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SCEDS: protein fragments for molecular replacement in Phaser
Airlie J McCoy1, Robert A Nicholls, Thomas R Schneider
1Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 0XY, England.
Acta Crystallographica. Section D, Biological Crystallography
|November 6, 2013
Summary
This study introduces a new method to generate protein fragments for molecular replacement (MR) modeling. These fragments, identified using normal mode analysis and a scoring system, improve structural refinement accuracy for proteins with conformational changes.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Molecular replacement (MR) is a crucial technique in X-ray crystallography for determining protein structures.
- Identifying suitable template models is essential for successful MR, especially for proteins exhibiting conformational flexibility.
- Existing methods may struggle with proteins that undergo significant conformational changes, impacting the accuracy of MR.
Purpose of the Study:
- To develop and validate a novel method for generating optimized protein fragments for MR template models.
- To enhance the accuracy of MR, particularly for proteins with conformational variability.
- To improve the efficiency and success rate of protein structure determination using MR.
Main Methods:
- Perturbation of template protein structures along low-frequency normal modes of an elastic network model.
- Identification of structurally invariant regions by analyzing difference distance matrices between perturbed and unperturbed structures.
- Scoring of identified fragments using the SCEDS metric, assessing sphericity, chain continuity, atom counts, and C(α) density.
- Implementation of the method in the Phaser software for practical application in MR.
Main Results:
- The SCEDS scoring effectively identifies protein fragments suitable for MR template models.
- Test cases demonstrated that fragments identified by this method lead to a lower R factor after refinement compared to the original template structure.
- This improvement is particularly notable for proteins containing fragments that change their relative positions (juxtaposition) between the template and target structures.
Conclusions:
- The described method provides a robust approach for generating improved MR template models from flexible proteins.
- Utilizing normal mode analysis and the SCEDS scoring system enhances the identification of invariant, yet conformationally relevant, protein fragments.
- The integration into Phaser software facilitates wider adoption and application in structural biology workflows.
