Ribosomal proteins of Deinococcus radiodurans: Their solvent accessibility and reactivity

Journal of Proteome Research

Volumn 8, Issue 3, 2009, Pages 1228-1246

  Running, William E ^a   Reilly, James P ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Chemical modification of proteins; Post translational modifications; Protein mass spectrometry; Protein nucleic acid interactions; Ribosomal proteins

Indexed keywords

ACETAMIDE DERIVATIVE; BACTERIAL PROTEIN; LYSINE; METHIONYL AMINOPEPTIDASE; RIBOSOME PROTEIN; RIBOSOME RNA;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DEINOCOCCUS RADIODURANS; ERROR; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SOLVENT EFFECT; THERMUS THERMOPHILUS;

AMINO ACID SEQUENCE; DEINOCOCCUS; IMIDOESTERS; LYSINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN CONFORMATION; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS, LARGE, BACTERIAL; RIBOSOME SUBUNITS, SMALL, BACTERIAL; SOLVENTS; THERMUS THERMOPHILUS;

DEINOCOCCUS RADIODURANS;

EID: 65249106020     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800544y     Document Type: Article

References (71)

1. Ray, P. S.; Arif, A.; Fox, P. L. Trends Biochem. Sci. 2007, 32, 158-164.
2. Downard, K. M. Proteomics 2006, 6, 5374-5384.
3. Sharon, M.; Robinson, C. V. Annu. Rev. Biochem. 2007, 76, 167-193.
4. Krause, R.; von Mering, C.; Bork, P.; Dandekar, T. BioEssays 2004, 26, 1333-1343.
5. Resing, K. A.; Ahn, N. G. FEBS Lett. 2005, 579, 885-889.
6. Kelleher, N. L.; Lin, H. Y.; Valaskovic, G. A.; Aaserud, D. J.; Fridriksson, E. K.; McLafferty, F. W. J. Am. Chem. Soc. 1999, 121, 806-812.
7. Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R., III Nat. Biotech. 1999, 17, 676-682.
8. Protein NMR Techniques. In Methods in Molecular Biology, Vol. 60; Reed, D. G., Ed.; Humana Press: Totowa, NJ, 1997; p 5.
9. Drenth, J. Principles of Protein X-ray Crystallography; Springer-Verlag: New York, 1994.
10. Akashi, S.; Sirouzu, M.; Terada, T.; Ito, Y.; Yokoyama, S.; Takio, K. Anal. Biochem. 1997, 248, 15-25.
11. Englander, S. W.; Mayne, L.; Sosnick, T. R. Protein Sci. 1997, 6, 1101-1109.
12. Ehring, H. Anal. Biochem. 1999, 267, 252-259.
13. Smith, D. L.; Deng, Y.; Zhang, Z. J. Mass. Spectrom. 1997, 32, 135-146.
14. Glocker, M. O.; Borchers, C.; Fiedler, W.; Suckau, D.; Przybylski, M. Bioconiueate Chem. 1994, 5, 583-590.
15. Glocker, M. O.; Nock, S.; Sprinzl, M.; Przybylski, M. Chem.-Eur. J. 1998, 4, 707-715.
16. Fiedler, W.; Borchers, C.; Macht, M.; Deininger, S.-O.; Przybylski, M. Bioconiueate Chem. 1998, 9, 236-241.
17. Mendoza, V. L.; Vachet, R. M. Anal. Chem. 2008, 80, 2895-2904.
18. Guan, J.-Q.; Chance, M. R. Trends Biochem. Sci. 2005, 30, 583-592.
19. Sharp, J. S.; Becker, J. M.; Hettich, R. L. Anal. Chem. 2004, 76, 672-683.
20. Sharp, J. S.; Guo, J.-T.; Uchiki, T.; Xu, Y.; Dealwis, C.; Hettich, R. L. Anal. Biochem. 2005, 340, 201-212.
21. Tong, X.; Wren, J. C.; Konerman, L. Anal. Chem. 2007, 79, 6376-6382.
22. Neurath, H. In Protein folding Jaenicke, R., Ed.; Elsevier, New York, 1980; pp 501-523.
23. Hubbard, S. J. BBA 1998, 1382, 191-206.
24. Suh, M.-J.; Pourshahian, S.; Limbach, P. A. J. Am. Soc. Mass Spectrom. 2007, 18, 1304-1317.
25. Beardsley, R. L.; Reilly, J. P. J. Proteome Res. 2003, 2, 15-21.
26. Janecki, D. J.; Beardsley, R. L.; Reilly, J. P. Anal. Chem. 2005, 77, 7274-7281.
27. Liu, X.; Broshears, W. C.; Reilly, J. P. Anal. Biochem. 2007, 367, 13-19.
28. Beardsley, R. L.; Running, W. E.; Reilly, J. P. J. Proteome Res. 2006, 5, 2935-2946.
29. Muller, E.-C.; Wittmann-Liebold, B. Cell. Mol. Life Sci. 1997, 53, 34-50.
30. Harms, J.; Schluenzen, F.; Zarivach, R.; Bashan, A.; Gat, S.; Agmon, I.; Bartels, H.; Franceshi, F.; Yonath, A. Cell 2001, 107, 679-688.
31. Harms, J. M.; Wilson, D. N.; Schluenzen, F.; Connell, S. R.; Stachelhaus, T.; Zaborowska, Z.; Spahn, C. M. T.; Fucini, P. Mol. Cell 2008, 30, 26-38.
