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A mass spectrometry–based hybrid method for structural modeling of protein complexes

Nature Methods volume 11, pages 403–406 (2014)Cite this article

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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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Figure 1: Workflow and benchmark of a hybrid method for structure determination of protein assemblies using complementary MS data.
Figure 2: Structural models of the intact proteasomal lid and two distinct submodules.
Figure 3: Structural models of chaperone-base assembly intermediates involved in the formation of the proteasomal base complex.

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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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Author notes

  1. Argyris Politis

    Present address: Current address: Department of Life and Health Sciences, School of Biomedical Sciences, University of Ulster, Londonderry, UK.,

  2. Argyris Politis and Florian Stengel: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, University of Oxford, Oxford, UK

    Argyris Politis, Zoe Hall, Helena Hernández & Carol V Robinson

  2. Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland

    Florian Stengel, Alexander Leitner, Thomas Walzthoeni & Ruedi Aebersold

  3. Faculty of Science, University of Zurich, Zurich, Switzerland

    Ruedi Aebersold

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  1. Argyris Politis
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  7. Carol V Robinson
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Contributions

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.

Corresponding authors

Correspondence to Carol V Robinson or Ruedi Aebersold.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–30, Supplementary Tables 1–12, Supplementary Results and Supplementary Notes 1–3 (PDF 14099 kb)

Supplementary Software

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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