title: Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.
abstract: For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.
authors.affiliation: Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, England.
authors.forename: Felix
authors.initials: F
authors.lastname: Simkovic
authors.affiliation: Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, England.
authors.forename: Jens M H
authors.initials: JM
authors.lastname: Thomas
authors.affiliation: Research Complex at Harwell, STFC Rutherford Appleton Laboratory , Didcot OX11 0FA, England.
authors.forename: Ronan M
authors.initials: RM
authors.lastname: Keegan
authors.affiliation: Science and Technology Facilities Council, Daresbury Laboratory , Warrington WA4 4AD, England.
authors.forename: Martyn D
authors.initials: MD
authors.lastname: Winn
authors.affiliation: Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, England.
authors.forename: Olga
authors.initials: O
authors.lastname: Mayans
authors.affiliation: Institute of Integrative Biology, University of Liverpool , Liverpool L69 7ZB, England.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Rigden
keywords: ab initio modelling; evolutionary covariation; molecular replacement; predicted contacts; protein structure prediction