On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys

Acta Crystallographica Section D: Biological Crystallography

Volumn 69, Issue 5, 2013, Pages 683-694

  Karaca, Ezgi ^a   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

Author keywords

collision cross section; HADDOCK; hybrid methods; ion mobility mass spectrometry; low resolution; small angle X ray scattering

Indexed keywords

ARTICLE; BIOLOGY; COLLISION CROSS-SECTION; COMPUTER PROGRAM; HADDOCK; HYBRID METHODS; ION-MOBILITY MASS SPECTROMETRY; LOW RESOLUTION; MASS SPECTROMETRY; METHODOLOGY; MOLECULAR DOCKING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; SMALL ANGLE SCATTERING; SMALL-ANGLE X-RAY SCATTERING; X RAY DIFFRACTION;

COLLISION CROSS-SECTION; HADDOCK; HYBRID METHODS; ION-MOBILITY MASS SPECTROMETRY; LOW RESOLUTION; SMALL-ANGLE X-RAY SCATTERING;

COMPUTATIONAL BIOLOGY; MASS SPECTROMETRY; MOLECULAR DOCKING SIMULATION; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; SCATTERING, SMALL ANGLE; SOFTWARE; X-RAY DIFFRACTION;

EID: 84877278835     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444913007063     Document Type: Article

References (76)

