Ions and the protein surface revisited: Extensive molecular dynamics simulations and analysis of protein structures in alkali-chloride solutions

Journal of Physical Chemistry B

Volumn 115, Issue 29, 2011, Pages 9213-9223

  Friedman, Ran ^a  

^a LINNAEUS UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; COMPUTER SIMULATION; METAL IONS; MOLECULAR DYNAMICS; SODIUM CHLORIDE;

ASPARTATE RESIDUE; BULK SOLUTIONS; ELECTROSTATIC POTENTIALS; ION-BINDING; MOLECULAR DYNAMICS SIMULATIONS; PLANNING AND EXECUTION; PROTEIN RESIDUES; PROTEIN STRUCTURES; PROTEIN SURFACE; PROTEIN-SALT INTERACTIONS; STRUCTURAL DETAILS; SURFACE RESIDUES;

PROTEINS;

EID: 79960623090     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp112155m     Document Type: Article

References (82)

1. Hofmeister, F. Arch. Exp. Pathol. Pharmakol. 1888, 24, 247-60
2. Kunz, W.; Henle, J.; Ninham, B. W. Curr. Opin. Colloid Interface Sci. 2004, 9, 19-37
3. Loeb, J. J. Gen. Physiol. 1920, 2, 673-687
4. Loeb, J. J. Gen. Physiol. 1920, 3, 85-106
5. Northrop, J. H.; Kunitz, M. J. Gen. Physiol. 1924, 7, 25-38
6. Scatchard, G.; Scheinberg, I. H.; Armstrong, S. H., Jr. J. Am. Chem. Soc. 1950, 72, 535-540
7. Scheraga, H. Annu. Rev. Phys. Chem. 1959, 10, 191-218
8. Kachmar, J. F.; Boyer, P. D. J. Biol. Chem. 1953, 200, 669-682
9. Young, D. A.; Cimasoni, G. Biochim. Biophys. Acta 1974, 342, 333-342
10. Juárez, J.; López, S. G.; Cambón, A.; Taboada, P.; Mosquera, V. J. Phys. Chem. B 2009, 113, 10521-10529
11. Xiong, K.; Asciutto, E. K.; Madura, J. D.; Asher, S. A. Biochemistry 2009, 48, 10818-10826
12. Maestre-Martínez, M.; Haupt, K.; Edlich, F.; Neumann, P.; Parthier, C.; Stubbs, M. T.; Fischer, G.; Lücke, C. J. Mol. Recognit. 2011, 24, 23-34
13. Hummel, J. P.; Dreyer, W. J. Biochim. Biophys. Acta 1962, 63, 530-532
14. Arakawa, T.; Timasheff, S. N. Biochemistry 1982, 21, 6545-6552
15. OuYang, B.; Pochapsky, S. S.; Pagani, G. M.; Pochapsky, T. C. Biochemistry 2006, 45, 14379-14388
16. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-42
17. Imbragimova, G. T.; Wade, R. C. Biophys. J. 1998, 74, 2906-2911
18. Marlow, G. E.; Pettitt, B. M. Biopolymers 2001, 60, 134-52
19. Friedman, R.; Nachliel, E.; Gutman, M. Biophys. J. 2005, 89, 768-81
20. Vrbka, L.; Jungwirth, P.; Bauduin, P.; Touraud, D.; Kunz, W. J. Phys. Chem. B 2006, 110, 7036-7043
21. Project, E.; Nachliel, E.; Gutman, M. J. Comput. Chem. 2008, 29, 1163-1169
22. Joung, I. S.; Cheatham, T. E. J. Phys. Chem. B 2008, 112, 9020-9041
23. Hess, B.; van der Vegt, N. F. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 13296-13300
24. Fyta, M.; Kalcher, I.; Dzubiella, J.; Vrbka, L.; Netz, R. R. J. Chem. Phys. 2010, 132, 024911-024911
25. Klasczyk, B.; Knecht, V. J. Chem. Phys. 2010, 132, 024109-024109
26. Sakharov, D. V.; Lim, C. J. Comput. Chem. 2009, 30, 191-202
27. Villa, A.; Hess, B.; Saint-Martin, H. J. Phys. Chem. B 2009, 113, 7270-7281
28. Uejio, J. S.; Schwartz, C. P.; Duffin, A. M.; Drisdell, W. S.; Cohen, R. C.; Saykally, R. J. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6809-6812
29. Aziz, E. F.; Ottosson, N.; Eisebitt, S.; Eberhardt, W.; Jagoda-Cwiklik, B.; Vácha, R.; Jungwirth, P.; Winter, B. J. Phys. Chem. B 2008, 112, 12567-12570
30. Kalcher, I.; Horinek, D.; Netz, R. R.; Dzubiella, J. J. Phys.: Condens. Matter 2009, 21, 424108
31. Schwierz, N.; Horinek, D.; Netz, R. R. Langmuir 2010, 26, 7370-7379
32. Tomé, L. I.; Jorge, M.; Gomes, J. R.; Coutinho, J. A. J. Phys. Chem. B 2010, 114, 16450-16459
33. Gutman, M.; Nachliel, E.; Friedman, R. Photochem. Photobiol. Sci. 2006, 5, 531-7
34. Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Model. 2001, 7, 306-17
35. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718
36. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236
