Theoretical assessment of the oligolysine model for ionic interactions in protein-DNA complexes

Journal of Physical Chemistry B

Volumn 115, Issue 32, 2011, Pages 9864-9872

  Fenley, Marcia O ^a   Russo, Cristina ^a   Manning, Gerald S ^b  

^a FLORIDA STATE UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOCHEMISTRY; COMPLEXATION; DNA; POLYELECTROLYTES;

ANTITHROMBIN; BINDING FREE ENERGY; BINDING INTERFACE; BULK SOLUTIONS; CATIONIC PROTEINS; CHARGED LIGANDS; CHARGED PROTEINS; COUNTERION CONDENSATION; COUNTERIONS; CUMULATIVE EFFECTS; EXPERIMENTAL DATA; IONIC INTERACTION; POISSON-BOLTZMANN; PROTEIN BINDING; PROTEIN RESIDUES; PROTEIN-DNA COMPLEXES; SALT DEPENDENCE; SIMPLE SYSTEM; SIMULATION METHODS;

PROTEINS;

EID: 80051726307     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp204915y     Document Type: Article

References (38)

1. Alberts, B.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walter, P. Mol. Biol. Cell 2007.
2. Jones, S.; van Heyningen, P.; Berman, H. M.; Thornton, J. M. J. Mol. Biol. 1999, 287, 877
3. Stawiski, E. W.; Gregoret, L. M.; Mandel-Gutfreund, Y. J. Mol. Biol. 2003, 326, 1065
4. Cherstvy, A. G. Phys. Chem. Chem. Phys. 2011, 13, 9942
5. Jayaram, B.; McConnell, K.; Dixit, S. B.; Beveridge, D. L. J. Comput. Chem. 2002, 23, 1
6. Privalov, P. L.; Dragan, A. I.; Crane-Robinson, C. Nucleic Acids Res. 2011, 39, 2483
7. Manning, G. S. Quart. Revs. Biophys. 1978, 11, 179
8. Record, M. T., Jr.; Lohman, T. M.; de Haseth, P. J. Mol. Biol. 1976, 107, 145
9. Record, M. T., Jr.; Zhang, W.; Anderson, C. F. Adv. Protein Chem. 1998, 51, 281
10. Seyrek, E.; Dubin, P. Adv. Colloid Interface Sci. 2010, 158, 119
11. Manning, G. S. Acc. Chem. Res. 1979, 12, 443
12. Manning, G. S. Ber. Bunsenges. Phys. Chem. 1996, 100, 909
13. Granot, J.; Feigon, J.; Kearns, D. R. Biopolymers 1982, 21, 181
14. Granot, J.; Kearns, D. R.. Biopolymers 1982, 21, 203
15. Granot, J.; Kearns, D. R.. Biopolymers 1982, 21, 219
16. Granot, J.; Assa-Munt, N.; Kearns, D. R.. Biopolymers 1982, 21, 873
17. Mattai, J.; Kwak, J. C. T. Biochim. Biophys. Acta 1981, 677, 303
18. Dais, P.; Peng, Z.-J.; Perlin, A. S. Carbohydr. Res. 1987, 168, 163
19. Dais, P.; Peng, Z.-J.; Perlin, A. S. Can. J. Chem. 1987, 65, 1739
20. Keyser, U. F.; Koeleman, S.; Van Dorp, D.; Krapf, R. M. M.; Smeets, S. G.; Lemay, N. H.; Dekker, N. H.; Dekker, C. Nat. Phys. 2006, 2, 473
21. Qiu, X.; Kwok, L. W.; Park, H. Y.; Lamb, J. S.; Andresen, K.; Pollack, L. Phys. Rev. Lett. 2006, 96, 138101
22. Young, M. A.; Jayaram, B.; Beveridge, D. L. J. Am. Chem. Soc. 1997, 119, 59
23. Manning, G. S. Biophys. Chem. 1977, 7, 141
24. Mascotti, D. P.; Lohman, T. M. Proc. Natl. Acad. Sci., U.S.A. 1990, 87, 3142
25. Lohman, T. M.; de Haseth, P. L.; Record, M. T., Jr. Biochemistry 1980, 19, 3522
26. Hallberg, R. K.; Dubin, P. L. J. Phys. Chem. B 1998, 102, 8629
27. Rouzina, I.; Bloomfield, V. A. Biophys. J. 1999, 77, 3242
28. Qian, H.; Schellman, J. A. J. Phys. Chem. B 2000, 104, 11528
29. Boschitsch, A. H.; Fenley, M. O. J. Chem. Theory Comput. 2011, 7, 1524
30. Boschitsch, A. H.; Fenley, M. O. J. Comput. Chem. 2007, 28, 909
31. Bredenberg, J.; Russo, C.; Fenley, M. O. Biophys. J. 2008, 94, 4634
32. Zimm, B. H.; Le Bret, M. J. Biomol. Struct. Dynam. 1983, 1, 461
33. Ramanathan, G. V. J. Chem. Phys. 1983, 78, 3223
34. Mohanty, U.; Ninham, B. W.; Oppenheim, I. Proc. Natl. Acad. Sci., U.S.A. 1996, 93, 4342
35. Rouzina, I.; Bloomfield, V. A. J. Phys. Chem. 1996, 100, 4292
36. Tracy, C. A.; Widom, H. Physica A 1997, 244, 402
37. Belloni, L. Colloids Surf. A 1998, 140, 227
38. Deserno, M.; Holm, C.; May, S. Macromolecules 2000, 33, 199