Development of a microsecond X-ray protein footprinting facility at the Advanced Light Source

Journal of Synchrotron Radiation

Volumn 21, Issue 4, 2014, Pages 690-699

  Gupta, Sayan ^a   Celestre, Richard ^a   Petzold, Christopher J ^a   Chance, Mark R ^b   Ralston, Corie ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

mass spectrometry; microsecond irradiation; protein structure; radiolytic labeling

Indexed keywords

LIGHT SOURCES; MASS SPECTROMETRY; NITROGEN OXIDES; NUCLEIC ACIDS; RADIOLYSIS;

ADVANCED LIGHT SOURCE; HIGH FLUX DENSITY; LABELING EFFICIENCIES; MICRO-CAPILLARY FLOWS; NATIONAL SYNCHROTRON LIGHT SOURCES; PROTEIN FOOTPRINTING; PROTEIN STRUCTURES; STRUCTURAL BIOLOGY;

PROTEINS;

PROTEIN; PROTEIN BINDING;

BINDING SITE; CHEMISTRY; DEVICE FAILURE ANALYSIS; DEVICES; EQUIPMENT DESIGN; PROTEIN CONFORMATION; PROTEIN FOOTPRINTING; SYNCHROTRON; ULTRASTRUCTURE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOOTPRINTING; PROTEINS; SYNCHROTRONS;

EID: 84903614620     PISSN: 09090495     EISSN: 16005775     Source Type: Journal    
DOI: 10.1107/S1600577514007000     Document Type: Article

References (57)

