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Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling

Lookup NU author(s): Dr Owen Davies

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular replacement approaches using ab initio models and ideal secondary structure components have greatly contributed to solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which relatively rigid α-helices provide very useful molecular replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, we report an expansion in the scope of coiled-coil structure solution by AMPLE, which has been achieved through general improvements in the pipeline, removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two/three/four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/anti-parallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting ‘coiled-coil’ mode.


Publication metadata

Author(s): Thomas JMH, Keegan RM, Rigden DJ, Davies OR

Publication type: Article

Publication status: Published

Journal: Acta Crystallographica Section D: Structural Biology

Year: 2020

Volume: D76

Online publication date: 14/01/2020

Acceptance date: 14/01/2020

Date deposited: 27/02/2020

ISSN (electronic): 2059-7983

Publisher: Wiley-Blackwell Publishing Ltd.

URL: https://doi.org/10.1107/S2059798320000443

DOI: 10.1107/S2059798320000443


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