Tumgik
#An integrated native mass spectrometry and top-down proteomics method that connect
naivelocus · 7 years
Text
An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes
1.
Sharon, M. How far can we go with structural mass spectrometry of protein complexes? J. Am. Soc. Mass Spectrom. 21, 487–500 (2010).
2.
Heck, A. J. R. Native mass spectrometry: a bridge between interactomics and structural biology. Nat. Methods 5, 927–933 (2008).
3.
Lorenzen, K. & Duijn, E. v. Current Protocols in Protein Science (Wiley, 2001).
4.
Van Duijn, E. Current limitations in native mass spectrometry based structural biology. J. Am. Soc. Mass Spectrom. 21, 971–978 (2010).
5.
Benesch, J. L. P., Ruotolo, B. T., Simmons, D. A. & Robinson, C. V. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem. Rev. 107, 3544–3567 (2007).
6.
Snijder, J., Rose, R. J., Veesler, D., Johnson, J. E. & Heck, A. J. R. Studying 18 MDa virus assemblies with native mass spectrometry. Angew. Chem. Int. Ed. 52, 4020–4023 (2013).
7.
Van Berkel, W. J. H., Van Den Heuvel, R. H. H., Versluis, C. & Heck, A. J. R. Detection of intact megaDalton protein assemblies of vanillyl-alcohol oxidase by mass spectrometry. Protein Sci. 9, 435–439 (2000).
8.
Rose, R. J., Damoc, E., Denisov, E., Makarov, A. & Heck, A. J. R. High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies. Nat. Methods 9, 1084–1086 (2012).
9.
Van de Waterbeemd, M. et al. High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles. Nat. Methods 14, 283–286 (2017).
10.
Snijder, J. et al. Defining the stoichiometry and cargo load of viral and bacterial nanoparticles by orbitrap mass spectrometry. J. Am. Chem. Soc. 136, 7295–7299 (2014).
11.
Gault, J. et al. High-resolution mass spectrometry of small molecules bound to membrane proteins. Nat. Methods 13, 333–336 (2016).
12.
Dyachenko, A. et al. Tandem native mass-spectrometry on antibody–drug conjugates and submillion Da antibody–antigen protein assemblies on an Orbitrap EMR equipped with a high-mass quadrupole mass selector. Anal. Chem. 87, 6095–6102 (2015).
13.
Rosati, S., Yang, Y., Barendregt, A. & Heck, A. J. R. Detailed mass analysis of structural heterogeneity in monoclonal antibodies using native mass spectrometry. Nat. Protoc. 9, 967–976 (2014).
14.
Walzthoeni, T., Leitner, A., Stengel, F. & Aebersold, R. Mass spectrometry supported determination of protein complex structure. Curr. Opin. Struct. Biol. 23, 252–260 (2013).
15.
Shi, Y. et al. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol. Cell Proteomics 13, 2927–2943 (2014).
16.
Savaryn, J., Catherman, A., Thomas, P., Abecassis, M. & Kelleher, N. The emergence of top-down proteomics in clinical research. Genome Med. 5, 53 (2013).
17.
Smith, L. M. & Kelleher, N. L. Proteoform: a single term describing protein complexity. Nat. Methods 10, 186–187 (2013).
18.
Li, H. et al. Use of top-down and bottom-up Fourier transform ion cyclotron resonance mass spectrometry for mapping calmodulin sites modified by platinum anticancer drugs. Anal. Chem. 83, 9507–9515 (2011).
19.
Siuti, N. & Kelleher, N. L. Decoding protein modifications using top-down mass spectrometry. Nat. Methods 4, 817–821 (2007).
20.
Tian, Z. et al. Enhanced top-down characterization of histone post-translational modifications. Genome Biol. 13, R86 (2012).
21.
Xie, Y., Zhang, J., Yin, S. & Loo, J. A. Top-down ESI-ECD-FT-ICR mass spectrometry localizes noncovalent protein–ligand binding sites. J. Am. Chem. Soc. 128, 14432–14433 (2006).
22.
