Top‐down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment
Open accessAbstract
Here we study the intact stoichiometry and top‐down fragmentation behavior of three integral membrane proteins which were natively reconstituted into detergent micelles: the mechano‐sensitive ion channel of large conductance (MscL), the Kirbac potassium channel and the p7 viroporin from the hepatitis C virus. By releasing the proteins under nondenaturing conditions inside the mass spectrometer, we obtained their oligomeric sizes. Increasing the ion activation (collision energy) causes unfolding and subsequent ejection of a highly charged monomer from the membrane protein complexes. Further increase of the ion activation then causes collision‐induced dissociation (CID) of the ejected monomers, with fragments observed which were predominantly found to stem from membrane‐embedded regions. These experiments show how in a single experiment, we can probe the relation between higher‐order structure and protein sequence, by combining the native MS data with fragmentation obtained from top‐down MS.
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Performing CID-based complex-down MS on MscL, Kirbac, and hepatitis C p7 viroporin, b and y fragment ions mainly stemmed from dissociation in the membrane-spanning regions of the monomers.
“Performing CID-based complex-down MS, they found that b and y fragment ions mainly stemmed from dissociation in the membrane-spanning regions of the monomers.110”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [110]
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Cites
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654 · see citing works
Electrospray Ionization for Mass Spectrometry of Large Biomolecules
Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., & Whitehouse, C. M. (1989) · Science · doi:10.1126/science.2675315 · Cited by 7,634 · see citing works
Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441 · see citing works
Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry
Tanaka, K., Waki, H., Ido, Y., Akita, S., Yoshida, Y., Yoshida, T., & Matsuo, T. (1988) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1290020802 · Cited by 3,005 · see citing works
A hidden Markov model for predicting transmembrane helices in protein sequences.
Sonnhammer, E. L. L., von HEIJNE, G., & Krogh, A. (1998) · PubMed · Cited by 2,483 · see citing works
Analytical Properties of the Nanoelectrospray Ion Source
Wilm, M. S., & Mann, M. (1996) · Analytical Chemistry · doi:10.1021/ac9509519 · Cited by 1,871 · see citing works
Proteoform: a single term describing protein complexity
The Consortium for Top Down Proteomics, Smith, L. M., & Kelleher, N. L. (2013) · Nature Methods · doi:10.1038/nmeth.2369 · Cited by 1,528 · see citing works
Studying noncovalent protein complexes by electrospray ionization mass spectrometry
Loo, J. A. (1997) · Mass Spectrometry Reviews · doi:10.1002/(sici)1098-2787(1997)16:1 · Cited by 1,152 · see citing works
Mobile and localized protons: a framework for understanding peptide dissociation
Wysocki, V. H., Tsaprailis, G., Smith, L. L., & Breci, L. A. (2000) · Journal of Mass Spectrometry · doi:10.1002/1096-9888(200012)35:12 · Cited by 998 · see citing works
Electrospray and Taylor-Cone theory, Dole's beam of macromolecules at last?
Wilm, M. S., & Mann, M. (1994) · International Journal of Mass Spectrometry and Ion Processes · doi:10.1016/0168-1176(94)04024-9 · Cited by 976 · see citing works
Membrane proteins bind lipids selectively to modulate their structure and function
Laganowsky, A. D., Reading, E., Allison, T. M., Ulmschneider, M. B., Degiacomi, M. T., Baldwin, A. J., & Robinson, C. V. (2014) · Nature · doi:10.1038/nature13419 · Cited by 786 · see citing works
Top Down versus Bottom Up Protein Characterization by Tandem High-Resolution Mass Spectrometry
Kelleher, N. L., Lin, H., Valaskovic, G. A., Aaserud, D. J., Fridriksson, E. K., & McLafferty, F. W. (1999) · Journal of the American Chemical Society · doi:10.1021/ja973655h · Cited by 606 · see citing works
Investigation of intact protein complexes by mass spectrometry
Heck, A. J. R., & van den Heuvel, R. H. H. (2004) · Mass Spectrometry Reviews · doi:10.1002/mas.10081 · Cited by 584 · see citing works
The molecular sociology of the cell
Robinson, C. V., Šali, A., & Baumeister, W. P. (2007) · Nature · doi:10.1038/nature06523 · Cited by 533 · see citing works
Assembly reflects evolution of protein complexes
Levy, E. D., Erba, E. B., Robinson, C. V., & Teichmann, S. A. (2008) · Nature · doi:10.1038/nature06942 · Cited by 420 · see citing works
Mass spectrometry of intact membrane protein complexes
