What is the dielectric constant of a protein when its backbone is fixed?

Journal of Chemical Theory and Computation

Volumn 9, Issue 10, 2013, Pages 4603-4608

  Simonson, Thomas ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84885395843     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400398e     Document Type: Article

References (75)

1. You, T.; Bashford, D. Biophys. J. 1995, 69, 1721-1733
2. Beroza, P.; Case, D. A. J. Phys. Chem. 1996, 100, 20156-20163
3. Georgescu, E. R.; Alexov, E.; Gunner, M. Biophys. J. 2002, 83, 1731-1748
4. Barth, P.; Alber, T.; Harbury, P. B. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4898-4903
5. Kieseritzky, G.; Knapp, E. W. Proteins 2008, 71, 1335-1348
6. Song, Y.; Mao, J.; Gunner, M. R. J. Comput. Chem. 2009, 30, 2231-2247
7. Aleksandrov, A.; Polydorides, S.; Archontis, G.; Simonson, T. J. Phys. Chem. B 2010, 114, 10634-10648
8. Gunner, M.; Zhu, X.; Klein, M. C. Proteins 2011, 79, 3306-3319
9. Polydorides, S.; Simonson, T. J. Comput. Chem. 2013, In Press
10. Vizcarra, C. L.; Mayo, S. L. Curr. Opin. Chem. Biol. 2005, 9, 622-626
11. Vizcarra, C. L.; Zhang, N. G.; Marshall, S. A.; Wingreen, N. S.; Zeng, C.; Mayo, S. L. J. Comput. Chem. 2008, 29, 1153-1162
12. Pantazes, R. J.; Greenwood, M. J.; Maranas, C. D. Curr. Opin. Struct. Biol. 2011, 21, 467-472
13. Samish, I.; MacDermaid, C. M.; Perez-Aguilar, J. M.; Saven, J. G. Annu. Rev. Phys. Chem. 2011, 62, 129-149
14. Fröhlich, H. Theory of Dielectrics; Clarendon Press: Oxford, 1949.
15. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149
16. Simonson, T. Rep. Prog. Phys. 2003, 66, 737-787
17. Simonson, T. Photosynth. Res. 2008, 97, 21-32
18. Gilson, M.; Honig, B. Biopolymers 1986, 25, 2097-2119
19. Nakamura, H.; Sakamoto, T.; Wada, A. Protein Eng. 1988, 2, 177-183
20. King, G.; Lee, F.; Warshel, A. J. Chem. Phys. 1991, 95, 4366-4377
21. Simonson, T.; Perahia, D.; Brünger, A. T. Biophys. J. 1991, 59, 670-90
22. Smith, P.; Brunne, R.; Mark, A.; van Gunsteren, W. J. Phys. Chem. 1993, 97, 2009-2014
23. Simonson, T.; Perahia, D. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 1082-1086
24. Simonson, T.; Perahia, D. J. Am. Chem. Soc. 1995, 117, 7987-8000
25. Simonson, T.; Brooks, C. L. J. Am. Chem. Soc. 1996, 118, 8452-8458
26. Simonson, T.; Archontis, G.; Karplus, M. J. Phys. Chem. B 1999, 103, 6142-6156
27. Krishtalik, L.; Kuznetsov, A. M.; Mertz, E. L. Biophys. J. 1996, 70, A225
28. Song, X.; Chandler, D.; Marcus, R. A. J. Phys. Chem. 1996, 100, 11954-11959
29. Voges, D.; Karshikoff, A. J. Chem. Phys. 1998, 108, 2219-2227
30. Boresch, S.; Höchtl, P.; Steinhauser, O. J. Phys. Chem. B 2000, 104, 8743-8752
31. Pitera, J.; Falta, M.; van Gunsteren, W. Biophys. J. 2001, 80, 2546-2555
32. Song, X. J. Chem. Phys. 2002, 116, 9359-9363
33. Park, H.; Jeon, Y. H. Phys. Rev. E 2007, 75 10.1103/PhysRevE.75.021916
34. Goh, G. B.; Garcia-Moreno, B.; Brooks, Charles L., I. J. Am. Chem. Soc. 2011, 133, 20072-20075
35. Guest, W. C.; Cashman, N. R.; Plotkin, S. S. Phys. Chem. Chem. Phys. 2011, 13, 6286-6295
36. Martin, D. R.; Matyushov, D. V. J. Chem. Phys. 2012, 137, 165101
37. Neumann, M. Mol. Phys. 1983, 50, 841-858
