Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method

Journal of Chemical Theory and Computation

Volumn 11, Issue 6, 2015, Pages 2560-2574

  Lee, Juyong ^a   Miller, Benjamin T ^a   Damjanović, Ana ^a,b   Brooks, Bernard R ^a  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; CARDIOTOXIN; GLUTAMIC ACID; LYSINE; PEPTIDE; SOLVENT;

ANIMAL; CHEMISTRY; MOLECULAR DYNAMICS; PH; SNAKE; THERMODYNAMICS;

ANIMALS; ASPARTIC ACID; CARDIOTOXINS; GLUTAMIC ACID; HYDROGEN-ION CONCENTRATION; LYSINE; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; SNAKES; SOLVENTS; THERMODYNAMICS;

EID: 84931274866     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct501101f     Document Type: Article

References (92)

1. Perutz, M. F. Science (Washington, DC, U. S.) 1978, 201, 1187
2. García-Moreno, B. J. Biol. 2009, 8, 98
3. Chimenti, M. S.; Khangulov, V. S.; Robinson, A. C.; Heroux, A.; Majumdar, A.; Schlessman, J. L.; García-Moreno, B. Structure 2012, 20, 1071
4. Rastogi, V. K.; Girvin, M. E. Nature 1999, 402, 263
5. Symersky, J.; Pagadala, V.; Osowski, D.; Krah, A.; Meier, T.; Faraldo-Gómez, J. D.; Mueller, D. M. Nat. Struct. Mol. Biol. 2012, 19, 485
6. Schulz, S.; Iglesias-Cans, M.; Krah, A.; Yildiz, Ö.; Leone, V.; Matthies, D.; Cook, G. M.; Faraldo-Gómez, J. D.; Meier, T. PLoS Biol. 2013, 11 e1001596
7. Wang, T.; Sessions, A. O.; Lunde, C. S.; Rouhani, S.; M, R.; Duan, Y.; Facciotti, M. T. Structure 2013, 21, 290
8. Yoshikawa, S.; Muramoto, K.; Shinzawa-Itoh, K. Annu. Rev. Biophys. 2011, 40, 205
9. Tripathi, S.; Šrajer, V.; Purwar, N.; Henning, R.; Schmidt, M. Biophys. J. 2012, 102, 325
10. Isom, D. G.; Castañeda, C. A.; Cannon, B. R.; García-Moreno, B. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 5260
11. Lee, D.; Lee, J.; Seok, C. Phys. Chem. Chem. Phys. 2013, 15, 5844
12. Yang, A. S.; Gunner, M. R.; Sampogna, R.; Sharp, K.; Honig, B. Proteins: Struct., Funct., Bioinf. 1993, 15, 252
13. Alexov, E. G.; Gunner, M. R. Biophys. J. 1997, 72, 2075
14. Carstensen, T.; Farrell, D.; Huang, Y.; Baker, N. A.; Nielsen, J. E. Proteins: Struct., Funct., Bioinf. 2011, 79, 3287
15. Warwicker, J. Proteins: Struct., Funct., Bioinf. 2011, 79, 3374
16. Baptista, A. M.; Teixeira, V. H.; Soares, C. M. J. Chem. Phys. 2002, 117, 4184
17. Bürgi, R.; Kollman, P. A.; Van Gunsteren, W. F. Proteins: Struct., Funct., Bioinf. 2002, 47, 469
18. Mongan, J.; Case, D. A.; McCammon, J. A. J. Comput. Chem. 2004, 25, 2038
19. Lee, M. S.; Salsbury, F. R.; Brooks, C. L. Proteins: Struct., Funct., Bioinf. 2004, 56, 738
20. Mongan, J.; Case, D. A. Curr. Opin. Struct. Biol. 2005, 15, 157
21. Khandogin, J.; Brooks, C. L. Biophys. J. 2005, 89, 141
22. Machuqueiro, M.; Baptista, A. M. J. Phys. Chem. B 2006, 110, 2927
23. Khandogin, J.; Brooks, C. L. Biochemistry 2006, 45, 9363
24. Itoh, S. G.; Damjanović, A.; Brooks, B. R. Proteins: Struct., Funct., Bioinf. 2011, 79, 3420
