Genesis and Application of Radical Probe Mass Spectrometry (RP-MS) to Study Protein Interactions

Mass Spectrometry of Protein Interactions

Volumn , Issue , 2006, Pages 109-133

  Maleknia, Simin D ^a   Downard, Kevin M ^b  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Amino acid side chain interactions; Radical oxidation in protein assembly study; Radical probe mass spectrometry genesis

Indexed keywords

EID: 84889286164     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470146330.ch6     Document Type: Chapter

References (37)

1. Tullius, T. D., and Dombroski, B. A. (1986). Hydroxyl radical "footprinting": highresolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proc. Natl. Acad. Sci. U.S.A. 83: 5469-5473.
2. Heyduk, E., and Heyduk, T. (1994). Mapping protein domains involved in macromolecular interactions: a novel protein footprinting approach. Biochemistry 33: 9643-9650.
3. Fenton, H. J. H. (1894). Oxidation of tartaric acid in the presence of iron. J. Chem. Soc. 65: 899.
4. Pierre, J. L. L., and Fontecave, M. (1999). Iron and activated oxygen species in biology: the basic chemistry. BioMetals 12: 195-199.
5. Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M., and Woodson, S. A. (1998). RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279: 1940-1943.
6. Sclavi, B., Woodson, S., Sullivan, M., Chance, M., and Brenowitz, M. (1998). Following the folding of RNA with time-resolved synchrotron X-ray footprinting. Methods Enzymol. 295: 379-402.
7. Maleknia, S. D., and Chance, M. R. (1998). Synchrotron radiolysis studies of peptides by mass spectrometry. In Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics, p. 972, Orlando, Florida.
8. Maleknia, S. D., Goldsmith, S., Vorobiev, S., Almo, S. A., Chance, M. R., and Downard, K. M. (1998). Examining protein-peptide interactions through synchrotron X-ray footprinting techniques. In Proceedings of the 46th ASMS Conference on Mass Spectrometry and Allied Topics, p. 973, Orlando, Florida.
9. Maleknia, S. D., and Downard, K. M. (2001). Radical approaches to probe protein structure, folding, and interactions by mass spectrometry. Mass Spectrom. Rev. 20: 388-401.
10. Maleknia, S. D., and Downard, K. M. (2001). Unfolding of apomyoglobin helices by synchrotron radiolysis and mass spectrometry. Eur. J. Biochem. 268: 5578-5588.
11. Maleknia, S. D., Wong, J. W. H., and Downard, K. M. (2004). Photochemical and electrophysical production of radicals on millisecond timescales to probe the structure, dynamics and interactions of proteins. Photochem. Photobiol. Sci. 3: 741-748.
12. Maleknia, S. D., Brenowitz, M., and Chance, M. R. (1999). Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry. Anal. Chem. 71: 3965-3973.
13. Buxton, G. V., Greenstock, C. L., Helman, W. P., and Ross, A. B. (1988). Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals in aqueous solution. J. Phys. Chem. Ref Data 270: 513-886.
14. Masuda, T., Nakano, S., and Kondo, M. (1973). Rate constants for the reaction of OH radicals with enzyme proteins as determined by the p-nitrodimethylanaline method. J. Radiat. Res. (Japan) 14: 339-345.
15. Xu, G., and Chance, M. R. (2004). Radiolytic modification of acidic amino acid residues in peptides: probes for examining protein-protein interactions. Anal. Chem. 76: 1213-1221.
16. Xu, G., and Chance, M. R. (2005). Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting. Anal. Chem. 77: 4549-4555.
17. Takamoto, K., and Chance, M. R. (2006). Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu. Rev. Biophys. Biomol. Struct. 35: 251-276.
