Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

Journal of Physical Chemistry A

Volumn 114, Issue 13, 2010, Pages 4471-4485

  Maisuradze, Gia G ^a   Senet, Patrick ^a,b   Czaplewski, Cezary ^a,c   Liwo, Adam ^a,c   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITÉ DE BOURGOGNE   (France)

^c UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEINS; COARSE-GRAINED MOLECULAR DYNAMICS; COARSE-GRAINED MOLECULAR DYNAMICS SIMULATIONS; DEGREES OF FREEDOM; DIHEDRAL ANGLES; ENERGY PROFILE; ENSEMBLE TECHNIQUES; EXPERIMENTAL DATA; EXPLICIT SOLVENTS; FOLDING MECHANISM; FOLDING PATHWAY; FORCE CALCULATION; FORCE FIELDS; HELIX BUNDLE; MASSIVELY PARALLEL COMPUTERS; N-TERMINALS; PARALLEL SIMULATIONS; PHYSICS-BASED; PHYSICS-BASED UNITED-RESIDUE FORCE FIELDS; POTENTIALS OF MEAN FORCES; PRINCIPAL COMPONENTS; PROTEIN STRUCTURES; REPLICA EXCHANGE METHOD; SIMULATION TIME; STAPHYLOCOCCAL PROTEIN; STRUCTURAL FEATURE; STRUCTURE SIMULATIONS; TIME-SCALES; TRANSITION TEMPERATURE; UNIMODAL; WW DOMAIN;

ABSTRACTING; COMPUTER SIMULATION; DYNAMICS; FREE ENERGY; MOLECULAR DYNAMICS; PROTEIN FOLDING;

PRINCIPAL COMPONENT ANALYSIS;

BACTERIAL PROTEIN; CARRIER PROTEIN; FORMIN BINDING PROTEIN 28, MOUSE; PROTEIN; SOLVENT;

ALGORITHM; ANIMAL; ARTICLE; CHEMISTRY; KINETICS; MOLECULAR DYNAMICS; MOUSE; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; ROTATION; STAPHYLOCOCCUS AUREUS; STATISTICAL MODEL; THERMODYNAMICS;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; CARRIER PROTEINS; KINETICS; MICE; MODELS, STATISTICAL; MOLECULAR DYNAMICS SIMULATION; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; ROTATION; SOLVENTS; STAPHYLOCOCCUS AUREUS; THERMODYNAMICS;

EID: 77950477912     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp9117776     Document Type: Article

References (108)