25. Wallace, J. A.; Shen, J. K. J. Chem. Theory Comput. 2011, 7, 2617
26. Donnini, S.; Tegeler, F.; Groenhof, G.; Grubmüller, H. J. Chem. Theory Comput. 2011, 7, 1962
27. Goh, G. B.; Knight, J. L.; Brooks, C. L. J. Chem. Theory Comput. 2012, 8, 36
28. Sabri Dashti, D.; Meng, Y.; Roitberg, A. E. J. Phys. Chem. B 2012, 116, 8805
29. Hu, H.; Shen, L. J. Comput. Chem. 2014, 35, 1491
30. Swails, J. M.; York, D. M.; Roitberg, A. E. J. Chem. Theory Comput. 2014, 10, 1341
31. Chen, W.; Morrow, B. H.; Shi, C.; Shen, J. K. Mol. Simul. 2014, 1
32. Kong, X.; Brooks, C. L. J. Chem. Phys. 1996, 105, 2414
33. Lee, J.; Miller, B. T.; Damjanovic, A.; Brooks, B. R. J. Chem. Theory Comput. 2014, 10, 2738
34. Christ, C. D.; van Gunsteren, W. F. J. Chem. Phys. 2007, 126 184110
35. Christ, C. D.; van Gunsteren, W. F. J. Chem. Phys. 2008, 128 174112
36. Fukunishi, H.; Watanabe, O.; Takada, S. J. Chem. Phys. 2002, 116, 9058
37. Sugita, Y.; Kitao, A.; Okamoto, Y. J. Chem. Phys. 2000, 113, 6042
38. Mitsutake, A. J. Chem. Phys. 2009, 131 094105
39. Mitsutake, A.; Okamoto, Y. J. Chem. Phys. 2009, 130 214105
40. Chodera, J. D.; Shirts, M. R. J. Chem. Phys. 2011, 135 194110
41. Gee, J.; Shell, M. S. J. Chem. Phys. 2011, 134 064112
42. Jeon, J.; Shell, M. S. Biophys. J. 2012, 102, 1952
43. Ostermeir, K.; Zacharias, M. J. Comput. Chem. 2014, 35, 150
44. Bergonzo, C.; Henriksen, N. M.; Roe, D. R.; Swails, J. M.; Roitberg, A. E.; Cheatham, T. E., III J. Chem. Theory Comput. 2013, 10, 492
45. Kokubo, H.; Tanaka, T.; Okamoto, Y. J. Comput. Chem. 2013, 34, 2601
46. Chiang, C. M.; Chien, K. Y.; Lin, H. J.; Lin, J. F.; Yeh, H. C.; Ho, P. L.; Wu, W. G. Biochemistry 1996, 35, 9167
47. Chiang, C. M.; Chang, S. L.; Lin, H. J.; Wu, W. G. Biochemistry 1996, 35, 9177
48. Won, H.; Kim, J.; Ko, K.; Won, Y. Bull. Korean Chem. Soc. 2002, 23, 80-81
49. 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: Struct., Funct., Bioinf. 2011, 79, 3260
50. Olsson, M. H. M.; Søndergaard, C. R.; Rostkowski, M.; Jensen, J. H. J. Chem. Theory Comput. 2011, 7, 525
51. König, G.; Hudson, P. S.; Boresch, S.; Woodcock, H. L. J. Chem. Theory Comput. 2014, 10, 1406
52. Baptista, A. M.; Martel, P. J.; Petersen, S. B. Proteins: Struct., Funct., Bioinf. 1997, 27, 523
53. Baptista, A. M. J. Chem. Phys. 2002, 116, 7766
54. Torrie, G.; Valleau, J. J. Comput. Phys. 1977, 23, 187
55. Christ, C. D.; van Gunsteren, W. F. J. Chem. Theory Comput. 2009, 5, 276
56. Nozaki, Y.; Tanford, C. Methods Enzymol. 1967, 69, 715
57. Kyte, J. Structure in Protein Chemistry; Structure in Protein Chemistry Series; Garland: New York, NY, USA, 1995.
58. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, 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.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wirkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586
