A quasichemical approach for protein-cluster free energies in dilute solution

Journal of Chemical Physics

Volumn 127, Issue 16, 2007, Pages

  Young, Teresa M ^a   Roberts, Christopher J ^a  

^a University of Delaware   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; OLIGOMERS; POLYMERIZATION; SOLUTIONS; STATISTICAL MECHANICS;

FIBRIL FORMATION; PROTEIN OLIGOMERS; QUASICHEMICAL (QC) APPROXIMATION;

PROTEINS;

PROTEIN;

ARTICLE; CHEMISTRY; HYDROPHOBICITY; MONTE CARLO METHOD; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

HYDROPHOBICITY; MONTE CARLO METHOD; PROTEINS; SOLUTIONS; THERMODYNAMICS;

EID: 36048930727     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2779323     Document Type: Article

References (59)

1. D. Thirumalai, D. Klimov, and R. Dima, Curr. Opin. Struct. Biol. 13, 146 (2003).
2. R. Wetzel, Acc. Chem. Res. 39, 671 (2006).
3. S. Tanaka, K. Ito, R. Hayakawa, and M. Ataka, J. Chem. Phys. 111, 10330 (1999).
4. P. G. Vekilov, Cryst. Growth Des. 4(4), 671 (2004).
5. F. Oosawa and S. Asakura, Thermodynamics of the Polymerization of Protein (Academic, New York, 1975).
6. P. G. Debenedetti, Metastable Liquids: Concepts and Principles (Princeton University Press, Princeton, NJ, 1996).
7. F. Ferrone, Methods Enzymol. 309, 256 (1999).
8. J. M. Andrews and C. J. Roberts, J. Phys. Chem. B 111, 7897 (2007).
9. A. L. Fink, Folding Des. 3, R9 (1998).
10. M. M. Pallitto and R. M. Murphy, Biophys. J. 81, 1805 (2001).
11. S. Chen, F. A. Ferrone, and R. Wetzel, Proc. Natl. Acad. Sci. U.S.A. 99, 11884 (2002).
12. C. J. Roberts, R. T. Darrington, and M. B. Whitley, J. Pharm. Sci. 92, 1095 (2003).
13. Z. Ignatova and L. M. Gierasch, Biochemistry 44, 7266 (2005).
14. J. M. Andrews and C. J. Roberts, Biochemistry 46, 7558 (2007).
15. A. O. Grillo, K.-L. T. Edwards, R. S. Kashi, K. M. Shipley, L. Hu, M. J. Besman, and C. R. Middaugh, Biochemistry 40, 586 (2001).
16. E. Y. Chi, S. Krishnan, B. S. Kendrick, B. S. Chang, J. F. Carpenter, and T. W. Randolph, Protein Sci. 12, 903 (2003).
17. C. M. Dobson, Semin Cell Dev. Biol. 15, 3 (2004).
18. R. Dima and D. Thirumalai, Protein Sci. 11, 1036 (2002).
19. T. Cellmer, D. Bratko, J. Prausnitz, and H. Blanch, J. Chem. Phys. 122, 174908 (2005).
20. N. L. Fawzi, V. Chubukov, L. A. Clark, S. Brown, and T. Head-Gordon, Protein Sci. 14, 993 (2005).
21. S. Ohnishi and K. Takano, Cell. Mol. Life Sci. 61, 511 (2004).
22. V. N. Uversky and A. L. Fink, Biochim. Biophys. Acta 1698, 131 (2004).
23. H.-H. G. Tsai, M. Reches, C.-J. Tsai, K. Gunasekaran, E. Gazit, and R. Nussinov, Proc. Natl. Acad. Sci. U.S.A. 102, 8174 (2005).
24. S. Jang and S. Shin, J. Phys. Chem. B 110, 1955 (2006).
25. A. Melquiond, N. Mousseau, and P. Derreumaux, Proteins: Struct., Funct., Bioinf. 65, 180 (2006).
26. B. Urbanc, J. Borreguero, L. Cruz, and H. E. Stanley, Methods Enzymol. 412, 314 (2006).
