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Related Concept Videos

Theories of Dissolution: The Danckwerts' Model and Interfacial Barrier Model01:09

Theories of Dissolution: The Danckwerts' Model and Interfacial Barrier Model

Various dissolution theories provide insight into the factors that influence the dissolution rate. Danckwerts' Model suggests that turbulence, rather than a stagnant layer, characterizes the dissolution medium at the solid-liquid interface. In this model, the agitated solvent contains macroscopic packets that move to the interface via eddy currents, facilitating the absorption and delivery of the drug to the bulk solution. The regular replenishment of solvent packets maintains the concentration...
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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
09:42

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Published on: January 16, 2016

On the application of structure-specific bulk-solvent models.

Nicholas M Glykos1

  • 1Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece. glykos@mbg.duth.gr

Acta Crystallographica. Section D, Biological Crystallography
|July 29, 2011
PubMed
Summary

Improving bulk solvent modeling in macromolecular crystallography using physics-based simulations significantly enhances crystallographic model accuracy. This detailed approach refines the agreement between experimental data and structural models.

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Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Chemistry

Background:

  • Macromolecular refinement often uses simplified bulk solvent models.
  • High R factors suggest limitations in current solvent modeling techniques.
  • Accurate modeling of the solvent environment is crucial for complex biomolecules.

Purpose of the Study:

  • To test the hypothesis that improved bulk solvent modeling enhances crystallographic model accuracy.
  • To construct a detailed, physics-based model of bulk solvent for a known crystal structure.
  • To evaluate the impact of this detailed solvent model on crystallographic refinement.

Main Methods:

  • Molecular-dynamics simulations were used to create a structure-specific bulk solvent model.
  • The simulation-derived water-distribution map was converted into a partial structure factor.
  • This detailed solvent model was incorporated into a re-refinement of a crystal structure.

Main Results:

  • A physics-based, structure-specific bulk solvent model was successfully generated.
  • Incorporating the detailed solvent model into refinement led to a 0.3% reduction in the free R value.
  • This improvement surpasses the results obtained with simple Babinet-based corrections.

Conclusions:

  • Detailed, physics-based modeling of bulk solvent can improve crystallographic refinement.
  • The findings support the hypothesis that enhanced solvent modeling is beneficial for macromolecular crystallography.
  • Further research can explore the implications for modeling complex biological systems.