59. Okamoto, Y. J. Mol. Graphics Modell. 2004, 22, 425
60. Kannan, S.; Zacharias, M. Proteins: Struct., Funct., Bioinf. 2009, 76, 448
61. Curuksu, J.; Zacharias, M. J. Chem. Phys. 2009, 130 104110
62. Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 13749
63. Itoh, S. S. G.; Okumura, H.; Okamoto, Y. J. Chem. Phys. 2010, 132 134105
64. Kokubo, H.; Tanaka, T.; Okamoto, Y. J. Comput. Chem. 2011, 32, 2810
65. Wallace, J. A.; Shen, J. K. J. Chem. Phys. 2012, 137 184105
66. Jiang, W.; Hodoscek, M.; Roux, B. J. Chem. Theory Comput. 2009, 5, 2583
67. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; 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
68. Wu, X.; Brooks, B. R. Chem. Phys. Lett. 2003, 381, 512
69. Wu, X.; Hodoscek, M.; Brooks, B. R. J. Chem. Phys. 2012, 137 044106
70. Singhal, A. K.; Chien, K. Y.; Wu, W. G.; Rule, G. S. Biochemistry 1993, 32, 8036
71. Miller, B. T.; Singh, R. P.; Klauda, J. B.; Hodoscek, M.; Brooks, B. R.; Woodcock, H. L. J. Chem. Inf. Model. 2008, 48, 1920
72. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
73. Chu, J.-W.; Trout, B. L.; Brooks, B. R. J. Chem. Phys. 2003, 119, 12708
74. König, G.; Miller, B. T.; Boresch, S.; Wu, X.; Brooks, B. R. J. Chem. Theory Comput. 2012, 8, 3650
75. Woodcock, H. L.; Miller, B. T.; Hodoscek, M.; Okur, A.; Larkin, J. D.; Ponder, J. W.; Brooks, B. R. J. Chem. Theory Comput. 2011, 7, 1208
76. Nose, S. J. Chem. Phys. 1984, 81, 511
77. Hoover, W. Phys. Rev. A 1985, 31, 1695
78. Bogusz, S.; Cheatham, T. E.; Brooks, B. R. J. Chem. Phys. 1998, 108, 7070
79. Lindstrom, M. J.; Bates, D. M. Biometrics 1990, 673
80. Pinheiro, J. C.; Bates, D. M. Stat. Comput. 1996, 6, 289
81. Pinheiro, J.; Bates, D.; DebRoy, S.; Sarkar, D. R Core Team nlme: Linear and Nonlinear Mixed Effects Models, R package version 3.1-120; R Foundation for Statistical Computing: Vienna, Austria, 2015.
82. R Core Team, R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2013.
83. Zuckerman, D. M.; Lyman, E. J. Chem. Theory Comput. 2006, 2, 1200
84. Okur, A.; Roe, D. R.; Cui, G.; Hornak, V.; Simmerling, C. J. Chem. Theory Comput. 2007, 3, 557
85. Roitberg, A. E.; Okur, A.; Simmerling, C. J. Phys. Chem. B 2007, 111, 2415
86. Okur, A.; Miller, B. T.; Joo, K.; Lee, J.; Brooks, B. R. J. Chem. Theory Comput. 2013, 9, 1115
87. Damjanović, A.; García-Moreno, B.; Lattman, E. E.; García, A. E. Proteins: Struct., Funct., Bioinf. 2005, 60, 433
88. Damjanović, A.; Wu, X.; García-Moreno E., B.; Brooks, B. R. Biophys. J. 2008, 95, 4091
89. Damjanović, A.; Brooks, B. R.; García-Moreno E., B. J. Phys. Chem. A 2011, 115, 4042
90. Karpen, M. E.; Tobias, D. J.; Brooks, C. L. Biochemistry 1993, 32, 412
91. Carpenter, G. A.; Grossberg, S. Appl. Opt. 1987, 26, 4919
92. Pao, Y.-H Adaptive Pattern Recognition and Neural Networks; Addison-Wesley Longman: Boston, MA, USA, 1989.