Ion mobility-mass spectrometry study of folded ubiquitin conformers induced by treatment with cis-[Pd(en)(H 2O) 2] 2+

Journal of the American Society for Mass Spectrometry

Volumn 22, Issue 2, 2011, Pages 300-309

  Giganti, Virginia G ^a   Kundoor, Sriramu ^a   Best, W Alex ^a   Angel, Laurence A ^a  

^a TEXAS A AND M UNIVERSITY COMMERCE   (United States)

Author keywords

Ion mobility; Mass spectrometry; Pd(II) complexes; Proteomic reagents; Ubiquitin conformers

Indexed keywords

ACTIVATED COMPLEX; CHARGE STATE; ETHYLENE DIAMINE; ION MOBILITY; ION MOBILITY-MASS SPECTROMETRY; MOLAR EXCESS; PALLADIUM COMPLEXES; PD(II) COMPLEXES; PEPTIDE BONDS; PROTEOMIC REAGENTS; UBIQUITIN; UBIQUITIN CONFORMERS;

AMIDES; AMINO ACIDS; BINDING SITES; BIOCHEMISTRY; IONS; MASS SPECTROMETRY; PEPTIDES;

PALLADIUM COMPOUNDS;

ETHYLENEDIAMINE; HISTIDINE; HYDROGEN; METHIONINE; OXYGEN; PALLADIUM COMPLEX; PEPTIDE; UBIQUITIN;

ARTICLE; BINDING SITE; HYDROLYSIS; ION MOBILITY SPECTROMETRY; LIGAND BINDING; MASS SPECTROMETRY; METAL BINDING; PROTEIN BINDING; PROTEIN CLEAVAGE; PROTEOMICS;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CATTLE; ETHYLENEDIAMINES; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; ORGANOMETALLIC COMPOUNDS; PALLADIUM; PEROXIDES; PROTEIN FOLDING; PROTEOMICS; UBIQUITIN;

BOVINAE;

EID: 79952531652     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-010-0044-1     Document Type: Article

References (35)

