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Microcrystallography of Protein Crystals and In Cellulo Diffraction
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Improving sampling of crystallographic disorder in ensemble refinement.

Nicoleta Ploscariu1, Tom Burnley2, Piet Gros1

  • 1Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Acta Crystallographica. Section D, Structural Biology
|November 2, 2021
PubMed
Summary
This summary is machine-generated.

Ensemble refinement improves macromolecular structures by modeling disorder. New DEN restraints and ECHT disorder models enhance sampling and physical interpretability in crystallographic refinement.

Keywords:
disorder modellingensemble refinementmolecular dynamicsstructure refinement

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Ensemble refinement uses molecular dynamics for crystallographic refinement, modeling macromolecular disorder for improved accuracy over single-model approaches.
  • Current limitations include suboptimal sampling and physically unrealistic models due to inadequate disorder modeling.

Purpose of the Study:

  • To introduce two key improvements to ensemble refinement within the Phenix software suite.
  • To enhance the accuracy, physical realism, and utility of ensemble refinement for macromolecular crystallography.

Main Methods:

  • Implementation of DEN (Disordered Ensemble) restraints to guide local conformational sampling.
  • Integration of ECHT (Ensemble Crystallographic Heterogeneity) disorder models for improved parameterization of continuous disorder.
  • Application and validation of the improved methods on various case studies, including the SARS-CoV-2 main protease.

Main Results:

  • DEN restraints facilitate more robust exploration of local conformational landscapes.
  • ECHT disorder models enable the selection of physically meaningful disorder parameterizations.
  • The enhanced ensemble refinement yields more consistent and interpretable simulations of macromolecules in crystalline environments.
  • Systematic exploration of structural heterogeneity and disorder across different scales is now possible.

Conclusions:

  • The presented improvements significantly advance ensemble refinement methodology in macromolecular crystallography.
  • These advancements lead to more accurate and physically realistic structural models, better capturing molecular heterogeneity.
  • The choice of disorder model critically influences the sampling of disorder in restrained molecular dynamics simulations.