.
  • To provide insights for engineering improved TetR ligands and proteins.

Main Methods:

  • Combined free-energy simulations and crystallographic analysis.
  • Quantum mechanical description of Tc in solution.
  • High-quality molecular mechanics model for Tc:TetR interactions.

Related Experiment Videos

  • Experimental determination of group orientations using Debye-Waller factors.

    • Main Results:

    • Simulations and experimental data showed strong agreement, validating the models.
    • Tetracycline prefers an extended, zwitterionic state in solution and when bound to TetR.
    • TetR exhibits lock-and-key binding for some regions and induced fit near the Mg2+ ion.

    Conclusions:

    • Tetracycline is preorganized for binding to TetR.
    • TetR employs a hybrid binding mechanism involving both rigid and flexible interactions.
    • The study offers valuable insights for developing novel antibiotics and gene regulation strategies.