1. Alber, F., Förster, F., Korkin, D., Topf, M. & Sali, A. (2008). Annu. Rev. Biochem. 77, 443-477.
2. Badger, J. et al. (2005). Proteins, 60, 787-796.
3. Benesch, J. L. & Ruotolo, B. T. (2011). Curr. Opin. Struct. Biol. 21, 641-649.
4. Bernadó, P. (2010). Eur. Biophys. J. 39, 769-780.
5. Bernstein, S. L., Dupuis, N. F., Lazo, N. D., Wyttenbach, T., Condron, M. M., Bitan, G., Teplow, D. B., Shea, J. E., Ruotolo, B. T., Robinson, C. V. & Bowers, M. T. (2009). Nature Chem. 1, 326-331.
6. Blobel, J., Bernadó, P., Svergun, D. I., Tauler, R. & Pons, M. (2009). J. Am. Chem. Soc. 131, 4378-4386.
7. Bonvin, A. M. (2006). Curr. Opin. Struct. Biol. 16, 194-200.
8. Bressanelli, S., Stiasny, K., Allison, S. L., Stura, E. A., Duquerroy, S., Lescar, J., Heinz, F. X. & Rey, F. A. (2004). EMBO J. 23, 728-738.
9. Brunger, A. T., Adams, P. D. & Rice, L. M. (1999). Prog. Biophys. Mol. Biol. 72, 135-155.
10. Brunger, A. T., Strop, P., Vrljic, M., Chu, S. & Weninger, K. R. (2011). J. Struct. Biol. 173, 497-505.
11. Buey, R. M., Chacón, P., Andreu, J. M. & Fernando Díaz, J. (2009). Applications of Synchrotron Light to Scattering and Diffraction in Materials and Life Sciences, edited by T. A. Ezquerra, M. C. García-Gutiérrez, A. Nogales & M. Gomez, pp. 245-263. Berlin Heidelberg: Springer.
12. Chen, Y. W., Stott, K. & Perutz, M. F. (1999). Proc. Natl Acad. Sci. USA, 96, 1257-1261.
13. Covaceuszach, S., Cassetta, A., Konarev, P. V., Gonfloni, S., Rudolph, R., Svergun, D. I., Lamba, D. & Cattaneo, A. (2008). J. Mol. Biol. 381, 881-896.
14. D'Abramo, M., Meyer, T., Bernadó, P., Pons, C., Recio, J. F. & Orozco, M. (2009). J. Chem. Theory Comput. 5, 3129-3137.
15. Dima, R. I. & Thirumalai, D. (2004). J. Phys. Chem. B, 108, 6564-6570.
16. Dominguez, C., Boelens, R. & Bonvin, A. M. (2003). J. Am. Chem. Soc. 125, 1731-1737.
17. Fernández-Recio, J., Totrov, M. & Abagyan, R. (2004). J. Mol. Biol. 335, 843-865.
18. Filgueira de Azevedo, W., dos Santos, G. C., dos Santos, D. M., Olivieri, J. R., Canduri, F., Silva, R. G., Basso, L. A., Renard, G., da Fonseca, I. O., Mendes, M. A., Palma, M. S. & Santos, D. S. (2003). Biochem. Biophys. Res. Commun. 309, 923-928.
19. Förster, F., Webb, B., Krukenberg, K. A., Tsuruta, H., Agard, D. A. & Sali, A. (2008). J. Mol. Biol. 382, 1089-1106.
20. Gabel, F. (2012). Eur. Biophys. J. 41, 1-11.
21. Garcia-Garcia, J., Bonet, J., Guney, E., Fornes, O., Planas, J. & Oliva, B. (2012). Mol. Informatics, 31, 342-362.
22. Grishaev, A., Wu, J., Trewhella, J. & Bax, A. (2005). J. Am. Chem. Soc. 127, 16621-16628.
23. Hamiaux, C., Pérez, J., Prangé, T., Veesler, S., Riès-Kautt, M. & Vachette, P. (2000). J. Mol. Biol. 297, 697-712.
24. Hura, G. L., Menon, A. L., Hammel, M., Rambo, R. P., Poole, F. L. II, Tsutakawa, S. E., Jenney, F. E. Jr, Classen, S., Frankel, K. A., Hopkins, R. C., Yang, S.-J., Scott, J. W., Dillard, B. D., Adams, M. W. W. & Tainer, J. A. (2009). Nature Methods, 6, 606-612.
25. Hwang, H., Vreven, T., Janin, J. & Weng, Z. (2010). Proteins, 78, 3111-3114.
26. Jorgensen, W. L. & Tirado-Rives, J. (1988). J. Am. Chem. Soc. 110, 1657-1666.
27. Jurneczko, E. & Barran, P. E. (2011). Analyst, 136, 20-28.
28. Karaca, E., Melquiond, A. S., de Vries, S. J., Kastritis, P. L. & Bonvin, A. M. (2010). Mol. Cell. Proteomics, 9, 1784-1794.
29. Lander, G. C., Saibil, H. R. & Nogales, E. (2012). Curr. Opin. Struct. Biol. 22, 627-635.
30. Liu, Y., Gotte, G., Libonati, M. & Eisenberg, D. (2002). Protein Sci. 11, 371-380.
31. Loris, R., Tielker, D., Jaeger, K. E. & Wyns, L. (2003). J. Mol. Biol. 331, 861-870.
32. Madl, T., Gabel, F. & Sattler, M. (2011). J. Struct. Biol. 173, 472-482.
33. Mashiach-Farkash, E., Nussinov, R. & Wolfson, H. J. (2011). Proteins, 79, 2607-2623.
34. Melquiond, A. S. J. & Bonvin, A. M. J. J. (2010). Protein-Protein Complexes: Analysis, Modeling and Drug Design, edited by M. Zacharias, pp. 183-209. London: Imperial College Press
35. Méndez, R., Leplae, R., De Maria, L. & Wodak, S. J. (2003). Proteins, 52, 51-67.
36. Mertens, H. D. & Svergun, D. I. (2010). J. Struct. Biol. 172, 128-141.
37. Mintseris, J., Pierce, B., Wiehe, K., Anderson, R., Chen, R. & Weng, Z. (2005). Proteins, 69, 511-520.