Laganowsky, A., Reading, E., Hopper, J. T. S., & Robinson, C. V. (2013) · Nature Protocols · doi:10.1038/nprot.2013.024 · Cited by 409 · see citing works
Regulation of Fas Alternative Splicing by Antagonistic Effects of TIA-1 and PTB on Exon Definition
Izquierdo, J. M., Oró, N. M., Bonnal, S., Martínez, C., Castelo, R., Guigó, R., Bilbao, D., & Valcárcel, J. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.06.015 · Cited by 364 · see citing works
Micelles Protect Membrane Complexes from Solution to Vacuum
Barrera, N. P., Bartolo, N. D. D., Booth, P. J., & Robinson, C. V. (2008) · Science · doi:10.1126/science.1159292 · Cited by 362 · see citing works
Mass spectrometry of peptides and proteins
Wysocki, V. H., Resing, K. A., Zhang, Q., & Cheng, G. C. (2005) · Methods · doi:10.1016/j.ymeth.2004.08.013 · Cited by 309 · see citing works
Mass spectrometry: come of age for structural and dynamical biology
Benesch, J. L. P., & Ruotolo, B. T. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.08.002 · Cited by 264 · see citing works
Unusual architecture of the p7 channel from hepatitis C virus
OuYang, B., Xie, S., Berardi, M. J., Zhao, X., Dev, J., Yu, W., Sun, B., & Chou, J. J. (2013) · Nature · doi:10.1038/nature12283 · Cited by 259 · see citing works
Finding one's way in proteomics: a protein species nomenclature
Schlüter, H., Apweiler, R., Holzhütter, H., & Jungblut, P. (2009) · Chemistry Central Journal · doi:10.1186/1752-153x-3-11 · Cited by 254 · see citing works
Native ion mobility-mass spectrometry and related methods in structural biology
Konijnenberg, A., Butterer, A., & Sobott, F. (2012) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2012.11.013 · Cited by 249 · see citing works
Self-citationProtein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways
Marsh, J. A., Hernández, H., Hall, Z., Ahnert, S. E., Perica, T., Robinson, C. V., & Teichmann, S. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.044 · Cited by 245 · see citing works
Collisional Cooling of Large Ions in Electrospray Mass Spectrometry
Chernushevich, I. V., & Thomson, B. A. (2004) · Analytical Chemistry · doi:10.1021/ac035406j · Cited by 235 · see citing works
Tandem Mass Spectrometry Reveals the Quaternary Organization of Macromolecular Assemblies
Benesch, J. L. P., Aquilina, J. A., Ruotolo, B. T., Sobott, F., & Robinson, C. V. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.04.006 · Cited by 223 · see citing works
Self-citationElectrospray‐ionization mass spectrometry of intact intrinsic membrane proteins
Whitelegge, J. P., Gundersen, C. B., & Faull, K. F. (1998) · Protein Science · doi:10.1002/pro.5560070619 · Cited by 198 · see citing works
Belov, M. E., Damoc, E., Denisov, E., Compton, P. D., Horning, S., Makarov, A. A., & Kelleher, N. L. (2013) · Analytical Chemistry · doi:10.1021/ac4029328 · Cited by 175 · see citing works
Marcoux, J., Wang, S. C., Politis, A., Reading, E., Ma, J., Biggin, P. C., Zhou, M., Tao, H., Zhang, Q., Chang, G. A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1303888110 · Cited by 170 · see citing works
The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy
Luik, P., Chew, C. F., Aittoniemi, J., Chang, J. P.-E., Wentworth, P., Dwek, R. A., Biggin, P. C., Vénien‐Bryan, C., & Zitzmann, N. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905966106 · Cited by 156 · see citing works
The role of lipids in defining membrane protein interactions: insights from mass spectrometry
Barrera, N. P., Zhou, M., & Robinson, C. V. (2012) · Trends in Cell Biology · doi:10.1016/j.tcb.2012.08.007 · Cited by 151 · see citing works
Wachs, T., & Henion, J. D. (2001) · Analytical Chemistry · doi:10.1021/ac000935y · Cited by 141 · see citing works
Hilton, G. R., & Benesch, J. L. P. (2012) · Journal of The Royal Society Interface · doi:10.1098/rsif.2011.0823 · Cited by 140 · see citing works
Bavro, V. N., Zorzi, R. D., Schmidt, M. R., et al. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2208 · Cited by 97 · see citing works
Muneeruddin, K., Thomas, J. J., Salinas, P. A., & Kaltashov, I. A. (2014) · Analytical Chemistry · doi:10.1021/ac502590h · Cited by 96 · see citing works
Wang, S. C., Politis, A., Bartolo, N. D. D., Bavro, V. N., Tucker, S. J., Booth, P. J., Barrera, N. P., & Robinson, C. V. (2010) · Journal of the American Chemical Society · doi:10.1021/ja104312e · Cited by 81 · see citing works
Top Down Proteomics of Human Membrane Proteins from Enriched Mitochondrial Fractions
Catherman, A. D., Li, M., Tran, J. C., Durbin, K. R., Compton, P. D., Early, B. P., Thomas, P. M., & Kelleher, N. L. (2013) · Analytical Chemistry · doi:10.1021/ac3031527 · Cited by 76 · see citing works
