Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

Journal of Chemical Physics

Volumn 134, Issue 2, 2011, Pages

  Oroguchi, Tomotaka ^a   Ikeguchia, Mitsunori ^a  

^a YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC RESOLUTION; CLOSED FORM; DIFFERENT SOLVENTS; HEN EGG WHITE LYSOZYME; ION CONCENTRATIONS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NACL CONCENTRATION; NOVEL METHODS; PROTEIN CONFORMATION; PURE WATER; SMALL-ANGLE X-RAYS;

MOLECULAR DYNAMICS; PROTEINS; SODIUM CHLORIDE;

IONIC STRENGTH;

HEN EGG LYSOZYME; LYSOZYME; SODIUM CHLORIDE;

ANIMAL; ARTICLE; CHEMISTRY; CHICKEN; METABOLISM; MOLECULAR DYNAMICS; OSMOLARITY; PROTEIN CONFORMATION; SMALL ANGLE SCATTERING; X RAY DIFFRACTION;

ANIMALS; CHICKENS; MOLECULAR DYNAMICS SIMULATION; MURAMIDASE; OSMOLAR CONCENTRATION; PROTEIN CONFORMATION; SCATTERING, SMALL ANGLE; SODIUM CHLORIDE; X-RAY DIFFRACTION;

EID: 78751525538     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3526488     Document Type: Article

References (32)

1. C. J. Tsai, S. Kumar, B. Ma, and R. Nussinov, Protein Sci. 8, 1181 (1999).
2. M. Ikeguchi, J. Ueno, M. Sato, and A. Kidera, Phys. Rev. Lett. 94, 078102 (2005).
3. K. A. Henzler-Wildman, V. Thai, M. Lei, M. Ott, M. Wolf-Watz, T. Fenn, E. Pozharski, M. A. Wilson, G. A. Petsko, M. Karplus, C. G. Hübner, and D. Kern, Nature (London) 450, 838 (2007).
4. D. I. Svergun and M. H. J. Koch, Q. Rev. Biophys. 36, 147 (2003).
5. C. D. Putnum, M. Hammel, G. L. Hura, and J. A. Tainer, Q. Rev. Biophys. 40, 191 (2007).
6. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002).
7. T. Oroguchi, H. Hashimoto, T. Shimizu, M. Sato, and M. Ikeguchi, Biophys. J. 96, 2808 (2009).
8. S. Yang, S. Park, L. Makowski, and B. Roux, Biophys. J. 96, 4449 (2009).
9. R. Zangi, M. Hagen, and B. J. Berne, J. Am. Chem. Soc. 129, 4678 (2007).
10. M. V. Athawale, S. Sarupria, and S. Garde, J. Phys. Chem. B 112, 5661 (2008).
11. J. Holzmann, R. Ludwig, A. Geiger, and D. Paschek, Chem. Phys. Chem. 9, 2722 (2008).
12. D. I. Svergun, C. Barberato, and M. H. J. Koch, J. Appl. Cryst. 28, 768 (1995).
13. F. Merzel and J. C. Smith, Acta. Cryst. D 58, 242 (2002).
14. Y. Seki, T. Tomizawa, N. N. Khechinashvili, and K. Soda, Biophys. Chem. 95, 235 (2002).
15. S. Park, J. P. Bardhan, B. Roux, and L. Makowski, J. Chem. Phys. 130, 134114 (2009).
16. R. W. Kriwacki, L. H. Hengst, L. Tennant, S. I. Reed, and P. E. Wright, Proc. Natl. Acad. Sci. U.S.A. 93, 11504 (1996).
17. M. V. Fedorov, J.M. Goodman, and S. Schumm, Phys. Chem. Chem. Phys. 9, 5423 (2007).
18. S. Y. Ponomarev, K. M. Thayer, and D. L. Beveridge, Proc. Natl. Acad. Sci. U.S.A. 101, 14771 (2004).
19. M. Ikeguchi, J. Comput. Chem. 25, 529 (2004).
20. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, andM. Karplus, J. Phys. Chem. B 102, 3586 (1998).
21. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
22. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995).
23. R. Diamond, J. Mol. Biol. 82, 371 (1974).
24. P. D. Jeffrey, M. C. Bewley, R. T. A. MacGillivray, A. B. Mason, R. C. Woodworth, and E. N. Baker, Biochemistry 37, 13978 (1998).
25. R. T. A. MacGillivray, S. A. Moore, J. Chen, B. F. Anderson, H. Baker, Y. Luo, M. Bewley, C. A. Smith, M. E. P. Murphy, Y. Wang, A. B. Mason, R. C. Woodworth, G. D. Brayer, and E. N. Baker, Biochemistry 37, 7919 (1998).
26. See supplementary material at http://dx.doi.org/10.1063/1.3526488 for supplement providing the time-resolved MD-SAXS I(Q) in terms of the similarity score S and some additional information that cannot be included in the text.
27. E. N. Maslen, A. G. Fox, and M. A. O'Keefe, in International Tables for Crystallography, edited by A. J. C. Wilson and E. Prince (Kluwer Academic Publishers, Dordrecht/Boston/London, 1999), Vol. C, p. 548.
28. D. J. Price, and C. L. Brooks III, J. Chem. Phys. 121, 10096 (2004).
29. A. Guinier and G. Fournet, Small-angle scattering of X-rays (John Wiley & Sons, New York, 1955).
30. K. Ibel and H. B. Stuhrmann, J. Mol. Biol. 93, 255 (1975).
31. C. Stanley, S. Krueger, V. A. Parsegian, and D. C. Rau, Biophys. J. 94, 2777 (2008).
32. R. D. B. Fraser, T. P. MacRae, and E. Suzuki, J. Appl. Crystallogr, 11, 693 (1978).