Related Experiment Video
Updated: Apr 15, 2026
14:04
Derivatization of Protein Crystals with I3C using Random Microseed Matrix Screening
Published on: January 16, 2021
5.1K
Routine phasing of coiled-coil protein crystal structures with AMPLE.
Jens M H Thomas1, Ronan M Keegan2, Jaclyn Bibby1
1Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, England.
Iucrj
|April 14, 2015
Summary
AMPLE, a novel computational tool, successfully solves complex coiled-coil protein structures using ab initio methods when homologous structures are unavailable. This breakthrough aids in determining the structure of abundant protein folds, improving crystallographic elucidation.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Coiled-coil protein folds are abundant but challenging to solve crystallographically.
- Traditional molecular replacement methods struggle with these structures due to lack of homologous templates.
Purpose of the Study:
- To introduce and validate the AMPLE program for solving coiled-coil crystal structures.
- To demonstrate AMPLE's capability in the absence of homologous protein structures.
Main Methods:
- Utilized ab initio search models for molecular replacement.
- Benchmarked AMPLE on a diverse dataset of coiled-coil crystal structures.
- Compared AMPLE's performance against single structure and ideal polyalanine helix phasing.
Main Results:
- AMPLE successfully solved 80% of tested coiled-coil structures.
- Achieved solutions for structures up to 253 residues and resolutions of 2.9 Å.
- Successfully phased macromolecular complexes containing coiled-coil components, including DNA.
Conclusions:
- AMPLE is a highly effective method for crystallographic elucidation of coiled-coil structures.
- Ab initio modeling and ensemble search models are key to AMPLE's success.
- AMPLE offers a viable route for phasing complex structures by leveraging coiled-coil motifs.
