Abstract
In native mass spectrometry, non-covalent interactions are preserved in solution and through transfer to the gas phase. This technique can be used to characterize the composition, stoichiometry, and architecture of protein nano-assemblies, such as those observed in vivo or constructed through protein engineering in nanotechnology and synthetic biology. Here we describe an implementation of native mass spectrometry for studying protein-based nanostructures, including membrane proteins. Unambiguous structural details of assemblies can be rapidly determined due to the high resolution and mass accuracy afforded by mass spectrometry measurements including protein nano-assembly stoichiometry, heterogeneity, and ligand binding characteristics.
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References
Leney AC, Heck AJR (2017) Native mass spectrometry: what is in the name? J Am Soc Mass Spectrom 28(1):5–13
Karas M, Bahr U, Dülcks T (2000) Nano-electrospray ionization mass spectrometry: addressing analytical problems beyond routine. Fresenius J Anal Chem 366(6):669–676
Benesch JLP (2009) Collisional activation of protein complexes: picking up the pieces. J Am Soc Mass Spectrom 20(3):341
O’Brien JP, Li W, Zhang Y, Brodbelt JS (2014) Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry. J Am Chem Soc 136(37):12920–12928
Zhou M, Wysocki VH (2014) Surface induced dissociation: dissecting noncovalent protein complexes in the gas phase. Acc Chem Res 47(4):1010–1018
Zhang H, Cui W, Gross ML, Blankenship RE (2013) Native mass spectrometry of photosynthetic pigment–protein complexes. FEBS Lett 587(8):1012–1020
Lermyte F, Konijnenberg A, Williams JP, Brown JM, Valkenborg D, Sobott F (2014) ETD allows for native surface mapping of a 150 kDa noncovalent complex on a commercial Q-TWIMS-TOF instrument. J Am Soc Mass Spectrom 25(3):343–350
Liko I, Allison TM, Hopper JTS, Robinson CV (2016) Mass spectrometry guided structural biology. Curr Opin Struct Biol 40(Suppl C):136–144
Lai Y-T, Reading E, Hura GL, Tsai K-L, Laganowsky A, Asturias FJ, Tainer JA, Robinson CV, Yeates TO (2014) Structure of a designed protein cage that self-assembles into a highly porous cube. Nat Chem 6:1065
Sciore A, Su M, Koldewey P, Eschweiler JD, Diffley KA, Linhares BM, Ruotolo BT, Bardwell JCA, Skiniotis G, Marsh ENG (2016) Flexible, symmetry-directed approach to assembling protein cages. Proc Natl Acad Sci 113(31):8681–8686
Sahasrabuddhe A, Hsia Y, Busch F, Sheffler W, King NP, Baker D, Wysocki VH (2018) Confirmation of inter-subunit connectivity and topology of designed protein complexes by native mass spectrometry. Proc Natl Acad Sci U S A 115(6):1268–1273
Cubrilovic D, Haap W, Barylyuk K, Ruf A, Badertscher M, Gubler M, Tetaz T, Joseph C, Benz J, Zenobi R (2014) Determination of protein–ligand binding constants of a cooperatively regulated tetrameric enzyme using electrospray mass spectrometry. ACS Chem Biol 9(1):218–226
Ishii K, Noda M, Uchiyama S (2016) Mass spectrometric analysis of protein–ligand interactions. Biophys Physicobiol 13:87–95
Sobott F, Hernandez H, McCammon MG, Tito MA, Robinson CV (2002) A tandem mass spectrometer for improved transmission and analysis of large macromolecular assemblies. Anal Chem 74(6):1402–1407
van de Waterbeemd M, Fort KL, Boll D, Reinhardt-Szyba M, Routh A, Makarov A, Heck AJR (2017) High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles. Nat Methods 14:283
Konermann L (2017) Addressing a common misconception: ammonium acetate as neutral pH “buffer” for native electrospray mass spectrometry. J Am Soc Mass Spectrom 28(9):1827–1835
Hernandez H, Robinson CV (2007) Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry. Nat Protoc 2(3):715–726
McKay AR, Ruotolo BT, Ilag LL, Robinson CV (2006) Mass measurements of increased accuracy resolve heterogeneous populations of intact ribosomes. J Am Chem Soc 128(35):11433–11442
