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

Acta Crystallographica. Section D, Structural Biology
Jens M H ThomasOwen R Davies

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 the 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 the 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, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the 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 the existing modelling p...Continue Reading

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Citations

Oct 7, 2020·Acta Crystallographica. Section D, Structural Biology·Filomeno Sánchez RodríguezDaniel J Rigden
Jun 16, 2021·Open Biology·C R MortonL Pellegrini
Aug 11, 2021·Nature Structural & Molecular Biology·James M DunceOwen R Davies

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Methods Mentioned

BETA
X-ray

Software Mentioned

PyMOL
SPICKER
SHELXE
Rosetta
SHELXE CC
SOCKET
CCP
Rosetta Fold - and - Dock
TWISTER
CCFold

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