Molecular replacement using structure predictions from databases

Abstract

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Where the lack of a suitable homologue precludes conventional MR, one option is to predict the target structure using bioinformatics. Such modelling, in the absence of homologous templates, is calledab initioorde novomodelling. Recently, the accuracy of such models has improved significantly as a result of the availability, in many cases, of residue-contact predictions derived from evolutionary covariance analysis. Covariance-assistedab initiomodels representing structurally uncharacterized Pfam families are now available on a large scale in databases, potentially representing a valuable and easily accessible supplement to the PDB as a source of search models. Here, the unconventional MR pipelineAMPLEis employed to explore the value of structure predictions in the GREMLIN and PconsFam databases. It was tested whether these deposited predictions, processed in various ways, could solve the structures of PDB entries that were subsequently deposited. The results were encouraging: nine of 27 GREMLIN cases were solved, covering target lengths of 109–355 residues and a resolution range of 1.4–2.9 Å, and with target–model shared sequence identity as low as 20%. The cluster-and-truncate approach inAMPLEproved to be essential for most successes. For the overall lower quality structure predictions in the PconsFam database, remodelling withRosettawithin theAMPLEpipeline proved to be the best approach, generating ensemble search models from single-structure deposits. Finally, it is shown that theAMPLE-obtained search models deriving from GREMLIN deposits are of sufficiently high quality to be selected by the sequence-independent MR pipelineSIMBAD. Overall, the results help to point the way towards the optimal use of the expanding databases ofab initiostructure predictions.