Yeo, M. G., Oh, H. J., Cho, H., Chun, J. S., Marcantonio, E. E., & Song, W. K. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22335 · Cited by 71 · see citing works
Drug Binding Revealed by Tandem Mass Spectrometry of a Protein−Micelle Complex
Ilag, L. L., Ubarretxena‐Belandia, I., Tate, C. G., & Robinson, C. V. (2004) · Journal of the American Chemical Society · doi:10.1021/ja0450307 · Cited by 65 · see citing works
Foster, T. L., Thompson, G. S., Kalverda, A. P., et al. (2013) · Hepatology · doi:10.1002/hep.26685 · Cited by 65 · see citing works
Konijnenberg, A., Yilmaz, D., Ingólfsson, H. I., Dimitrova, A. I., Marrink, . J., Li, Z., Vénien‐Bryan, C., Sobott, F., & Koçer, A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1413118111 · Cited by 64 · see citing works
Self-citationBorysik, A. J., Hewitt, D., & Robinson, C. V. (2013) · Journal of the American Chemical Society · doi:10.1021/ja401736v · Cited by 63 · see citing works
Identification of membrane proteins by tandem mass spectrometry of protein ions
Carroll, J., Altman, M. C., Fearnley, I., & Walker, J. (2007) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0706817104 · Cited by 60 · see citing works
Benesch, J. L. P., Ruotolo, B. T., Sobott, F., Wildgoose, J. L., Gilbert, A. A., Bateman, R. H., & Robinson, C. V. (2008) · Analytical Chemistry · doi:10.1021/ac801950u · Cited by 60 · see citing works
Self-citationEvidence for Micellar Structure in the Gas Phase
Sharon, M., Ilag, L. L., & Robinson, C. V. (2007) · Journal of the American Chemical Society · doi:10.1021/ja067820h · Cited by 54 · see citing works
Whitelegge, J. P. (2003) · Photosynthesis Research · doi:10.1023/b:pres.0000006828.65688.0d · Cited by 47 · see citing works
Thangaraj, B., Ryan, C., Souda, P., Krause, K., Faull, K. F., Weber, A. P. M., Fromme, P., & Whitelegge, J. P. (2010) · Proteomics · doi:10.1002/pmic.201000190 · Cited by 41 · see citing works
Fragmentation of Integral Membrane Proteins in the Gas Phase
Skinner, O. S., Catherman, A. D., Early, B. P., Thomas, P. M., Compton, P. D., & Kelleher, N. L. (2014) · Analytical Chemistry · doi:10.1021/ac500864w · Cited by 29 · see citing works
Berridge, G., Chalk, R., D’Avanzo, N., et al. (2010) · Analytical Biochemistry · doi:10.1016/j.ab.2010.11.008 · Cited by 25 · see citing works
Newton, K. A., Pitteri, S. J., Laskowski, M. C., et al. (2004) · Journal of Proteome Research · doi:10.1021/pr049910w · Cited by 18 · see citing works
Fearnley, I. M., Skehel, M. J., & Walker, J. E. (1994) · Biochemical Society Transactions · doi:10.1042/bst0220551 · Cited by 17 · see citing works
Rathore, D., & Dodds, E. D. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-014-0946-4 · Cited by 11 · see citing works
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Standard Proteoforms and Their Complexes for Native Mass Spectrometry
Schachner, L. F., Ives, A. N., McGee, J. P., Melani, R. D., Kafader, J. O., Compton, P. D., Patrie, S. M., & Kelleher, N. L. (2019) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-019-02191-w · Cited by 48 · see citing works
Sipe, S. N., Patrick, J. W., Laganowsky, A., & Brodbelt, J. S. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b03689 · Cited by 39 · see citing works
- Authors
- Konijnenberg, A., Bannwarth, L., Yilmaz, D., Koçer, A., Venien‐Bryan, C., & Sobott, F.
- Affiliations
- University of Antwerp (BE)
- Institut de minéralogie, de physique des matériaux et de cosmochimie (FR)
- University of Groningen (NL)
- Bioinformatique et BioPhysique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Université Pierre et Marie Curie Paris France
- Corresponding author
- Sobott, Frank
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2015-05-29
- Volume
- 24
- Issue
- 8
- Pages
- 1292-1300
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC4534180
- OpenAlex
- W2115690303
- Cited by
- 45
- References
- 52
- Citations by year
- 2025: 4 · 2024: 1 · 2023: 8 · 2022: 3 · 2021: 4 · 2020: 7 · 2019: 7 · 2018: 3 · 2017: 5 · 2016: 1 · 2015: 2
- FWCI
- 1.64
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- HAL (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Funders
- Hercules foundation
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- top-down mass spectrometry, native mass spectrometry, membrane protein complexes, oligomeric state, hepatitis C virus, detergent micelles, collision-induced dissociation, ion activation, protein unfolding, protein stoichiometry
- MeSH terms
- Amino Acid Sequence, Hepatitis C, Humans, Ion Channels, Models, Molecular, Molecular Sequence Data, Viral Proteins, Potassium Channels, Hepacivirus, Spectrometry, Mass, Electrospray Ionization, Protein Multimerization
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