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Related Experiment Videos

The hydration shell of myoglobin.

F Parak1, H Hartmann, M Schmidt

  • 1J. Gutenberg-Universität, Institut für Molekulare Biophysik, Mainz, Federal Republic of Germany.

European Biophysics Journal : EBJ
|January 1, 1992
PubMed
Summary

Monte Carlo calculations accurately modeled water molecules within metmyoglobin crystals, improving crystallographic refinement. This method better represents crystal water than homogeneous electron density, yielding superior structural data.

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Area of Science:

  • Biophysics
  • Crystallography
  • Computational Chemistry

Background:

  • Crystallographic studies often face challenges in accurately modeling solvent molecules within unit cells.
  • The precise location and density of water molecules can significantly impact protein structure refinement.

Purpose of the Study:

  • To investigate the utility of Monte Carlo (MC) simulations for modeling water molecules in metmyoglobin crystals.
  • To compare the effectiveness of MC-simulated water with homogeneous electron density models for crystallographic refinement.

Main Methods:

  • Monte Carlo calculations were employed to fill unoccupied space within the metmyoglobin unit cell with water molecules.
  • Structure factors were computed using obtained water coordinates and known myoglobin atomic coordinates.

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  • Comparison of calculated structure factors with experimental data was performed.

    • Main Results:

    • A model with 814 MC water molecules per unit cell and a B-value of 50 Ų effectively reproduced both low and high-resolution experimental structure factors.
    • The MC water model resulted in a significantly lower R-value (0.166) compared to a homogeneous electron density model (R = 0.212).
    • Reciprocal space refinement using MC water and protein coordinates improved the overall structural model.

    Conclusions:

    • Monte Carlo calculations provide valuable information for crystallographically invisible regions, such as solvent molecules.
    • This computational approach enhances the refinement of visible protein coordinates by accurately representing crystal water.
    • MC simulations offer a superior method for modeling crystal water compared to traditional homogeneous electron density approaches.