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Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.

Siyuan Du1, Stephanie A Wankowicz2, Filip Yabukarski3

  • 1Department of Biochemistry, Stanford University, Stanford, CA, United States; Department of Chemistry, Stanford University, Stanford, CA, United States.

Methods in Enzymology
|September 25, 2023
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Summary
This summary is machine-generated.

Understanding protein function requires atomic-level models of conformational ensembles. This study refines multiconformer models from X-ray diffraction data, revealing temperature-driven protein changes and their functional implications.

Keywords:
Conformational ensemblesMulti-temperature X-ray crystallographyMulticonformer modelRoom temperature X-rayStructural model refinement

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Area of Science:

  • Structural Biology
  • Biophysics
  • X-ray Crystallography

Background:

  • Protein conformational ensembles are crucial for function.
  • Traditional crystallography limits understanding of protein dynamics.
  • Recent advances allow data collection at ambient temperatures.

Purpose of the Study:

  • To provide a tutorial for refining multiconformer ensemble models from X-ray diffraction data.
  • To investigate temperature-driven conformational changes in Proteinase K.
  • To link protein ensemble information to function.

Main Methods:

  • Collected X-ray diffraction datasets for Proteinase K at temperatures from 313 to 363 K.
  • Integrated automated sampling and refinement tools with manual adjustments.
  • Developed multiconformer models detailing backbone and sidechain conformations, occupancies, and interconnections.

Main Results:

  • Obtained multiconformer models capturing extensive and diverse conformational changes.
  • Observed increased bound peptide ligand occupancies with temperature.
  • Identified altered calcium (Ca2+) binding site configurations and rotameric distributions.

Conclusions:

  • Multiconformer model refinement is essential for extracting ensemble information from diffraction data.
  • Temperature significantly influences protein conformation and ligand binding.
  • Understanding ensemble-function relationships is vital for protein science.