Laganowsky A, Reading E, Hopper JT, Robinson CV (2013) Mass spectrometry of intact membrane protein complexes. Nat Protoc 8(4):639–651
Reading E, Liko I, Allison TM, Benesch JLP, Laganowsky A, Robinson CV (2015) The role of the detergent Micelle in preserving the structure of membrane proteins in the gas phase. Angew Chem Int Ed 54(15):4577–4581
Laganowsky A, Reading E, Allison TM, Ulmschneider MB, Degiacomi MT, Baldwin AJ, Robinson CV (2014) Membrane proteins bind lipids selectively to modulate their structure and function. Nature 510(7503):172–175
Kirshenbaum N, Michaelevski I, Sharon M (2010) Analyzing large protein complexes by structural mass spectrometry. J Vis Exp 40:e1954
Fong KWY, Chan TWD (1999) A novel nonmetallized tip for electrospray mass spectrometry at nanoliter flow rate. J Am Soc Mass Spectrom 10(1):72–75
Marty MT, Baldwin AJ, Marklund EG, Hochberg GKA, Benesch JLP, Robinson CV (2015) Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. Anal Chem 87(8):4370–4376
Liko I, Hopper JTS, Allison TM, Benesch JLP, Robinson CV (2016) Negative ions enhance survival of membrane protein complexes. J Am Soc Mass Spectrom 27(6):1099–1104
Yen H-Y, Hopper JTS, Liko I, Allison TM, Zhu Y, Wang D, Stegmann M, Mohammed S, Wu B, Robinson CV (2017) Ligand binding to a G protein–coupled receptor captured in a mass spectrometer. Sci Adv 3(6):e1701016
Mehmood S, Corradi V, Choudhury HG, Hussain R, Becker P, Axford D, Zirah S, Rebuffat S, Tieleman DP, Robinson CV, Beis K (2016) Structural and functional basis for lipid synergy on the activity of the antibacterial peptide ABC transporter McjD. J Biol Chem 291(41):21656–21668
Mehmood S, Marcoux J, Gault J, Quigley A, Michaelis S, Young SG, Carpenter EP, Robinson CV (2016) Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24. Nat Chem 8:1152
Landreh M, Liko I, Uzdavinys P, Coincon M, Hopper JTS, Drew D, Robinson CV (2015) Controlling release, unfolding and dissociation of membrane protein complexes in the gas phase through collisional cooling. Chem Commun 51(85):15582–15584
Hopper JT, Yu YT, Li D, Raymond A, Bostock M, Liko I, Mikhailov V, Laganowsky A, Benesch JL, Caffrey M, Nietlispach D, Robinson CV (2013) Detergent-free mass spectrometry of membrane protein complexes. Nat Methods 10(12):1206–1208
Ruotolo BT, Benesch JL, Sandercock AM, Hyung SJ, Robinson CV (2008) Ion mobility-mass spectrometry analysis of large protein complexes. Nat Protoc 3(7):1139–1152
Juraschek R, Dülcks T, Karas M (1999) Nanoelectrospray—more than just a minimized-flow electrospray ionization source. J Am Soc Mass Spectrom 10(4):300–308
Susa AC, Xia Z, Williams ER (2017) Small emitter tips for native mass spectrometry of proteins and protein complexes from nonvolatile buffers that mimic the intracellular environment. Anal Chem 89(5):3116–3122
Chernushevich IV, Bahr U, Karas M (2004) Nanospray ‘taxation’ and how to avoid it. Rapid Commun Mass Spectrom 18(20):2479–2485
Mortensen DN, Williams ER (2016) Surface-induced protein unfolding in submicron electrospray emitters. Anal Chem 88(19):9662–9668
Testa L, Brocca S, Grandori R (2011) Charge-surface correlation in electrospray ionization of folded and unfolded proteins. Anal Chem 83(17):6459–6463
Konermann L, Ahadi E, Rodriguez AD, Vahidi S (2013) Unraveling the mechanism of electrospray ionization. Anal Chem 85(1):2–9
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Allison, T.M., Agasid, M.T. (2020). Native Protein Mass Spectrometry. In: Gerrard, J., Domigan, L. (eds) Protein Nanotechnology. Methods in Molecular Biology, vol 2073. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9869-2_15
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DOI: https://doi.org/10.1007/978-1-4939-9869-2_15
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