DNA duplex formation with a coarse-grained model

Journal of Chemical Theory and Computation

Volumn 10, Issue 11, 2014, Pages 5020-5035

  Maciejczyk, Maciej ^a,b   Spasic, Aleksandar ^a,c   Liwo, Adam ^a,d   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF WARMIA AND MAZURY IN OLSZTYN   (Poland)

^c UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^d UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84909589749     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct4006689     Document Type: Article

References (77)

1. Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737-738
2. Brooks, B. R.; 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
3. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668-1688
4. Lavery, R.; Zakrzewska, K.; Beveridge, D.; Bishop, T. C.; Case, D. A.; Cheatham, T., III; Dixit, S.; Jayaram, B.; Lankas, F.; Laughton, C.; Maddocks, J. H.; Michon, A.; Osman, R.; Orozco, M.; Perez, A.; Singh, T.; Spackova, N.; Sponer, J. Nucleic Acids Res. 2010, 38, 299-313
5. Perez, A.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 2007, 129, 14739-14745
6. Mura, C.; McCammon, J. A. Nucleic Acids Res. 2008, 36, 4941-4955
7. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151
8. Kannan, S.; Zacharias, M. Phys. Chem. Chem. Phys. 2009, 11, 10589-10595
9. Laio, A.; Parinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562-12566
10. Piana, S.; Laio, A. J. Phys. Chem. B 2007, 111, 4553-4559
11. Piana, S. J. Phys. Chem. A 2007, 111, 12349-12354
12. Zimm, B. H.; Rice, S. A. Mol. Phys. 1960, 3, 391-407
13. Poland, D.; Scheraga, H. A. Physiol. Chem. Phys. 1969, 1, 389-446
14. Marko, J. F.; Siggia, E. D. Macromolecules 1994, 27, 981-988
15. Balaeff, A.; Mahadevan, L.; Schulten, K. Phys. Rev. Lett. 1999, 83, 4900-4903
16. Balaeff, A.; Koudella, C. R.; Mahadevan, L.; Schulten, K. Philos. Trans. R. Soc., A 2004, 362, 1355-1371
17. Vorobjev, Y. N. Biopolymers 1990, 29, 1503-1518
18. Olson, W. K. Curr. Opin. Struct. Biol. 1996, 6, 242-256
19. Rudnicki, W. R.; Bakalarski, G.; Lesyng, B. J. Biomol. Struct. Dyn. 2000, 17, 1097-1108
20. Maciejczyk, M.; Rudnicki, W. R.; Lesyng, B. J. Biomol. Struct. Dyn. 2000, 17, 1109-1116
21. Drukker, K.; Wu, G.; Schatz, G. C. J. Chem. Phys. 2001, 114, 579-590
22. Jendrejack, R. M.; de Pablo, J. J.; Graham, M. D. J. Chem. Phys. 2002, 116, 7752-7759
23. Jendrejack, R. M.; Schwartz, D. C.; Graham, M. D.; de Pablo, J. J. J. Chem. Phys. 2003, 119, 1165-1173
24. Jendrejack, R. M.; Schwartz, D. C.; de Pablo, J. J.; Graham, M. D. J. Chem. Phys. 2004, 120, 2513-2529
25. Chen, Y. L.; Graham, M. D.; de Pablo, J. J. Macromolecules 2005, 38, 6680-6687
26. Tepper, H. L.; Voth, G. A. J. Chem. Phys. 2005, 122, 124906
27. Knotts, T. A., IV; Rathore, N.; Schwartz, D. C.; de Pablo, J. J. J. Chem. Phys. 2007, 126, 084901
28. Voltz, K.; Trylska, J.; Tozzini, V.; Kurkal-Siebert, V.; Langowski, J.; Smith, J. J. Comput. Chem. 2008, 29, 1429-1439
29. Niewieczerzal, S.; Cieplak, M. J. Phys.: Condens. Matter 2009, 21, 474221
30. Sambirski, E. J.; Schwartz, D. C.; de Pablo, J. J. Biophys. J. 2009, 96, 1675-1690
31. Sambirski, E. J.; Ortiz, V.; de Pablo, J. J. J. Phys.: Condens. Matter 2009, 21, 034105
32. Ouldridge, T. E.; Johnston, I. G.; Louis, A. A.; Doye, J. P. J. Chem. Phys. 2009, 130, 065101
33. Dans, P. D.; Zeida, A.; Machado, M. R.; Pantano, S. J. Chem. Theory Comput. 2010, 6, 1711-1725
34. Morriss-Andrews, A.; Rottler, J.; Plotkin, S. S. J. Chem. Phys. 2010, 132, 035105
35. Linak, M. C.; Dorfman, K. D. J. Chem. Phys. 2010, 133, 125101
36. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. Phys. Rev. Lett. 2010, 104, 178101
37. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. J. Chem. Phys. 2011, 134, 085101
38. Freeman, G. S.; Hinckley, D. M.; de Pablo, J. J. J. Chem. Phys. 2011, 135, 165104
39. Linak, M. C.; Tourdot, R.; Dorfman, K. D. J. Chem. Phys. 2011, 135, 205102
40. Hsu, C. W.; Fyta, M.; Lakatos, G.; Melchionna, S.; Kaxiras, E. J. Chem. Phys. 2012, 137, 105102
41. Edens, L. E.; Brozik, J. A.; Keller, D. J. J. Phys. Chem. B 2012, 116, 14735-14743
42. Gonzalez, O.; Petkevičiu¯tè, D.; Maddocks, J. H. J. Chem. Phys. 2013, 138, 055102
43. He, Y.; Maciejczyk, M.; Oldziej, S.; Scheraga, H. A.; Liwo, A. Phys. Rev. Lett. 2013, 110, 098101
44. Ouldridge, T. E.; Šulc, P.; Romano, F.; Doye, P. K. J.; Louis, A. A. Nucleic Acids Res. 2013, 41, 8886-8895
45. Cragnolini, T.; Derreumaux, P.; Pasquali, S. J. Phys. Chem. B 2013, 117, 8047-8060
46. Hoang, T. X.; Cieplak, M. J. Chem. Phys. 2000, 112, 6851-6862
47. Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H. A. J. Comput. Chem. 2010, 31, 1644-1655
48. Leimkuhler, B. J.; Reich, S. Simulating Hamiltonian Dynamics; Cambridge University Press: Cambridge, U.K., 2004; pp 199-233.
49. Andersen, H. C. J. Comput. Phys. 1983, 52, 24-34
50. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341
51. Kol, A.; Laird, B. B.; Leimkuhler, B. J. J. Chem. Phys. 1997, 107, 2580-2588
52. Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Chem. Phys. 2001, 115, 2323-2347
53. Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. Protein Sci. 1993, 2, 1715-1731
54. Tsonchev, S.; Schatz, G. C.; Ratner, M. A. Chem. Phys. Lett. 2004, 400, 221-225
55. Mazur, J.; Jernigan, R. L. Biopolymers 1991, 31, 1615-1629
56. Schlick, T. Molecular Modeling and Simulation: An Interdisciplinary Guide; Springer: New York, 2010; p 177.
57. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. J. Am. Chem. Soc. 1995, 117, 5179-5197
58. Cheatham, T. E., III; Cieplak, P.; Kollman, P. A. J. Biomol. Struct. Dyn. 1999, 16, 845-862
59. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
60. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
61. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1339-1350
62. Roux, B. Comput. Phys. Commun. 1995, 91, 275-278
63. Grossfield, A. WHAM: the weighted histogram analysis method, http://membrane.urmc.rochester.edu/content/wham (accessed June 1, 2012).
64. Boggs, P. T.; Byrd, R. H.; Schnabel, R. B. Numerical Optimization 1984: Proceedings of the Siam Conference on Numerical Optimization, Boulder, Colorado; 1984; pp 71-83.
65. Arnott, S.; Hukins, D. W. L. Biochem. Bioph. Res. Commun. 1972, 47, 1504-1509
66. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690
67. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671-680
68. Černý, V. J. Opt. Theory Appl. 1985, 45, 41-51
69. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes. The Art of Scientific Computing; Cambridge University Press: New York, 2007; pp 509-514.
70. Doi, M.; Edwards, S. F. The Theory of Polymer Dynamics; Oxford University Press: New York, 1988; pp 316-317.
71. Fathizadeh, A.; Eslami-Mossollam, B.; Ejtehadi, M. R. Phys. Rev. E 2012, 86, 051907
72. Quinn, M. J. Parallel Programming in C with MPI and OpenMP; McGraw-Hill Companies: New York, 2004; pp 404-435.
73. Tinland, B.; Pluen, A.; Sturm, J.; Weill, G. Macromolecules 1997, 30, 5763-5765
74. Bustamante, C.; Marko, J. F.; Siggia, E. D.; Smith, S. Science 1994, 265, 1599-1600
75. Smith, S. B.; Cui, Y.; Bustamante, C. Science 1996, 271, 795-799
76. Baumann, C. G.; Smith, S. B.; Boomfield, V. A.; Bustamante, C. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 6185-6190
77. Geggier, S.; Kotlyar, A.; Vologodskii, A. Nucleic Acids Res. 2011, 4, 1419-1426