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Determination of Crystal Structures01:29

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In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
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Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules.

Timothy D Fenn1, Michael J Schnieders, Axel T Brunger

  • 1Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, USA.

Biophysical Journal
|June 17, 2010
PubMed
Summary

A new polarizable atomic multipole refinement method using the AMOEBA force field improves macromolecular models. This approach enhances biomolecular electron density description and aids in predicting protein function and interactions.

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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Macromolecular crystallography is crucial for understanding biomolecular structure and function.
  • Standard refinement procedures may not fully capture the nuances of electron density and electrostatic interactions.
  • Accurate atomic models are essential for reliable functional predictions.

Purpose of the Study:

  • To introduce and validate a novel polarizable atomic multipole refinement method assisted by the AMOEBA force field for macromolecular crystallography.
  • To assess the method's ability to improve the description of biomolecular electron density and atomic models.
  • To demonstrate the utility of the method in predicting protein-ligand interactions and active site behavior.

Main Methods:

  • Development of a polarizable atomic multipole refinement method incorporating the AMOEBA force field.
  • Application of the method to high-resolution lysozyme and trypsin crystal structures.
  • Re-refinement of a DNA crystal structure to evaluate its capability in modeling hydrogen bonding patterns.

Main Results:

  • The AMOEBA-assisted refinement led to a 0.4-0.6% decrease in R- and R(free)-values, indicating improved model accuracy.
  • A corresponding decrease in relative energy (0.4-0.8 Kcal/mol/residue) was observed, signifying a more stable and accurate model.
  • The method successfully oriented water networks and catalytically relevant hydrogens, enabling functional predictions.
  • Accurate modeling of DNA minor groove hydrogen bonding was achieved without manual intervention.

Conclusions:

  • The polarizable atomic multipole refinement method offers a more rigorous treatment of X-ray scattering and electrostatics than standard methods.
  • This approach significantly enhances the information content of atomic models derived from macromolecular crystallography.
  • The AMOEBA force field's polarizable electrostatics model is broadly applicable and informative for crystal structures across all resolution ranges.