38. De Leeuw, S.; Perram, J.; Smith, E. Annu. Rev. Phys. Chem. 1986, 37, 245-270
39. Perram, J.; Smith, E. J. Stat. Phys. 1986, 46, 179-190
40. Jackson, J. Classical Electrodynamics; Wiley: New York, 1975.
41. Netz, R. R.; Orland, H. Eur. Phys. J. E 2000, 1, 203-214
42. Gascoyne, P.; Pethig, R. J. Chem. Soc., Faraday Trans. 1981, 77, 1733-1735
43. Bone, S.; Pethig, R. J. Mol. Biol. 1982, 157, 571-575
44. Zhou, H. J. Chem. Phys. 1996, 105, 3726-3733
45. Mertz, E. L.; Krishtalik, L. I. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2081-2086
46. Archontis, G.; Simonson, T. J. Am. Chem. Soc. 2001, 123, 11047-11056
47. Simonson, T. Curr. Opin. Struct. Biol. 2001, 11, 243-252
48. Simonson, T. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6544-6549
49. Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt am Busch, M.; Lopes, A.; Amara, N.; Polydorides, S.; Sedano, A.; Druart, K.; Archontis, G. J. Comput. Chem. 2013, 10.1002/jcc.23418
50. Landau, L.; Lifschitz, E. Statistical Mechanics; Pergamon Press: New York, 1980.
51. Simonson, T. Int. J. Quantum Chem. 1999, 73, 45-57
52. Kusalik, P. Mol. Phys. 1993, 80, 225-231
53. Kusalik, P.; Mandy, M.; Svishchev, I. J. Chem. Phys. 1994, 100, 7654-7664
54. Simonson, T.; Perahia, D. Farad. Disc 1996, 103, 71-90
55. Bas, D. C.; Rogers, D. M.; Jensen, J. H. Proteins 2008, 73, 765-783
56. Olsson, M. H. M.; Sondergaard, C. R.; Rostowski, M.; Jensen, J. H. J. Chem. Theory Comput. 2011, 7, 525-537
57. Hawkins, G. D.; Cramer, C.; Truhlar, D. Chem. Phys. Lett. 1995, 246, 122-129
58. Lopes, A.; Aleksandrov, A.; Bathelt, C.; Archontis, G.; Simonson, T. Proteins 2007, 67, 853-867
59. Schmidt am Busch, M.; Lopes, A.; Amara, N.; Bathelt, C.; Simonson, T. BMC Bioinformatics 2008, 9, 148-163
60. Tuffery, P.; Etchebest, C.; Hazout, S.; Lavery, R. J. Biomol. Struct. Dyn. 1991, 8, 1267
61. Aleksandrov, A.; Thompson, D.; Simonson, T. J. Mol. Recog. 2010, 23, 117-127
62. Polydorides, S.; Amara, N.; Simonson, T.; Archontis, G. Proteins 2011, 79, 3448-3468
63. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82-87
64. Pokala, N.; Handel, T. M. J. Mol. Biol. 2005, 347, 203-227
65. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1092
66. Frenkel, D.; Smit, B. Understanding Molecular Simulation; Academic Press: New York, 1996.
67. Brünger, A. T. X-plor version 3.1, A System for X-ray Crystallography and NMR; Yale University Press: New Haven, CT, 1992.
68. Jorgensen, W.; Chandrasekar, J.; Madura, J.; Impey, R.; Klein, M. J. Chem. Phys. 1983, 79, 926-935
69. Bogusz, S.; Cheatham, T. E.; Brooks, B. R. J. Chem. Phys. 1998, 108, 7070-7084
70. Brooks, B.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614
71. Mackerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616
72. Alexov, E.; Mehler, E. L.; Baker, N.; Baptista, A. M.; Huang, Y.; Milletti, F.; Nielsen, J. E.; Farrell, D.; Carstensen, T.; Olsson, M. H. M.; Shen, J. K.; Warwicker, J.; Williams, S.; Word, J. M. Proteins 2011, 79, 3260-3275
73. Bashford, D.; Karplus, M. Biochemistry 1990, 29, 10219-10225
74. Krishtalik, L. Russ. J. Electrochem. 2006, 42, 1006-1016
75. Mandell; Kortemme, T. Curr. Opin. Biotechnol. 2009, 20, 420-428