Stable isotope labeling strategy for protein-ligand binding analysis in multi-component protein mixtures

Journal of the American Society for Mass Spectrometry

Volumn 22, Issue 3, 2011, Pages 418-430

  DeArmond, Patrick D ^a   West, Graham M ^a   Huang, Hai Tsang ^a   Fitzgerald, Michael C ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

Calcineurin; Covalent labeling; Cyclophilin A; Cyclosporin A; Ligand binding; Protein folding; Quantitative proteomics; Thermodynamics

Indexed keywords

CALCINEURIN; COVALENT LABELING; CYCLOPHILIN A; CYCLOSPORIN A; LIGAND BINDING; QUANTITATIVE PROTEOMICS;

AMINO ACIDS; BINDING ENERGY; CHEMICAL ANALYSIS; CHEMICAL MODIFICATION; ISOTOPES; LIGANDS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; OXIDATION; PROTEIN FOLDING; THERMODYNAMICS;

PROTEINS;

CALCINEURIN; CYCLOPHILIN A; CYCLOSPORIN A; METHIONINE; OXYGEN; OXYGEN 18;

AQUEOUS SOLUTION; ARTICLE; BINDING AFFINITY; BINDING ASSAY; CHEMICAL MODIFICATION; COMPLEX FORMATION; CONTROLLED STUDY; DRUG PROTEIN BINDING; ISOTOPE LABELING; LIGAND BINDING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; OXIDATION; PROTEIN ANALYSIS; PROTEIN DENATURATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEOMICS; SACCHAROMYCES CEREVISIAE;

AMINO ACID SEQUENCE; CALCINEURIN; CYCLOPHILIN A; CYCLOSPORINE; ISOTOPE LABELING; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; OXYGEN ISOTOPES; PROTEIN BINDING; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 79955752626     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-010-0060-1     Document Type: Article

References (25)

1. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M.J., Johnston, M., Fields, S., Rothberg, J.M.: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000) (Pubitemid 30103994)
2. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C.A., Finley Jr., R.L., White, K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J., Rothberg, J.M.: A protein interaction map of Drosophila melanogaster. Science 302, 1727-1736 (2003) (Pubitemid 37505730)
3. Li, S.M., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D.J., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S. L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q.R., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H.Y., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., van den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J. W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M.: A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004) (Pubitemid 38120855)
4. Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L.V., Wong, S.L., Franklin, G., Li, S.M., Albala, J.S., Lim, J.H., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M.E., Hill, D. E., Roth, F.P., Vidal, M.: Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178 (2005) (Pubitemid 41509356)
5. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L.Y., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B. D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W.V., Figeys, D., Tyers, M.: Systematic identification of protein complexes in Saccharomyces cerevisiae by Mass Spectrometry. Nature 415, 180-183 (2002) (Pubitemid 34059520)
6. Graumann, J., Dunipace, L.A., Seol, J.H., McDonald, W.H., Yates, J.R., Wold, B.J., Deshaies, R.J.: Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Mol. Cell. Proteom. 3, 226-237 (2004) (Pubitemid 38714278)
7. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., Superti-Furga, G.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002) (Pubitemid 34059510)
8. Powell, K.D., Ghaemmaghami, S., Wang, M.Z., Ma, L.Y., Oas, T.G., Fitzgerald, M.C.: A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution. J. Am. Chem. Soc. 124, 10256-10257 (2002) (Pubitemid 34977364)
9. Zhu, M.M., Rempel, D.L., Du, Z.H., Gross, M.L.: Quantification of protein-ligand interactions by mass spectrometry, titration, and H/D exchange: PLIMSTEX. J. Am. Chem. Soc. 125, 5252-5253 (2003) (Pubitemid 36582715)
10. Charvatova, O., Foley, B.L., Bern, M.W., Sharp, J.S., Orlando, R., Woods, R.J.: Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: Application to Galectin-1. J. Am. Soc. Mass Spectrom. 19, 1692-1705 (2008)
11. Takamoto, K., Chance, M.R.: Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biophys. Biomol. Struct. 35, 251-276 (2006) (Pubitemid 43877378)
12. West, G.M., Tang, L., Fitzgerald, M.C.: Thermodynamic analysis of protein stability and ligand binding using a chemical modificationand mass spectrometry-based strategy. Anal. Chem. 80, 4175-4185 (2008) (Pubitemid 351812772)
13. West, G.M., Tucker, C.L., Xu, T., Park, S.K., Han, X.M., Yates, J. R., Fitzgerald, M.C.: Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements. Proc. Natl. Acad. Sci. U. S. A. 107, 9078-9082 (2010)
14. West, G.M., Thompson, J.W., Soderblom, E.J., Dubois, L.G., DeArmond, P.D., Moseley, M.A., Fitzgerald, M.C.: Mass spectrometry-based thermal shift assay for protein-ligand binding analysis. Anal. Chem. 82, 5573-5581 (2010)
15. Gelperin, D.M., White, M.A., Wilkinson, M.L., Kon, Y., Kung, L.A., Wise, K.J., Lopez-Hoyo, N., Jiang, L.X., Piccirillo, S., Yu, H.Y., Gerstein, M., Dumont, M.E., Phizicky, E.M., Snyder, M., Grayhack, E. J.: Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev. 19, 2816-2826 (2005) (Pubitemid 41739967)
16. Bradford, M.M.: Rapid and sensitive method for quantitation of microgram quantities of protein utilizing principle of protein-dye binding. Anal. Biochem. 72, 248-254 (1976)
17. Nozaki, Y.: The preparation of guanidine hydrochloride. Method Enzymol. 26, 43-50 (1972)
18. Handschumacher, R.E., Harding, M.W., Rice, J., Drugge, R.J.: Cyclophilin-a specific cytosolic binding-protein for cyclosporin A. Science 226, 544-547 (1984) (Pubitemid 14018525)
19. Harding, M.W., Handschumacher, R.E.: Cyclophilin, a primary molecular target for cyclosporine-structural and functional implications. Transplantation 46, S29-S35 (1988)
20. Liu, J., Albers, M.W., Chen, C.M., Schreiber, S.L., Walsh, C.T.: Cloning, expression, and purification of human cyclophilin in Escherichia coli and assessment of the catalytic role of cysteines by site-directed mutagenesis. Proc. Natl. Acad. Sci. U. S. A. 87, 2304-2308 (1990)
21. Holzman, T.F., Egan, D.A., Edalji, R., Simmer, R.L., Helfrich, R., Taylor, A., Burres, N.S.: Preliminary characterization of a cloned neutral isoelectric form of the human peptidyl prolyl isomerase cyclophilin. J. Biol. Chem. 266, 2474-2479 (1991)
22. Wang, M.Z., Shetty, J.T., Howard, B.A., Campa, M.J., Patz, E.F., Fitzgerald, M.C.: Thermodynamic analysis of Cyclosporin A binding to Cyclophilin A in a lung tumor tissue lysate. Anal. Chem. 76, 4343-4348 (2004) (Pubitemid 39014004)
23. Liu, J., Albers, M.W., Wandless, T.J., Luan, S., Alberg, D.G., Belshaw, P.J., Cohen, P.,Mackintosh, C., Klee, C.B., Schreiber, S.L.: Inhibition of T cell signaling by imunophilin-ligand complexes correlates with loss of calcineurin phosphatase activity. Biochemistry 31, 3896-3901 (1992)
24. Liu, J., Farmer Jr., J.D., Lane, W.S., Friedman, J., Weissman, I., Schreiber, S.L.: Calcineurin is a common target of cyclophilin-cyclosporin A and Fkbp-Fk506 complexes. Cell 66, 807-815 (1991) (Pubitemid 121001714)
25. Jin, L., Harrison, S.C.: Crystal structure of human calcineurin complexed with cyclosporin A and human cyclophilin. Proc. Natl. Acad. Sci. U. S. A. 99, 13522-13526 (2002) (Pubitemid 35215414)