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Default Structure-based protein NMR assignments using native structural ensembles

Structure-based protein NMR assignments using native structural ensembles
Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald
Journal of Biomolecular NMR; 2008; 40(4); pp 263-276

Abstract:

An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange rates, TOCSY) and has high accuracy when the template is close to the target protein’s structure (less than 2 Å backbone RMSD). However, a close template may not always be available. We extend the circle of convergence of NVR for distant templates by using an ensemble of structures. This ensemble corresponds to the low-frequency perturbations of the given template and is obtained using normal mode analysis (NMA). Our algorithm assigns resonances and sparse NOEs using each of the structures in the ensemble separately, and aggregates the results using a voting scheme based on maximum bipartite matching. Experimental results on human ubiquitin, using four distant template structures show an increase in the assignment accuracy. Our algorithm also improves the robustness of NVR with respect to structural noise. We provide a confidence measure for each assignment using the percentage of the structures that agree on that assignment. We use this measure to assign a subset of the peaks with even higher accuracy. We further validate our algorithm on data for two additional proteins with NVR. We then show the general applicability of our approach by applying our NMA ensemble-based voting scheme to another SBA tool, MARS. For three test proteins with corresponding templates, including the 370-residue maltose binding protein, we increase the number of reliable assignments made by MARS. Finally, we show that our voting scheme is sound and optimal, by proving that it is a maximum likelihood estimator of the correct assignments.
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