38. Muradov, D., Kobe, B., Dixon, E. N. & Huber, T. (2010). Introduction to Protein Structure Prediction: Methods and Algorithms, edited by H. Rangwala & G. Karypis, pp. 265-277. Hoboken: John Wiley & Sons.
39. Nishimura, N., Hitomi, K., Arvai, A. S., Rambo, R. P., Hitomi, C., Cutler, S. R., Schroeder, J. I. & Getzoff, E. D. (2009). Science, 326, 1373-1379.
40. Pertz, O., Bozic, D., Koch, A. W., Fauser, C., Brancaccio, A. & Engel, J. (1999). EMBO J. 18, 1738-1747.
41. Petoukhov, M. V., Franke, D., Shkumatov, A. V., Tria, G., Kikhney, A. G., Gajda, M., Gorba, C., Mertens, H. D. T., Konarev, P. V. & Svergun, D. I. (2012). J. Appl. Cryst. 45, 342-350.
42. Petoukhov, M. V. & Svergun, D. I. (2005). Biophys. J. 89, 1237-1250.
43. Pinotsis, N., Lange, S., Perriard, J.-C., Svergun, D. I. & Wilmanns, M. (2008). EMBO J. 27, 253-264.
44. Politis, A., Park, A. Y., Hyung, S.-J., Barsky, D., Ruotolo, B. T. & Robinson, C. V. (2010). PLoS One, 5, e12080.
45. Pons, C., D'Abramo, M., Svergun, D. I., Orozco, M., Bernadó, P. & Fernández-Recio, J. (2010). J. Mol. Biol. 403, 217-230.
46. Pukala, T. L., Ruotolo, B. T., Zhou, M., Politis, A., Stefanescu, R., Leary, J. A. & Robinson, C. V. (2009). Structure, 17, 1235-1243.
47. Putnam, C. D., Hammel, M., Hura, G. L. & Tainer, J. A. (2007). Q. Rev. Biophys. 40, 191-285.
48. Rappsilber, J. (2011). J. Struct. Biol. 173, 530-540.
49. Rawat, N. & Biswas, P. (2011). Phys. Chem. Chem. Phys. 13, 9632-9643.
50. Robinson, C. V., Sali, A. & Baumeister, W. (2007). Nature (London), 450, 973-982.
51. Ruotolo, B. T., Benesch, J. L., Sandercock, A. M., Hyung, S.-J. & Robinson, C. V. (2008). Nature Protoc. 3, 1139-1152.
52. Ruotolo, B., Hyung, S., Robinson, P., Giles, K., Bateman, R. & Robinson, C. (2007). Angew. Chem. Int. Ed. 46, 8001-8004.
53. Scarff, C. A., Thalassinos, K., Hilton, G. R. & Scrivens, J. H. (2008). Rapid Commun. Mass Spectrom. 22, 3297-3304.
54. Schneidman-Duhovny, D., Hammel, M. & Sali, A. (2010). J. Struct. Biol. 173, 461-471.
55. Schneidman-Duhovny, D. et al. (2012). Bioinformatics, 28, 3282-3289.
56. Schubert, W. D., Urbanke, C., Ziehm, T., Beier, V., Machner, M. P., Domann, E., Wehland, J., Chakraborty, T. & Heinz, D. W. (2002). Cell, 111, 825-836.
57. Segelke, B. W., Nguyen, D., Chee, R., Xuong, N. H. & Dennis, E. A. (1998). J. Mol. Biol. 279, 223-232.
58. Shvartsburg, A. A., Hudgins, R. R., Dugourd, P. & Jarrold, M. F. (2001). Chem. Soc. Rev. 30, 26-35.
59. Shvartsburg, A. A. & Jarrold, M. F. (1996). Chem. Phys. Lett. 261, 86-91.
60. Smith, D. P., Knapman, T. W., Campuzano, I., Malham, R. W., Berryman, J. T., Radford, S. E. & Ashcroft, A. E. (2008). Eur. J. Mass Spectrom. 15, 113-130.
61. Sondermann, H., Nagar, B., Bar-Sagi, D. & Kuriyan, J. (2005). Proc. Natl Acad. Sci. USA, 102, 16632-16637.
62. Stehle, T. & Harrison, S. C. (1997). EMBO J. 16, 5139-5148.
63. Steinhoff, H. J. (2004). Biol. Chem. 385, 913-920.
64. Svergun, D., Barberato, C. & Koch, M. H. J. (1995). J. Appl. Cryst. 28, 768-773.
65. Svergun, D. I., Petoukhov, M. V. & Koch, M. H. J. (2001). Biophys. J. 80, 2946-2953.
66. Uetrecht, C., Barbu, I. M., Shoemaker, G. K., van Duijn, E. & Heck, A. J. (2010). Nature Chem. 3, 126-132.
67. Uetrecht, C., Rose, R. J., van Duijn, E., Lorenzen, K. & Heck, A. J. (2010). Chem. Soc. Rev. 39, 1633-1655.
68. Volz, K. (1999). Protein Sci. 8, 2428-2437.
69. Vries, S. J. de & Bonvin, A. M. J. J. (2011). PLoS One, 6, e17695.
70. Vries, S. J. de, van Dijk, M. & Bonvin, A. M. J. J. (2010). Nature Protoc. 5, 883-897.
71. Vries, S. J. de, van Dijk, A. D., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T. & Bonvin, A. M. J. J. (2007). Proteins, 69, 726-733.
72. Wang, X., Lee, H.-W., Liu, Y. & Prestegard, J. H. (2011). J. Struct. Biol. 173, 515-529.
73. Williamson, T. E., Craig, B. A., Kondrashkina, E., Bailey-Kellogg, C. & Friedman, A. M. (2008). Biophys. J. 94, 4906-4923.
74. Wyttenbach, T., Helden, G., Batka, J. J., Carlat, D. & Bowers, M. T. (1997). J. Am. Soc. Mass Spectrom. 8, 275-282.
75. Wyttenbach, T., Witt, M. & Bowers, M. T. (2000). J. Am. Chem. Soc. 122, 3458-3464.
76. Zhou, M. & Robinson, C. V. (2010). Trends Biochem. Sci. 35, 522-529.