Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment
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Multiprotein complexes are central to our understanding of cellular biology, as they play critical roles in nearly every biological process. Despite many impressive advances associated with structural characterization techniques, large and highly-dynamic protein complexes are too often refractory to analysis by conventional, high-resolution approaches. To fill this gap, ion mobility-mass spectrometry (IM-MS) methods have emerged as a promising approach for characterizing the structures of challenging assemblies due in large part to the ability of these methods to characterize the composition, connectivity, and topology of large, labile complexes. In this Critical Insight, we present a series of bioinformatics studies aimed at assessing the information content of IM-MS datasets for building models of multiprotein structure. Our computational data highlights the limits of current coarse-graining approaches, and compelled us to develop an improved workflow for multiprotein topology modeling, which we benchmark against a subset of the multiprotein complexes within the PDB. This improved workflow has allowed us to ascertain both the minimal experimental restraint sets required for generation of high-confidence multiprotein topologies, and quantify the ambiguity in models where insufficient IM-MS information is available. We conclude by projecting the future of IM-MS in the context of protein quaternary structure assignment, where we predict that a more complete knowledge of the ultimate information content and ambiguity within such models will undoubtedly lead to applications for a broader array of challenging biomolecular assemblies.
KeywordsNative mass spectrometry Structural proteomics Bioinformatics Molecular dynamics simulations Protein network
Protein topology modeling efforts in the Ruotolo lab are supported through the National Institute of General Medical Sciences, National Institutes of Health (R01 GM095832). Additionally, the authors gratefully acknowledge the support of Erik Marklund (Uppsala), Matteo Degiacomi (Oxford), and Justin Benesch (Oxford), who helped the authors to integrate IMPACT CCS calculations into their computational workflows.
- 8.Russel, D., Lasker, K., Webb, B., Velázquez-Muriel, J., Tjioe, E., Schneidman-Duhovny, D., Peterson, B., Sali, A.: Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 10(1) (2012). doi: 10.1371/journal.pbio.1001244
- 9.Shi, Y., Fernandez-Martinez, J., Tjioe, E., Pellarin, R., Kim, S.J., Williams, R., Schneidman-Duhovny, D., Sali, A., Rout, M.P., Chait, B.T.: Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol. Cell. Proteom. 13(11), 2927–2943 (2014)CrossRefGoogle Scholar
- 10.Stengel, F., Aebersold, R., Robinson, C.V.: Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol. Cell. Proteom. 11(3), 1-13 (2012). doi: 10.1074/mcp.R111.014027
- 21.Marsh, J.A., Hernández, H., Hall, Z., Ahnert, S.E., Perica, T., Robinson, C.V., Teichmann, S.A.: Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell 153(2), 461-470 (2013)Google Scholar
- 31.Politis, A., Park, A., Hyung, S.-J., Barsky, D., Ruotolo, B.T., Robinson, C.V.: Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes. PLoS ONE 5(8) (2010). doi: 10.1371/journal.pone.0012080
- 34.Politis, A., Park, A., Hall, Z., Ruotolo, B.T., Robinson, C.V.: Integrative modeling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein. J. Mol. Biol. 425(23), 4790-4801 (2013)Google Scholar
- 35.Politis, A., Schmidt, C., Tjioe, E., Sandercock, A.M., Lasker, K., Gordiyenko, Y., Russel, D., Sali, A., Robinson, C.V.: Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex. Chem. Biol. 22(1), 117-128 (2015). doi: 10.1016/j.chembiol.2014.11.010
- 43.Arthur, D., Vassilvitskii, S.: k-means++: the advantages of careful seeding. Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA (2007)Google Scholar
- 44.Jones, E., Oliphant, T., Peterson, P., et al.: SciPy: Open source scientific tools for Python. http://www.scipy.org/ (2001). Accessed 1 April 2017
- 62.Hamid, A.M., Garimella, S.V.B., Ibrahim, Y.M., Deng, L.L., Zheng, X.Y., Webb, I.K., Anderson, G.A., Prost, S.A., Norheim, R.V., Tolmachev, A.V., Baker, E.S., Smith, R.D.: Achieving high resolution ion mobility separations using traveling waves in compact multiturn structures for lossless ion manipulations. Anal. Chem. 88(18), 8949–8956 (2016)CrossRefGoogle Scholar