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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
Detection of alternative conformations by unrestrained refinement
Oleg V Sobolev1, Vladimir Y Lunin
1Laboratory of Macromolecular Crystallography, Institute of Mathematical Problems of Biology, RAS, Pushchino, Moscow Region, Russian Federation. sobolev@impb.psn.ru
Acta Crystallographica. Section D, Biological Crystallography
|September 6, 2012
Summary
Analyzing atomic shifts during unrestrained refinement can reveal residues with alternative conformations. This method aids in improving crystallographic models by identifying and refining disordered or multi-conformation residues.
Area of Science:
- Crystallography
- Structural Biology
- X-ray Diffraction
Background:
- Unrestrained refinement is generally stable at atomic resolution.
- Geometrical restraints are crucial for residues with multiple conformations to prevent model deterioration.
- Identifying residues with alternative conformations is essential for accurate structural analysis.
Purpose of the Study:
- To develop routine methods for identifying residues likely present in alternative conformations or disordered states.
- To provide a quantitative approach for analyzing atomic shifts during unrestrained refinement.
- To enhance the accuracy of crystallographic models by systematically addressing problematic residues.
Main Methods:
- Two methods analyzing atomic center shifts from unrestrained refinement cycles were developed.
- A simple diagram plotting atomic shifts against residue number for qualitative assessment.
- Decision-making procedures were created and tested for quantitative identification of residues needing further examination.
Main Results:
- Analysis of atomic shifts reliably identifies residues likely in alternative conformations or disordered.
- Procedures based on atomic shifts proved more dependable than those using atomic displacement parameters or density values.
- Tested on 203 Protein Data Bank structures refined better than 1.2 Å, confirming reliability.
Conclusions:
- Atomic shift analysis is a robust method for detecting residues with alternative conformations.
- These methods facilitate the routine identification and proper modeling of disordered or multi-conformation residues.
- Improved crystallographic model accuracy can be achieved by systematically applying these analytical procedures.
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