1. Adilakshmi, T., Bellur, D. L. & Woodson, S. A. (2008). Nature (London), 455, 1268-1272.
2. Adilakshmi, T., Lease, R. A. & Woodson, S. A. (2006). Nucleic Acids Res. 34, e64.
3. Adilakshmi, T., Soper, S. F. & Woodson, S. A. (2009). Methods Enzymol. 468, 239-258.
4. Angel, T. E., Gupta, S., Jastrzebska, B., Palczewski, K. & Chance, M. R. (2009). Proc. Natl Acad. Sci. USA, 106, 14367-14372.
5. Aye, T. T., Low, T. Y. & Sze, S. K. (2005). Anal. Chem. 77, 5814-5822.
6. Bohon, J., D'Mello, R., Ralston, C., Gupta, S. & Chance, M. R. (2014). J. Synchrotron Rad. 21, 24-31.
7. Bohon, J., Jennings, L. D., Phillips, C. M., Licht, S. & Chance, M. R. (2008). Structure, 16, 1157-1165.
8. Buxton, G. V., Greenstock, C. L., Helman, W. P. & Ross, A. B. (1988). J. Phys. Chem. Ref. Data, 17, 374.
9. Chaudhuri, B. N., Gupta, S., Urban, V. S., Chance, M. R., D'Mello, R., Smith, L., Lyons, K. & Gee, J. (2011). Biochemistry, 50, 1799-1807.
10. Clatterbuck Soper, S. F., Dator, R. P., Limbach, P. A. & Woodson, S. A. (2013). Mol. Cell, 52, 506-516.
11. Deperalta, G., Alvarez, M., Bechtel, C., Dong, K., McDonald, R. & Ling, V. (2013). mAbs 5, 86-101.
12. Dhavan, G. M., Crothers, D. M., Chance, M. R. & Brenowitz, M. (2002). J. Mol. Biol. 315, 1027-1037.
13. Downard, K. M., Maleknia, S. D. & Akashi, S. (2012). Rapid Commun. Mass Spectrom. 26, 226-230.
14. Gerega, S. K. & Downard, K. M. (2006). Bioinformatics, 22, 1702-1709.
15. Guan, J. Q., Takamoto, K., Almo, S. C., Reisler, E. & Chance, M. R. (2005). Biochemistry, 44, 3166-3175.
16. Gupta, S., Bavro, V. N., D'Mello, R., Tucker, S. J., Vénien-Bryan, C. & Chance, M. R. (2010). Structure, 18, 839-846.
17. Gupta, S., Chai, J., Cheng, J., D'Mello, R., Chance, M. R. & Fu, D. (2014). Nature (London). In the Press.
18. Gupta, S., Cheng, H., Mollah, A. K., Jamison, E., Morris, S., Chance, M. R., Khrapunov, S. & Brenowitz, M. (2007b). Biochemistry, 46, 9886-9898.
19. Gupta, S., D'Mello, R. & Chance, M. R. (2012). Proc. Natl Acad. Sci. USA, 109, 14882-14887.
20. Gupta, S., Mangel, W. F., McGrath, W. J., Perek, J. L., Lee, D. W., Takamoto, K. & Chance, M. R. (2004). Mol. Cell. Proteom. 3, 950-959.
21. Gupta, S., Sullivan, M., Toomey, J., Kiselar, J. & Chance, M. R. (2007a). J. Synchrotron Rad. 14, 233-243.
22. Hambly, D. M. & Gross, M. L. (2005). J. Am. Soc. Mass Spectrom. 16, 2057-2063.
23. Janik, I., Bartels, D. M. & Jonah, C. D. (2007). J. Phys. Chem. A, 111, 1835-1843.
24. Jones, L. M., Sperry, J. B., Carroll, J. A. & Gross, M. L. (2011). Anal. Chem. 83, 7657-7661.
25. Kamal, J. K., Benchaar, S. A., Takamoto, K., Reisler, E. & Chance, M. R. (2007). Proc. Natl Acad. Sci. USA, 104, 7910-7915.
26. Kamal, J. K. & Chance, M. R. (2008). Protein Sci. 17, 79-94.
27. Kiselar, J. G. & Chance, M. R. (2010). J. Mass Spectrom. 45, 1373-1382.
28. Kiselar, J. G., Datt, M., Chance, M. R. & Weiss, M. A. (2011). J. Biol. Chem. 286, 43710-43716.
29. Kiselar, J. G., Janmey, P. A., Almo, S. C. & Chance, M. R. (2003a). Mol. Cell. Proteom. 2, 1120-1132.
30. Kiselar, J. G., Janmey, P. A., Almo, S. C. & Chance, M. R. (2003b). Proc. Natl Acad. Sci. USA, 100, 3942-3947.
31. Kiselar, J. G., Mahaffy, R., Pollard, T. D., Almo, S. C. & Chance, M. R. (2007). Proc. Natl Acad. Sci. USA, 104, 1552-1557.
32. Konermann, L., Ahadi, E., Rodriguez, A. D. & Vahidi, S. (2013). Anal. Chem. 85, 2-9.
33. Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992). J. Mol. Biol. 228, 13-22.
34. Kuntz, I. D. Jr, Brassfield, T. S., Law, G. D. & Purcell, G. V. (1969). Science, 163, 1329-1331.
35. Laganowsky, A., Reading, E., Hopper, J. T. & Robinson, C. V. (2013). Nat. Protocols, 8, 639-651.
36. Liljenzin, J. (2002). Radiochemistry and Nuclear Chemistry, 3rd ed. Oxford: Butterworth-Heinemann.
37. Ling, J., Cho, C., Guo, L. T., Aerni, H. R., Rinehart, J. & Söll, D. (2012). Mol. Cell, 48, 713-722.
38. Maleknia, S. D., Chance, M. R. & Downard, K. M. (1999). Rapid Commun. Mass Spectrom. 13, 2352-2358.
39. Maleknia, S. D. & Downard, K. (2001). Mass Spectrom. Rev. 20, 388-401.
40. Maleknia, S. D. & Downard, K. M. (2012). Rapid Commun. Mass Spectrom. 26, 2311-2318.
41. Maleknia, S. D., Reixach, N. & Buxbaum, J. N. (2006). FEBS J. 273, 5400-5406.
42. Orban, T., Jastrzebska, B., Gupta, S., Wang, B., Miyagi, M., Chance, M. R. & Palczewski, K. (2012). Structure, 20, 826-840.
43. Oztug Durer, Z. A., Kamal, J. K., Benchaar, S., Chance, M. R. & Reisler, E. (2011). J. Mol. Biol. 414, 204-216.
44. Padayatti, P. S., Wang, L., Gupta, S., Orban, T., Sun, W., Salom, D., Jordan, S. R., Palczewski, K. & Chance, M. R. (2013). Mol. Cell. Proteom. 12, 1259-1271.
45. Pearson, R. G. & Williams, E. L. (1987). J. Polym. Sci. A 25, 565-573.
46. Pereira, J. H., Ralston, C. Y., Douglas, N. R., Meyer, D., Knee, K. M., Goulet, D. R., King, J. A., Frydman, J. & Adams, P. D. (2010). J. Biol. Chem. 285, 27958-27966.
47. Pryor, W. A. (1986). Annu. Rev. Physiol. 48, 657-667.
48. Ralston, C. Y., Sclavi, B., Sullivan, M., Deras, M. L., Woodson, S. A., Chance, M. R. & Brenowitz, M. (2000). Methods Enzymol. 317, 353-368.
49. Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M. & Woodson, S. A. (1998a). Science, 279, 1940-1943.
50. Sclavi, B., Woodson, S., Sullivan, M., Chance, M. & Brenowitz, M. (1998b). Methods Enzymol. 295, 379-402.
51. Shacter, E. (2000). Drug Metab. Rev. 32, 307-326.
52. Sullivan, M. R., Rekhi, S., Bohon, J., Gupta, S., Abel, D., Toomey, J. & Chance, M. R. (2008). Rev. Sci. Instrum. 79, 025101.
53. Takahashi, K., Ohgami, S., Koyama, Y., Sawamura, S., Marin, T. W., Bartels, D. M. & Jonah, C. D. (2004). Chem. Phys. Lett. 383, 445-450.
54. Watson, C., Janik, I., Zhuang, T., Charvátová, O., Woods, R. J. & Sharp, J. S. (2009). Anal. Chem. 81, 2496-2505.
55. Wong, J. W., Maleknia, S. D. & Downard, K. M. (2005). J. Am. Soc. Mass Spectrom. 16, 225-233.
56. Xu, G. & Chance, M. R. (2007). Chem. Rev. 107, 3514-3543.
57. Yuan, S., Goldberg, K. A., Yashchuk, V. V., Celectre, R., Warwick, T. & McKinney, W. R. (2011). Nucl. Instrum. Methods Phys. Res. A, 635, S58-S63.