37. Lindahl, M.; Svensson, L. A.; Liljas, A.; Sedelnikova, S. E.; Eliseikina, I. A.; Fomenkova, N. P.; Nevskaya, N.; Nikonov, S. V.; Garber, M. B.; Muranova, T. A. EMBO J. 1994, 13, 1249-54
38. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. J. Phys. Chem. 1987, 91, 6269-6271
39. Weerasinghe, S.; Smith, P. E. J. Chem. Phys. 2003, 119, 11342-11349
40. Åqvist, J. J. Chem. Phys. 1990, 94, 8021-4
41. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J. Comput. Chem. 1997, 18, 1463-72
42. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952-962
43. Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126, 014101
44. Berendsen, H. J. C.; Postma, J. P. M.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-90
45. Parrinello, M.; Rahman, A. J. Appl. Phys. 1981, 52, 7182-7190
46. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-92
47. Friedman, R.; Caflisch, A. Proteins 2010, 78, 1575-82
48. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
49. Chandrasekhar, J.; Spellmeyer, D. C.; Jorgensen, W. L. J. Am. Chem. Soc. 1984, 106, 903-910
50. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J. Comput. Chem. 1999, 20, 786-798
51. Wasmer, C.; Lange, A.; Van Melckebeke, H.; Siemer, A. B.; Riek, R.; Meier, B. H. Science 2008, 319, 1523-1526
52. Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
53. Golovin, A.; Henrick, K. BMC Bioinf. 2008, 9, 312-312
54. Roux, B. Biophys. J. 2010, 98, 2877-2885
55. Lund, M.; Jagoda-Cwiklik, B.; Woodward, C. E.; Vacha, R.; Jungwirth, P. J. Phys. Chem. Lett. 2010, 1, 300-303
56. Collins, K. D. Biophys. Chem. 2006, 119, 271-281
57. Rempe, S. B.; Pratt, L. R.; Hummer, G.; Kress, J. D.; Martin, R. L.; Redondo, A. J. Am. Chem. Soc. 2000, 122, 966-967
58. Rempe, S. B.; Pratt, L. R. Fluid Phase Equilib. 2001, 183-184, 121-132
59. Lyubartsev, A. P.; Laasonen, K.; Laaksonen, A. J. Chem. Phys. 2001, 114, 3120-3126
60. Leung, K.; Rempe, S. B. Phys. Chem. Chem. Phys. 2006, 8, 2153-2162
61. Mapother, D.; Crooks, H. N.; Maurer, R. J. Chem. Phys. 1950, 18, 1231-1236
62. Mills, R.; Kennedy, J. W. J. Am. Chem. Soc. 1953, 75, 5696-5701
63. Tanaka, K.; Nomura, M. J. Chem. Soc., Faraday Trans. 1 1987, 83, 1779-1782
64. Lin, C.-l.; Lee, L.-s. Fluid Phase Equilib. 2003, 205, 69-88
65. Archer, D. W.; Monk, C. B. J. Chem. Soc. 1964, 3117-22
66. Daniele, P. G.; Derobertis, A.; Destefano, C.; Sammartano, S.; Rigano, C. J. Chem. Soc., Dalton Trans. 1985, 2353-2361
67. Merzel, F.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378-5383
68. Pfeiffer, S.; Fushman, D.; Cowburn, D. Proteins 1999, 35, 206-17
69. Dzubiella, J. J. Am. Chem. Soc. 2008, 130, 14000-14007
70. Dzubiella, J. J. Phys. Chem. B 2009, 113, 16689-16694
71. Gutman, M.; Nachliel, E.; Friedman, R. Biochim. Biophys. Acta 2006, 1757, 931-941
72. Friedman, R.; Caflisch, A. FEBS Lett. 2007, 581, 4120-4124
73. Zhou, T.; Huang, D.; Caflisch, A. J. Med. Chem. 2008, 51, 4280-4288
74. Heyda, J.; Pokorná, J.; Vrbka, L.; Vácha, R.; Jagoda-Cwiklik, B.; Konvalinka, J.; Jungwirth, P.; Vondrásek, J. Phys. Chem. Chem. Phys. 2009, 11, 7599-7604
75. Otzen, D. E.; Nesgaard, L. W.; Andersen, K. K.; Hansen, J. H.; Christiansen, G.; Doe, H.; Sehgal, P. Biochim. Biophys. Acta 2008, 1784, 400-414
76. Swiss Bioinformatic Institute. UniProtKB/Swiss-Prot Protein Knowledge Base Release 2010-06 Statistics. http://expasy.org/sprot/relnotes/relstat.html. 2010.
77. Auffinger, P.; Cheatham, T. E.; Vaiana, A. C. J. Chem. Theory Comput. 2007, 3, 1851-1859
78. Cordomi, A.; Edholm, O.; Perez, J. J. J. Chem. Theory Comput. 2009, 5, 2125-2134
79. Timko, J.; Bucher, D.; Kuyucak, S. J. Chem. Phys. 2010, 132, 114510
80. Pejov, L.; Spångberg, D.; Hermansson, K. J. Chem. Phys. 2010, 133, 174513
81. Noy, A.; Soteras, I.; Luque, F. J.; Orozco, M. Phys. Chem. Chem. Phys. 2009, 11, 10596-10607
82. Pezeshki, S.; Chimerel, C.; Bessonov, A. N.; Winterhalter, M.; Kleinekathöfer, U. Biophys. J. 2009, 97, 1898-1906