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Updated: Oct 7, 2025

Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
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Integral equation models for solvent in macromolecular crystals.

Jonathon G Gray1, George M Giambaşu2, David A Case1

  • 1Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.

The Journal of Chemical Physics
|January 9, 2022
PubMed
Summary
This summary is machine-generated.

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A new periodic 3D-reference interaction site model (RISM) accurately predicts solvent and ion distributions in crystals. This computational method improves crystallographic data interpretation by modeling complex solvent environments in periodic systems.

Area of Science:

  • Crystallography
  • Computational Chemistry
  • Biophysics

Background:

  • Solvent constitutes a significant portion (up to 70%) of macromolecular crystals, impacting crystallographic data interpretation.
  • Existing implicit solvent models are limited for periodic solutes, often relying on simplified flat solvent models.
  • Accurate modeling of solvent distribution is crucial for understanding crystal structures and refining data.

Purpose of the Study:

  • To develop and present a periodic version of the 3D-reference interaction site model (RISM) integral equation method.
  • To enable efficient and accurate prediction of water and ion distributions in periodic systems.
  • To provide a computational tool for improved interpretation of crystallographic data, especially for charged systems.

Main Methods:

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  • Developed a periodic 3D-RISM integral equation method, extending the Ornstein-Zernike equation for charge neutrality.
  • Implemented gradient computation for use in minimization and molecular dynamics simulations.
  • Applied the method to model solvent distributions in protein, RNA, and small molecule crystals.

Main Results:

  • The periodic 3D-RISM model accurately describes water and ion distributions in periodic systems.
  • Calculations showed improved agreement between predicted and experimental X-ray scattering intensities compared to flat solvent models.
  • The greatest improvement in agreement was observed in the 2 to 4 Å resolution range.

Conclusions:

  • The periodic 3D-RISM method offers a significant advancement for modeling solvent in crystallographic studies.
  • This approach enhances the interpretation of crystallographic data by providing a more realistic solvent model.
  • Future integration of integral equation models into crystallographic refinement holds promise for further improvements.