1. Bellotti, V., Stoppini, M.: Protein misfolding diseases. Open. Biol. J. 2, 228-234 (2009)
2. Dobson, C.M.: Protein folding and misfolding. Nature 426, 884-890 (2003)
3. Hershko, A., Ciechanover, A.: The ubiquitin system. Annu. Rev. Biochem. 67, 425-479 (1998)
4. Bohrer, B.C., Merenbloom, S.I., Koeniger, S.L., Hilderbrand, A.E., Clemmer, D.E.: Biomolecule analysis by ion mobility spectrometry. Annu. Rev. Anal. Chem. 1, 293-327 (2008)
5. Uetrecht, C., Rose, R.J., van Duijn, E., Lorenzen, K., Heck, A.J.R.: Ion mobility mass spectrometry of proteins and protein assemblies. Chem. Soc. Rev. 39, 1633-1655 (2010)
6. Pringle, S.D., Giles, K., Wildgoose, J.L., Williams, J.P., Slade, S.E., Thalassinos, K., Batemann, R.H., Bowers, M.T., Scrivens, J.H.: An investigation of the mobility separation of some peptide and protein ions using a new hybrid quadrupole/traveling wave IMS/oa-TOF instrument. Int. J. Mass Spectrom. 261, 1-12 (2007)
7. Smith, D.P., Giles, K., Bateman, R.H., Radford, S.E., Ashcroft, A.E.: Monitoring co-populated conformational states during protein folding events using electrospray ionization-ion mobility spectrometry-mass spectrometry. J. Am. Soc. Mass Spectrom. 18, 2180-2190 (2007)
8. Benesch, J.L.P.: Collisional activation of protein complexes: picking up the pieces. J. Am. Soc. Mass Spectrom. 20, 341-348 (2009)
9. Hopper, J.T.S., Oldham, N.J.: Collision induced unfolding of protein ions in the gas phase studied by ion mobility-mass spectrometry: the effect of ligand binding on conformational stability. J. Am. Soc. Mass Spectrom. 20, 1851-1858 (2009)
10. Smith, D.P., Knapman, T.W., Campuzano, I., Malham, R.W., Berryman, J.T., Radford, S.E., Ashcroft, A.E.: Deciphering drift time measurements from traveling wave ion mobility spectrometry-mass spectrometry studies. Eur. J. Mass Spectrom. 15, 113-130 (2009)
11. Scarff, C.A., Thalassinos, K., Hilton, I., Scrivens, J.H.: Traveling wave ion mobility mass spectrometry studies of protein structure: biological significance and comparison with x-ray crystallography and nuclear magnetic resonance spectroscopy measurements. Rapid Commun. Mass Spectrom. 22, 3297-3304 (2008)
12. Thalassinos, K., Grabenauer, M., Slade, S.E., Hilton, G.R., Bowers, M. T., Scrivens, J.H.: Characterization of phosphorylated peptides using traveling wave-based and drift cell ion mobility mass spectrometry. Anal. Chem. 81, 248-254 (2009)
13. Hilton, G.R., Thalassinos, K., Grabenauer, M., Sanghera, N., Slade, S. E., Wytennbach, T., Robinson, P.J., Pinheiro, T.J.T., Bowers, M.T., Scrivens, J.H.: Structural analysis of prion proteins by means of drift cell and traveling wave ion mobility mass spectrometry. J. Am. Soc. Mass Spectrom. 5, 845-854 (2010)
14. Williams, J.P., Lough, J.A., Campuzano, I., Richardson, K., Sadler, P. J.: Use of ion mobility mass spectrometry and a collision cross-section algorithm to study an organometallic ruthenium anticancer complex and its adducts with a DNA oligonucleotide. Rapid Commun. Mass Spectrom. 23, 3563-3569 (2009)
15. Milović, N.M., Kostić, N.M.: Palladium(II) complexes, as synthetic peptidases, regioselectively cleave the second peptide bond "upstream" from methionine and histidine side chains. J. Am. Chem. Soc. 124, 4759-4769 (2002)
16. Milović, N.M., Kostić, N.M.: Palladium(II) complex as a sequence-specific peptidase: hydrolytic cleavage under mild conditions of x-pro peptide bonds in x-pro-met and x-pro-his segments. J. Am. Chem. Soc. 125, 781-788 (2003)
17. Ahrends, R., Pieper, S., Neumann, B., Scheler, C., Linscheld, M.W.: Metal-coded affinity tag labeling: a demonstration of analytical robustness and suitability for biological applications. Anal. Chem. 81, 2176-2184 (2009)
18. Zhu, L., Kostić, N.M.: Sequence-dependent cleavage of albumins with palladium(II) complexes: role of serine residue in controlling the high regioselectivity of protein cleavage. Inorg. Chim. Acta 339, 104-110 (2002)
19. hu, L., Bakhtiar, R., Kostić, N.M.: Transition-metal complexes as alternatives to proteolytic enzymes. regioselective cleavage of myoglobin by palladium(II) aqua complexes. J. Biol. Inorg. Chem. 3, 383-391 (1998)
20. Milović, N.M., Kostić, N.M.: Interplay of terminal amino group and coordinating side chains in directing regioselective cleavage of natural peptides and proteins with palladium(II) complexes. Inorg. Chem. 41, 7053-7063 (2002)
21. Milardi, D., Arnesano, F., Grasso, G., Magri, A., Tabbi, G., Scintilla, S., Natile, G., Rizzarelli, E.: Ubiquitin stability and the Lys63-linked polyubiquitination site are compromised on copper binding. Angew. Chem. Int. Ed. 46, 7993-7995 (2007)
22. Vijay-Kumar, S., Bugg, C.E., Cook, W.J.: Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194, 531-544 (1987)
23. Falini, G., Fermani, S., Tosi, G., Arnesano, F., Natile, G.: Structural probing of Zn(II), Cd(II), and Hg(II) binding to human ubiquitin. Chem. Commun. 45, 5960-5962 (2008)
24. Hoaglund, C.S., Valentine, S.J., Sporleder, C.R., Reilly, J.P., Clemmer, D.E.: Three-dimensional ion mobility TOFMS analysis of electrosprayed biomolecules. Anal. Chem. 70, 2236-2242 (1998)
25. Valentine, S.J., Counterman, A.E., Clemmer, D.E.: Conformer-dependent proton-transfer reactions of ubiquitin ions. J. Am. Soc. Mass Spectrom. 8, 954-961 (1997)
26. Clemmer, D. E. http://www.indiana.edu/~clemmer/Research/research.htm
27. Koeniger, S.L., Clemmer, D.E.: Resolution and structural transitions of elongated states of ubiquitin. J. Am. Soc.Mass Spectrom. 18, 322-331 (2007)
28. Koeniger, S.L., Merenbloom, S.I., Clemmer, D.E.: Evidence for many resolvable structures within conformational types of electrosprayed ubiquitin ions. J. Phys. Chem. B 110, 7017-7021 (2006)
29. Koeniger, S.L., Merenbloom, S.I., Sundarapandian, S., Clemmer, D.E.: Transfer of structural elements from compact to extended states in unsolvated ubiquitin. J. Am. Chem. Soc. 128, 11713-11719 (2006)
30. Purves, R.W., Barnett, D.A., Ells, B., Guevremont, R.: Investigation of bovine ubiquitin conformers separated by high-field asymmetric waveform ion mobility spectrometry: cross section measurements using energy-loss experiments with a triple quadrupole mass spectrometer. J. Am. Soc. Mass Spectrom. 11, 738-745 (2000)
31. Robinson, E.W., Leib, R.D., Williams, E.R.: The role of conformation on electron capture dissociation of ubiquitin. J. Am. Soc. Mass Spectrom. 17, 1469-1479 (2006)
32. Hong, J., Miao, R., Zhao, C., Jiang, J., Tang, H., Zhu, L.: Mass spectrometry assisted assignments of binding and cleavage sites of copper(II) and platinum(II) complexes towards oxidized insulin B chain. J. Mass Spectrom. 41, 1061-1072 (2006)
33. Basolo, F., Bailar Jr., J.C., Tarr, B.R.: The stereochemistry of complex inorganic compounds. X. The stereoisomers of dichlorobis(ethylenediamine) platinum(IV) chloride. J. Am. Chem. Soc. 72, 2433-2438 (1950)
34. Heneghan, L.F., Bailar Jr., J.C.: The stereoisomerism of complex inorganic compounds. XVI. The stereoisomers of dichlorobis(ethylenediamine) platinum(IV) salts. J. Am. Chem. Soc. 75, 1840-1841 (1953)
35. Broennum, B., Johansen, H.S., Skibsted, L.H.: Ammine ligand exchange in tetra-amminepalladium(II) in aqueous solution. Acta Chem. Scand. 43, 975-980 (1989)