18. Sharp, J. S., Becker, J. M., and Hettich, R. L. (2003). Protein surface mapping by chemical oxidation: structural analysis by mass spectrometry. Anal. Biochem. 313: 216-225.
19. Maleknia, S. D., Chance, M. R., and Downard, K. M. (1999). Electrosprayassisted modification of proteins: a radical probe of protein structure. Rapid Commun. Mass Spectrom. 13: 2352-2358.
20. Kiselar, J. G., Maleknia, S. D., Sullivan, M., Downard, K. M., and Chance, M. R. (2002). Hydroxyl radical probe of protein surfaces using synchrotron Xray radiolysis and mass spectrometry. Int. J. Radiat. Biol. 78: 101-114.
21. Thomas, M. C., Mitchell, T. W., and Blanksby, S. J. (2006). Ozonolysis of phospholipid double bonds during electrospray ionization: a new tool for structure determination. J. Am. Chem. Soc. 128: 58-59.
22. Hambly, D. M., and Gross, M. L. (2005). Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale J. Am. Soc. Mass. Spectrom. 16: 2057-2063.
23. Hughson, F. M., Wright, P. E., and Baldwin, R. L. (1990). Structural characterization of a partly folded apomyoglobin intermediate. Science 249: 1544-1548.
24. Goldsmith, S., Maleknia, S. D., Almo, S. C., and Chance, M. R. (1999). Synchrotron X-ray footprinting of profilin poly-proline peptide complex. Biophysical J. 76: A172.
25. Goldsmith, S. C., Maleknia, S. D., Almo, S. C., and Chance, M. R. (2000). Synchrotron X-ray footprinting of the gelsolin-actin complex. Biophysical J. 78: 213.
26. Wong, J. W., Maleknia, S. D., and Downard, K. M. (2003). Study of the ribonuclease-S-proteinpeptide complex using a radical probe and electrospray ionization mass spectrometry. Anal. Chem. 75: 1557-1563.
27. Wong, J. W., Maleknia, S. D., and Downard, K. M. (2005). Hydroxyl radical probe of the calmodulin-melittin complex interface by electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 16: 225-233.
28. Scaloni, A., Miraglia, N., Orru, S., Amodeo, P., Motta, A., Marino, G., and Pucci, P. (1998). Topology of the calmodulin-melittin complex. J. Mol. Biol. 277: 945-958.
29. Guan, J. Q., Almo, S. C., Reisler, E. and Chance, M. R. (2003). Structural reorganization of proteins revealed by radiolysis and mass spectrometry: G-actin solution structure is divalent cation dependent. Biochemistry 42: 11992-12000.
30. Kiselar, J. G., Janmey, P. A., Almo, S. C., and Chance, M. R., (2003). Visualizing the Ca2+/-dependent activation of gelsolin by using synchrotron footprinting. Proc. Natl. Acad. Sci. U.S.A 100: 3942-3947.
31. Stadtman, E. R. (1992). Protein oxidation and aging. Science 257: 1220-1224.
32. Berlett, B. S., and Stadtman, E. R. (1997). Protein oxidation in aging, disease, and oxidative stress. J. Biol. Chem. 272: 20313-20316.
33. Shum, W. -K., Maleknia, S. D., and Downard, K. M. (2005). Onset of oxidative damage in α-crystallin by radical probe mass spectrometry. Anal. Biochem. 344: 247-256.
34. Horwitz, J. (2003). Alpha-crystallin. Exp. Eye Res. 76: 145-153.
35. Issa, S., and Downard, K. M. (2006). Interaction between alpha and upsiloncrystallin common to the eye of the Australian platypus by radical probe mass spectrometry. J. Mass Spectrom., 41: 1298-1303.
36. Maleknia, S. D., Reixach, N., and Buxbaum, J. N. (2006). Protein oxidation inhibits amyloid fibril formation of transthyretin. FEBS J. 273: 5400-5406.
37. Gerega, S. K., and Downard, K. M. (2006). PROXIMO - a docking new algorithm to model protein complexes using data from radical probe mass spectrometry. Bioinformatics 22: 1702-1709.