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A Molecular Mechanics Model for Flavins.

Alexey Aleksandrov1

  • 1Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, IP Paris, 91128, Palaiseau, France.

Journal of Computational Chemistry
|September 1, 2019
PubMed
Summary
This summary is machine-generated.

New molecular mechanics force field parameters were developed for flavins, essential cofactors in enzymatic reactions. This model accurately simulates flavin cofactors in various protonation and redox states for enhanced biological simulations.

Keywords:
CHAMMflavinflavin adenine nucleotideflavin mononucleotideflavoproteinforce fieldmolecular dynamicsriboflavin

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Area of Science:

  • Biochemistry and Molecular Biophysics
  • Computational Chemistry

Background:

  • Flavin-containing molecules are crucial cofactors in numerous enzymatic reactions.
  • The isoalloxazine system in flavins facilitates one- and two-electron transfer and exists in multiple protonation states.

Purpose of the Study:

  • To derive molecular mechanics force field parameters for CHARMM36 compatible with biologically significant flavins.
  • To develop a model accounting for key protonation and redox states of the isoalloxazine group.

Main Methods:

  • Utilized CHARMM force field parametrization strategy with quantum mechanics for water-solute interactions.
  • Optimized partial charges using monohydrate energies, geometries, and electrostatic potential restraints.
  • Parametrized bonded terms, including stiff terms and torsion angles, via potential energy surface scans.

Main Results:

  • Developed parameters for riboflavin, flavin mononucleotide, and flavin adenine dinucleotide.
  • Model accurately reproduces isoalloxazine butterfly motion in oxidized and reduced states.
  • Validated model through simulations of four flavoproteins.

Conclusions:

  • The presented molecular mechanics model is suitable for simulating flavin cofactors in diverse redox states.
  • This work provides a valuable tool for computational studies involving flavoproteins and flavin chemistry.