Castro, M. E., Russell, D. H., Amster, I. J. & McLafferty, F. W. Detection of mass 16241 ions by Fourier-transform mass spectrometry. Anal. Chem. 58, 483–485 (1986).
23.
Karabacak, N. M. et al. Sensitive and specific identification of wild type and variant proteins from 8 to 669 kDa using top-down mass spectrometry. Mol. Cell Proteomics 8, 846–856 (2009).
24.
Zhang, H., Cui, W., Gross, M. L. & Blankenship, R. E. Native mass spectrometry of photosynthetic pigment–protein complexes. FEBS Lett. 587, 1012–1020 (2013).
25.
Li, H., Wolff, J. J., Van Orden, S. L. & Loo, J. A. Native top-down electrospray ionization-mass spectrometry of 158 kDa protein complex by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 86, 317–320 (2014).
26.
Li, H., Wongkongkathep, P., Van Orden, S., Ogorzalek Loo, R. & Loo, J. Revealing ligand binding sites and quantifying subunit variants of noncovalent protein complexes in a single native top-down FTICR MS experiment. J. Am. Soc. Mass Spectrom. 25, 2060–2068 (2014).
27.
Zhang, H., Cui, W., Wen, J., Blankenship, R. E. & Gross, M. L. Native electrospray and electron-capture dissociation FTICR mass spectrometry for top-down studies of protein assemblies. Anal. Chem. 83, 5598–5606 (2011).
28.
Geels, R. B. J., van der Vies, S. M., Heck, A. J. R. & Heeren, R. M. A. Electron capture dissociation as structural probe for noncovalent gas-phase protein assemblies. Anal. Chem. 78, 7191–7196 (2006).
29.
Barford, D., Hu, S. H. & Johnson, L. N. Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP. J. Mol. Biol. 218, 233–260 (1991).
30.
Horn, D. M., Ge, Y. & McLafferty, F. W. Activated ion electron capture dissociation for mass spectral sequencing of larger (42 kDa) proteins. Anal. Chem. 72, 4778–4784 (2000).
31.
Schennach, M. & Breuker, K. Probing protein structure and folding in the gas phase by electron capture dissociation. J. Am. Soc. Mass Spectrom. 26, 1059–1067 (2015).
32.
Johnson, L. N. Glycogen phosphorylase: control by phosphorylation and allosteric effectors. FASEB J. 6, 2274–2282 (1992).
33.
Tsaprailis, G., Somogyi, Á., Nikolaev, E. N. & Wysocki, V. H. Refining the model for selective cleavage at acidic residues in arginine-containing protonated peptides2. Int. J. Mass Spectrom. 195–196, 467–479 (2000).
34.
Breci, L. A., Tabb, D. L., Yates, J. R. & Wysocki, V. H. Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal. Chem. 75, 1963–1971 (2003).
35.
Rose, G., Geselowitz, A., Lesser, G., Lee, R. & Zehfus, M. Hydrophobicity of amino acid residues in globular proteins. Science 229, 834–838 (1985).
36.
Carrigan, J. B. & Engel, P. C. The structural basis of proteolytic activation of bovine glutamate dehydrogenase. Protein Sci. 17, 1346–1353 (2008).
37.
Banerjee, S., Schmidt, T., Fang, J., Stanley, C. A. & Smith, T. J. Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation. Biochemistry 42, 3446–3456 (2003).
38.
Smith, T. J. & Stanley, C. A. Untangling the glutamate dehydrogenase allosteric nightmare. Trends Biochem. Sci. 33, 557–564 (2008).
39.
Jacobson, R. H., Zhang, X. J., DuBose, R. F. & Matthews, B. W. Three-dimensional structure of β-galactosidase from E. coli. Nature 369, 761–766 (1994).
40.
Matthews, B. W. The structure of E. coli β-galactosidase. C. R. Biol. 328, 549–556 (2005).
41.
Cui, W., Zhang, H., Blankenship, R. E. & Gross, M. L. Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly. Protein Sci. 24, 1325–1332 (2015).
42.
Lermyte, F. et al. 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, 343–350 (2014).
43.
Li, H. et al. Structural characterization of native proteins and protein complexes by electron ionization dissociation-mass spectrometry. Anal. Chem. 89, 2731–2738 (2017).
