A fragmentation and reassembly method for ab initio phasing. (1st February 2015)

• Record Type: Journal Article
• Authors: Shrestha, Rojan; Zhang, Kam Y. J.
• Is Part Of: Acta crystallographica. Volume 71:Part 2(2015:Feb.)
• Page Start: 304
• Page End: 312
• Publication Date: 2015-02-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004714025449
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p> <italic>Ab initio</italic> phasing with <italic>de novo</italic> models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts <italic>de novo</italic> models and uses them for structure determination by molecular replacement. However, even the current state‐of‐the‐art <italic>de novo</italic> modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment‐assembly phasing method has been developed that starts from an ensemble of low‐accuracy <italic>de novo</italic> models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted <italic>de novo</italic> models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the <italic>ab initio</italic> phasing by <italic>de novo</italic> models approach. The method can be used to solve structures when the best <italic>de novo</italic> models are still of low accuracy.</p> </abstract>