27. J. K. Cheung and T. M. Truskett, Biophys. J. 89, 2372 (2005).
28. A. J. Marchut and C. K. Hall, Biophys. J. 90, 4574 (2006).
29. A. Lomakin, D. B. Teplow, D. A. Kirschner, and G. B. Benedek, Proc. Natl. Acad. Sci. U.S.A. 94, 7942 (1997).
30. D. Rosenbaum, A. Kulkarni, S. Ramakrishnan, and C. Zukoski, J. Chem. Phys. 111, 9882 (1999).
31. A. M. Kulkami and C. F. Zukoski, Langmuir 18, 3090 (2002).
32. P. M. Tessier, A. M. Lenhoff, and S. I. Sandler, Biophys. J. 82, 1620 (2002).
33. C. A. Teske, H. W. Blanch, and J. M. Prausnitz, J. Phys. Chem. B 108, 7437 (2004).
34. T. Ahamed, M. Ottens, G. W. van Dedem, and L. A. van der Wielen, J. Chromatogr., A 1089, 111 (2005).
35. J. J. Valente, K. S. Verma, M. C. Manning, W. W. Wilson, and C. S. Henry, Biophys. J. 89, 4211 (2005).
36. E. A. Guggenheim, and M. McGlashan, Proc. R. Soc. London, Ser. A 206, 448 (1951).
37. R. Goldstein and L. Stryer, Biophys. J. 50, 583 (1986).
38. P. G. Debenedetti, V. Raghavan, and S. S. Borick, J. Phys. Chem. 95, 4540 (1991).
39. C. J. Roberts and P. G. Debenedetti, J. Chem. Phys. 105, 658 (1996).
40. L. R. Pratt and R. A. LaViolette, Mol. Phys. 94, 909 (1998).
41. L. R. Pratt, R. A. LaViolette, M. A. Gomez, and M. E. Gentile, J. Phys. Chem. B 105, 11662 (2001).
42. C. J. Roberts, J. Phys. Chem. B 108, 19843 (2004).
43. E. T. Powers and D. L. Powers, Biophys. J. 91, 122 (2006).
44. G. Soto-Campos, D. S. Corti, and H. Reiss, J. Chem. Phys. 108, 2563 (1998).
45. A. Ben-Naim, Statistical Thermodynamics for Chemists and Biochemists (Plenum, New York, 1992).
46. D. A. McQuarrie, Statistical Mechanics (University Science Books, Sausalito, CA, 2000).
47. F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001).
48. D. Jayasri, V. Sastry, and K. Murthy, Phys. Rev. E 72, 036702 (2005).
49. M. P. Allen and D. Tildesley, Computer Simulation of Liquids (Oxford Science, Oxford, 1987).
50. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithm to Applications (Academic, New York, 1996).
51. I. M. Plaza del Pino, B. Ibarra-Molero, and J. M. Sanchez-Ruiz, Proteins: Struct., Funct., Genet. 40, 58 (2000).
52. K. Gekko and H. Noguchi, J. Phys. Chem. 83, 2706 (1979).
53. P. H. Stothart, Biochem. J. 219, 1049 (1984).
54. H. Durchschlag, Colloid Polym. Sci. 267, 1139 (1989).
55. W. Dzwolak, S. Grudzielanek, V. Smimovas, R. Ravindra, C. Nicolini, R. Jansen, A. Loksztejn, S. Porowski, and R. Winter, Biochemistry 44, 8948 (2005).
56. R. L. Remmele, Jr., J. Zhang-van Enk, V. Dharmavaram, D. Balaban, M. Durst, A. Shoshitaishvili, and H. Rand, J. Am. Chem. Soc. 127, 8328 (2005).
57. S. E. Radford, C. M. Dobson, and P. A. Evans, Nature (London) 358, 302 (1992).
58. T. L. Hill, An Introduction to Statistical Thermodynamics (Dover, Mineola, NY, 1986).
59. C. Haas, J. Drenth, and W. W. Wilson, J. Phys. Chem. B 103, 2808 (1999).