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Helical ensembles outperform ideal helices in molecular replacement

Lookup NU author(s): Dr Owen Davies

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Abstract

© 2020 Sánchez Rodríguez et al.The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: Transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the 'helical ensembles' mode.


Publication metadata

Author(s): Rodriguez FS, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ

Publication type: Article

Publication status: Published

Journal: Acta Crystallographica Section D: Structural Biology

Year: 2020

Volume: 76

Issue: 10

Pages: 962-970

Print publication date: 01/10/2020

Online publication date: 15/10/2020

Acceptance date: 18/08/2020

ISSN (electronic): 2059-7983

Publisher: International Union of Crystallography

URL: https://doi.org/10.1107/S205979832001133X

DOI: 10.1107/S205979832001133X

PubMed id: 33021498


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