44.
Jacob, E. & Unger, R. A tale of two tails: why are terminal residues of proteins exposed? Bioinformatics 23, e225–e230 (2007).
45.
van der Spoel, D., Marklund, E. G., Larsson, D. S. D. & Caleman, C. Proteins, lipids, and water in the gas phase. Macromol. Biosci. 11, 50–59 (2011).
46.
Faull, P. A. et al. Gas-phase metalloprotein complexes interrogated by ion mobility-mass spectrometry. Int. J. Mass Spectrom. 283, 140–148 (2009).
47.
Haverland, N. A. et al. Defining gas-phase fragmentation propensities of intact proteins during native top-down mass spectrometry. J. Am. Soc. Mass Spectrom. 28, 1203–1215 (2017).
48.
Brodbelt, J. S. & Wilson, J. J. Infrared multiphoton dissociation in quadrupole ion traps. Mass Spectrom. Rev. 28, 390–424 (2009).
49.
Bourgoin-Voillard, S., Leymarie, N. & Costello, C. E. Top-down tandem mass spectrometry on RNase A and B using a Qh/FT-ICR hybrid mass spectrometer. Proteomics 14, 1174–1184 (2014).
50.
Ahlf, D. et al. Evaluation of the compact high-field Orbitrap for top-down proteomics of human cells. J. Proteome Res. 11, 4308–4314 (2012).
51.
Holzmann, J., Hausberger, A., Rupprechter, A. & Toll, H. Top-down MS for rapid methionine oxidation site assignment in filgrastim. Anal. Bioanal. Chem. 405, 6667–6674 (2013).
52.
Belov, M. E. et al. From protein complexes to subunit backbone fragments: a multi-stage approach to native mass spectrometry. Anal. Chem. 85, 11163–11173 (2013).
53.
Brodbelt, J. S. Ion activation methods for peptides and proteins. Anal. Chem. 88, 30–51 (2016).
54.
Durbin, K. R., Skinner, O. S., Fellers, R. T. & Kelleher, N. L. Analyzing internal fragmentation of electrosprayed ubiquitin ions during beam-type collisional dissociation. J. Am. Soc. Mass Spectrom. 26, 782–787 (2015).
55.
Ogorzalek Loo, R. R. & Loo, J. A. Protein complexes: breaking up is hard to do well. Structure 21, 1265–1266 (2013).
56.
Schennach, M. & Breuker, K. Proteins with highly similar native folds can show vastly dissimilar folding behavior when desolvated. Angew. Chem. Int. Ed. 53, 164–168 (2014).
57.
Campuzano, I. & Giles, K. Nanoproteomics: Methods and Protocols (eds Toms, S.A. & Weil, R.J.) 57–70 (Humana, 2011).
58.
Marshall, A. G., Hendrickson, C. L. & Jackson, G. S. Fourier transform ion cyclotron resonance mass spectrometry: a primer. Mass Spectrom. Rev. 17, 1–35 (1998).
59.
Rayleigh, L. XX. On the equilibrium of liquid conducting masses charged with electricity. Philos. Mag. 14, 184–186 (1882).
60.
Ma, X., Zhou, M. & Wysocki, V. Surface induced dissociation yields quaternary substructure of refractory noncovalent phosphorylase B and glutamate dehydrogenase complexes. J. Am. Soc. Mass Spectrom. 25, 368–379 (2014).
61.
Rostom, A. A. & Robinson, C. V. Detection of the intact GroEL chaperonin assembly by mass spectrometry. J. Am. Chem. Soc. 121, 4718–4719 (1999).
62.
Sobott, F. & Robinson, C. V. Characterising electrosprayed biomolecules using tandem-MS—the noncovalent GroEL chaperonin assembly. Int. J. Mass Spectrom. 236, 25–32 (2004).
63.
Zubarev, R. A. Electron-capture dissociation tandem mass spectrometry. Curr. Opin. Biotechnol. 15, 12–16 (2004).
— Nature Chemistry
0 notes
sisiad · 7 years
Text
An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes
http://dlvr.it/Q8RkJ3
0 notes