Laboratory for Structural Bioinformatics

A fragmentation and reassembly method for ab initio phasing

Ab initio phasing with de novo models has become a viable approach for the structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modeling 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. We have developed a fragment assembly phasing method that starts from an ensemble of low accuracy de novo 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 the complete structure determination by automated model building. Tests on ten protein targets have shown that our method can solve structures for eight of these targets, although the predicted de novo 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. Our method has extended the applicability of the ab initio phasing by de novo models approach. Our method can be used to solve structures when the best de novo models are still of low accuracy. This work has been published in Acta Cryst. D. (publication).
Our method is illustrated in the figure below. Please see our paper for details.
The effect of fragmentation and reassembly in ab initio phasing is demonstrated below. The best full models (pink), native structures (cyan) and assembled partial models (green) for (a) 1ctf and (b) 1ew4 are shown. The structures for each target are shown in the same orientation. The overall RMSDs between each pair of structures are shown. The rotation angles between each pair of labelled secondary-structure elements are also indicated.