Abstract
We describe a method that integrates data derived from different mass spectrometry (MS)-based techniques with a modeling strategy for structural characterization of protein assemblies. We encoded structural data derived from native MS, bottom-up proteomics, ion mobility–MS and chemical cross-linking MS into modeling restraints to compute the most likely structure of a protein assembly. We used the method to generate near-native models for three known structures and characterized an assembly intermediate of the proteasomal base.
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Acknowledgements
MMOH and ToMOH were a gift of S.J. Lippard (Massachusetts Institute of Technology). Urease from K. aerogenes was a gift from R.P. Hausinger (Michigan State University). This work was supported by funding from PROSPECTS (Proteomics Specification in Space and Time Grant HEALTH-F4-2008-201648) within the European Union 7th Framework Program (A.P., C.V.R. and R.A.) and from European Research Council advanced grants “Proteomics v3.0” (233226) and “IMPRESS” (268851) to R.A. and C.V.R. H.H. is funded by Medical Research Council programme grant (G1000819). F.S. is a Sir Henry Wellcome Fellow funded by the Wellcome Trust (grant 095951), and C.V.R. is funded by the Royal Society.
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F.S. and A.P. conceived the study; F.S., A.P., C.V.R. and R.A. designed the research; A.P. performed all modeling and developed the software; F.S. carried out the experiments; Z.H. and H.H. performed part of the IM-MS and native MS experiments. A.L. and T.W. supported CX-MS experiments and analysis; F.S. and A.P. analyzed the data; A.P., F.S., C.V.R. and R.A. wrote the paper; all authors commented on and edited the final version of the paper.
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Supplementary Figures 1–30, Supplementary Tables 1–12, Supplementary Results and Supplementary Notes 1–3 (PDF 14099 kb)
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Software package for modeling protein complexes from hybrid mass spectrometry data (ZIP 217 kb)
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Politis, A., Stengel, F., Hall, Z. et al. A mass spectrometry–based hybrid method for structural modeling of protein complexes. Nat Methods 11, 403–406 (2014). https://doi.org/10.1038/nmeth.2841
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DOI: https://doi.org/10.1038/nmeth.2841
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