32. Selmer, M.; Dunham, C. M.; Murphy, F. V. IV.; Weixlbaumer, A.; Petry, S.; Kelley, A. C.; Weir, J. R.; Ramakrishnan, V. Science 2006, 313, 1935-1942.
33. Woese, C. R. Microbiol. Rev. 1987, 51, 221-271.
34. Arnold, R. J.; Reilly, J. P. Anal. Biochem. 1999, 269, 105-112.
35. Running, W. E.; Ravipaty, S.; Karty, J. A.; Reilly, J. P. J. Proteome Res. 2007, 6, 337-347.
36. Barritault, D.; Expert-Bezancon, A.; Guerin, M F.; Hayes, D. Eur. J. Biochem. 1976, 63, 131-135.
37. Karty, J. A.; Running, W. E.; Reilly, J. P. J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2007, 847, 103-113.
38. Martz, E. Trends Biochem. Sci. 2002, 27, 107-109, http://protein-explorer.org.
39. Connolly, M. L. J. Appl. Crystallogr. 1983, 16, 548-558.
40. White, O.; Eisen, J. A.; Heidelberg, J. F.; et al. Science 1999, 286, 1571-1577.
41. Kleinjung, J.; Fraternali, F. Nucleic Acids Res. 2005, 33, W342-W346.
42. Lipton, M. S.; Pasa-Tolic, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049-11054.
43. Zhang, C.; Wei, J.; Zheng, Z.; Ying, N.; Shaeng, D.; Hua, Y. Proteomics 2005, 5, 138-143.
44. Schmid, A. K.; Lipton, M. S.; Mottaz, H.; Monroe, M. E.; Smith, R. D.; Lidstrom, M. E. J. Proteome Res. 2005, 4, 709-718.
45. Sherman, F.; Stewart, J. W.; Tsunasawa, S. BioEssays 1985, 3, 27-31.
46. Frottin, F.; Martinez, A.; Peynot, P.; Mitra, S.; Holz, R. C.; Giglione, C.; Meinnel, T. Mol. Cell. Proteomics 2005, 5, 2336-2349.
47. Karty, J. A.; Ireland, M. M. E.; Brun, Y. V.; Reilly, J. P. J. Proteome Res. 2002, 1, 325-335.
48. Zabrouskov, V.; Senko, M. W.; Du, Y.; Leduc, R. D.; Kelleher, N. L. J. Am. Soc. Mass Spectrom. 2005, 16, 2027-2038.
49. Strader, M. B.; VerBerkmoes, N. C.; Tabb, D. L.; Connelly, H. M.; Barton, J. W.; Bruce, B. D.; Pelletier, D. A.; Davison, B. H.; Hettich, R. L.; Larimer, F. W.; Hurst, G. B. J. Proteome Res. 2004, 3, 965-978.
50. Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. J. Am. Soc. Mass Spectrom. 2000, 11, 320-332.
51. Miller, J. H. Cell 1974, 1, 73-76.
52. Makarova, K. S.; Omelchenko, M. V.; Gaidamakova, E. K.; Ma-trosova, V. Y.; Vasilenko, A. PLoS ONE 2007, 2, e955, doi:10.1371/ journal.pone.0000955.
53. Luer, C. A.; Wong, K.-P. Biochemistry 1980, 19, 176-183.
54. Diedrich, G.; Burkhardt, N.; Nierhaus, K. H. Protein Expression Purif. 1997, 10, 42-50.
55. Moore, P. B.; Steitz, T. A. Annu. Rev. Biochem. 2003, 72, 813-850.
56. Klein, D. J.; Moore, P. B.; Steitz, T. A. J. Mol. Biol. 2004, 340, 141-177.
57. Brodersen, D. E.; Clemens, W. M., Jr.; Carter, A. P.; Wimberly, B. T.; Ramakrishnan, V. J. Mol. Biol. 2002, 316, 725-768.
58. Jones, S.; Daly, D. T. A.; Luscombe, N. M.; Berman, H. M.; Thornton, J. M. Nucleic Acids Res. 2001, 29, 943-954.
59. Treger, M.; Westhof, E. J. Mol. Recognit. 2001, 14, 199-214.
60. Ellis, J. J.; Broom, M.; Jones, S. Proteins 2007, 66, 903-911.
61. Alix, J.-H. Adv. Exper. Biol. Med. 1988, 231, 371-385.
62. Cameron, D. M.; Gregory, S. T.; Thompson, J.; Suh, M.-J.; Limbach, P. A.; Dahlberg, A. E. J. Bacteriol. 2004, 186, 5819-5825.
63. Herold, M.; Nierhaus, K. H. J. Biol. Chem. 1987, 262, 8826-8833.
64. Semrad, K.; Green, R.; Schroeder, R. RNA 2004, 10, 1855-1860.
65. Held, W. A.; Ballou, B.; Mizushima, S.; Nomura, M. J. Biol. Chem. 1974, 249, 3103-3111.
66. Culver, G. Biopolymers 2003, 68, 234-249.
67. Wimberly, B. T.; Brodersen, D. E.; Clemmons, W. M., Jr.; Morgan-Warren, R. J.; Carter, A. P.; Vonrhein, C.; Hartsch, T.; Ramakrish-nan, V. Nature 2001, 407, 327-339.
68. Schuwirth, B. S.; Borovinskaya, M. A.; Hau, C. W.; Zhang, W.; Vila, S.; Holton, J. M.; Doudna Cate, J. H. Science 2005, 310, 827-834.
69. Lauber, M. A., Running, W. E., Reilly, J. P. manuscript in preparation.
70. th ASMS Conference on Mass Spec-trometry and Allied Topics, Denver, CO, June 1-5, 2008; Abstract 101 (A082979.4500.VER.3.pdf).
71. Clemons, W. M., Jr.; Brodersen, D. E.; McCutcheon, J. P.; May, J. L. C.; Carter, A. P.; Morgan-Warren, R. J.; Wimberly, B. T.; Ramakrishnan, V. J. Mol. Biol. 2001, 310, 827-843.