Simulated x-ray scattering of protein solutions using explicit-solvent models

Journal of Chemical Physics

Volumn 130, Issue 13, 2009, Pages

  Park, Sanghyun ^a   Bardhan, Jaydeep P ^a   Roux, Benòt ^a,b   Makowski, Lee ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC COORDINATES; ATOMISTIC MODELS; COMPUTATIONAL SCHEMES; CONTINUUM MODELS; EXPERIMENTAL TECHNIQUES; LENGTH-SCALE; PROTEIN SOLUTIONS; PROTEIN STRUCTURES; QUATERNARY STRUCTURES; SCATTERING PATTERNS; SOLVENT MODELS; X -RAY SCATTERINGS;

CONTINUUM MECHANICS; MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE; SCATTERING;

X RAY CRYSTALLOGRAPHY;

LYSOZYME; MYOGLOBIN; WATER;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; RADIATION SCATTERING; X RAY; X RAY CRYSTALLOGRAPHY;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; MURAMIDASE; MYOGLOBIN; PROTEIN CONFORMATION; SCATTERING, RADIATION; WATER; X-RAYS;

EID: 64549083267     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3099611     Document Type: Article

References (26)

1. S. Doniach, Chem. Rev. (Washington, D.C.) 0009-2665 10.1021/cr990071k 101, 1763 (2001).
2. C. D. Putnam, M. Hammel, G. L. Hura, and J. A. Tainer, Q. Rev. Biophys. 40, 191 (2007). 0033-5835
3. D. M. Tiede, R. Zhang, and S. Seifert, Biochemistry 41, 6605 (2002). 0006-2960
4. R. F. Fischetti, D. J. Rodi, D. B. Gore, and L. Makowski, Chem. Biol. 11, 1431 (2004). 1074-5521
5. L. Makowski, D. J. Rodi, S. Mandava, S. Devarapalli, and R. F. Fischetti, J. Mol. Biol. 383, 731 (2008). 0022-2836
6. R. D. B. Fraser, T. P. MacRae, and E. Suzuki, J. Appl. Crystallogr. 0021-8898 10.1107/S0021889878014296 11, 693 (1978).
7. D. Svergun, C. Barberato, and M. H. J. Koch, J. Appl. Crystallogr. 0021-8898 10.1107/S0021889895007047 28, 768 (1995).
8. E. Lattman, Proteins 5, 149 (1989). 0887-3585
9. F. Merzel and J. C. Smith, Acta Crystallogr., Sect. D: Biol. Crystallogr. 58, 242 (2002). 0907-4449
10. T. Head-Gordon and G. Hura, Chem. Rev. (Washington, D.C.) 0009-2665 10.1021/cr0006831 102, 2651 (2002).
11. R. F. Fischetti, D. J. Rodi, A. Mirza, T. C. Irving, E. Kondrashkina, and L. Makowski, J. Synchrotron Radiat. 0909-0495 10.1107/S0909049503016583 10, 398 (2003).
12. P. M. Chaikin and T. C. Lubensky, Principles of Condensed Matter Physics (Cambridge University Press, Cambridge, England, 1995).
13. L. Makowski, D. J. Rodi, S. Mandava, D. D. L. Minh, D. B. Gore, and R. F. Fischetti, J. Mol. Biol. 375, 529 (2008). 0022-2836
14. Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, edited by, Q. Cui, and, I. Bahar, (CRC, Boca Raton, FL, 2006).
15. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 0263-7855 10.1016/0263-7855(96)00018-5 14, 33 (1996).
16. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten, J. Comput. Chem. 0192-8651 10.1002/jcc.20289 26, 1781 (2005).
17. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 0021-9606 10.1063/1.445869 79, 926 (1983).
18. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. 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. Wirkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 1089-5647 10.1021/jp973084f 102, 3586 (1998).
19. T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 0021-9606 10.1063/1.464397 98, 10089 (1993).
20. International Tables for Crystallography, edited by, A. J. C. Wilson, (Kluwer Academic, Boston, 1992), Vol. C.
21. J. F. Kenney and E. S. Keeping, Mathematics of Statistics, 2nd ed. (Van Nostrand, Princeton, 1951).
22. A. Ponti, J. Magn. Reson. 1090-7807 10.1006/jmre.1999.1758 138, 288 (1999).
23. D. Sezer, J. H. Freed, and B. Roux, J. Chem. Phys. 0021-9606 10.1063/1.2908075 128, 165106 (2008).
24. K. Hermansson, Chem. Phys. Lett. 0009-2614 10.1016/0009-2614(96)00854-8 260, 229 (1996).
25. J. M. Sorenson, G. Hura, R. M. Glaeser, and T. Head-Gordon, J. Chem. Phys. 0021-9606 10.1063/1.1319615 113, 9149 (2000).
26. M. Krack, A. Gambirasio, and M. Parrinello, J. Chem. Phys. 0021-9606 10.1063/1.1517040 117, 9409 (2002).