1. Leach, A. L. Molecular modelling. Principles and Applications. Pearson, Prentice Hall: New York, 2001; pp 303 - 558.
2. Duan, V.; Kollman, P. A. Science 1998, 282, 740 - 744
3. Pande, V. S.; Rokhsar, D. S. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9062 - 9067
4. Daggett, V. Chem. Rev. 2006, 106, 1898 - 1916
5. Scheraga, H. A.; Khalili, M.; Liwo, A. Annu. Rev. Phys. Chem. 2007, 58, 57 - 83
6. Anfinsen, C. B.; Haber, E.; Sela, M.; White, F. H. Proc. Natl. Acad. Sci. U.S.A. 1961, 47, 1309 - 1314
7. Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. Protein Sci. 1993, 2, 1715 - 1731
8. Liwo, A.; Ołdziej, S.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A. J. Comput. Chem. 1997, 18, 849 - 873
9. Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Ołdziej, S.; Scheraga, H. A. J. Comput. Chem. 1997, 18, 874 - 887
10. Liwo, A.; Kazìmierkiewicz, R.; Czaplewski, C.; Groth, M.; Ołdziej, S.; Wawak, R. J.; Rackovsky, S.; Pincus, M. R.; Scheraga, H. A. J. Comput. Chem. 1998, 19, 259 - 276
11. Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Chem. Phys. 2001, 115, 2323 - 2347
12. Liwo, A.; Arłukowicz, P.; Czaplewski, C.; Ołdziej, S.; Pillardy, J.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1937 - 1942
13. Ołdziej, S.; Kozłowska, U.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. A 2003, 107, 8035 - 8046
14. Ołdziej, S.; Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16934 - 16949
15. Ołdziej, S.; Aaìgiewka, J.; Liwo, A.; Czaplewski, C.; Chinchio, M.; Nanias, M.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 16950 - 16959
16. Liwo, A.; Ołdziej, S.; Czaplewski, C.; Kozłowska, U.; Scheraga, H. A. J. Phys. Chem. B 2004, 108, 9421 - 9438
17. Kozłowska, U.; Liwo, A.; Scheraga, H. A. J. Phys: Condens. Matter 2007, 19, 285203-1 - 285203-15
18. Liwo, A.; Khalili, M.; Czaplewski, C.; Kalinowski, S.; Ołdziej, S.; Wachucik, K.; Scheraga, H. A. J. Phys. Chem. B 2007, 111, 260 - 285
19. Chinchio, M.; Czaplewski, C.; Liwo, A.; Ołdziej, S.; Scheraga, H. A. J. Chem. Theory Comput. 2007, 3, 1236 - 1248
20. Liwo, A.; Czaplewski, C.; Ołdziej, S.; Rojas, A. V.; Kazìmierkiewicz, R.; Makowski, M.; Murarka, R. K.; Scheraga, H. A. Simulation of protein structure and dynamics with the coarse-grained UNRES force field. In Coarse-Graining of Condensed Phase and Biomolecular systems; Voth, G. A., Ed.; CRC Press: Boca Raton, FL, 2008; pp 107 - 122.
21. Shen, H.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. B 2009, 113, 8738 - 8744
22. Kozłowska, U.; Liwo, A.; Scheraga, H. A. J. Comput. Chem. [Online early access]. DOI: 10.1002/jcc.21399.
23. Kozłowska, U.; Maisuradze, G. G.; Liwo, A.; Scheraga, H. A. J. Comput. Chem. [Online early access]. DOI: 10.1002/jcc.21402.
24. Makowski, M.; Sobolewski, E.; Czapiewski, C.; Liwo, A.; Odziej, S.; No, J. H.; Scheraga, H. A. J. Phys. Chem. B 2007, 111, 2925 - 2931
25. Makowski, M.; Sobolewski, E.; Czapiewski, C.; Odziej, S.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. B 2008, 112, 11385 - 11395
26. Noid, W.; Chu, J.-W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. J. Chem. Phys. 2008, 128, 244114
27. Noid, W. G.; Liu, P.; Wang, Y.; Chu, J.-W.; Ayton, G. S.; Izvekov, S.; Andersen, H. C.; Voth, G. A. J. Chem. Phys. 2008, 128, 244115
28. Gay, J. G.; Berne, B. J. J. Chem. Phys. 1981, 74, 3316 - 3319
29. Khalili, M.; Liwo, A.; Rakowski, F.; Grochowski, P.; Scheraga, H. A. J. Phys. Chem. B 2005, 109, 13785 - 13797
30. Kolinski, A.; Godzik, A.; Skolnick, J. J. Chem. Phys. 1993, 98, 7420 - 7433
31. Kubo, R. J. Phys. Soc. Jpn. 1962, 17, 1100 - 1120
32. Lee, J.; Liwo, A.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 2025 - 2030
33. Ołdziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J. A.; Khalili, M.; Arnautova, Y. A.; Jagielska, A.; Makowski, M.; Schafroth, H. D.; Kazìmierkiewicz, R.; Ripoll, D. R.; Pillardy, J.; Saunders, J. A.; Kang, Y. K.; Gibson, K. D.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 7547 - 7552
34. Khalili, M.; Liwo, A.; Jagielska, A.; Scheraga, H. A. J. Phys. Chem. B 2005, 109, 13798 - 13810
35. Liwo, A.; Khalili, M.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362 - 2367
36. Rakowski, F.; Grochowski, P.; Lesyng, B.; Liwo, A.; Scheraga, H. A. J. Chem. Phys. 2006, 125, 204107-1 - 204107-10
37. Kubo, R. Rep. Prog. Phys. 1966, 29, 255 - 284
38. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637 - 649
39. Guarnieri, F.; Still, W. C. J. Comput. Chem. 1994, 15, 1302 - 1310
40. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684 - 3690
41. Kleinerman, D. S.; Czaplewski, C.; Liwo, A.; Scheraga, H. A. J. Chem. Phys. 2008, 128, 245103
42. Noseì, S. Mol. Phys. 1984, 52, 255 - 268
43. Hoover, W. G. Phys. Rev. A 1985, 31, 1695 - 1697
44. Noseì, S. J. Phys. Soc. Jpn. 2001, 70, 75 - 77
45. Murarka, R. K.; Liwo, A.; Scheraga, H. A. J. Chem. Phys. 2007, 127, 155103-1 - 155103-16
46. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr. Opinion Struct. Biol. 2004, 14, 76 - 88
47. Gouda, H.; Torigoe, H.; Saito, A.; Sato, M.; Arata, Y.; Shimada, I. Biochemistry 1992, 31, 9665 - 9672
48. Karplus, M.; Weaver, D. L. Biopolymers 1979, 18, 1421 - 1437
49. Liwo, A.; Ołdziej, S.; Czaplewski, C.; Kleinerman, D. S.; Blood, P.; Scheraga, H. A. J. Chem. Theory Comput. [Online early access]. DOI: 10.1021/ct9004068.
50. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435 - 447
51. Khalili, M.; Liwo, A.; Scheraga, H. A. J. Mol. Biol. 2006, 355, 536 - 547
52. Bai, Y. W.; Karimi, A.; Dyson, H. J.; Wright, P. E. Protein Sci. 1997, 6, 1449 - 1457
53. Sato, S.; Religa, T. L.; Daggett, V.; Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 6952 - 6956
54. Jagielska, A.; Scheraga, H. A. J. Comput. Chem. 2007, 28, 1068 - 1082
55. Maisuradze, G. G.; Liwo, A.; Scheraga, H. A. Phys. Rev. Lett. 2009, 102, 238102-1 - 238102-4
56. Maisuradze, G. G.; Liwo, A.; Scheraga, H. A. J. Mol. Biol. 2009, 385, 312 - 329
57. Maisuradze, G. G.; Liwo, A.; Scheraga, H. A. J. Chem. Theory Comput. 2010, 6, 583-595.
58. Macias, M. J.; Gervais, V.; Civera, C.; Oschkinat, H. Nat. Struct. Biol. 2000, 7, 375 - 379
59. Mitsutake, A.; Sugita, Y.; Okamoto, Y. Biopolymers 2001, 60, 96 - 123
60. Berg, B. A.; Neuhaus, T. Phys. Lett. B 1991, 267, 249 - 253
61. Berg, B. A.; Neuhaus, T. Phys. Rev. Lett. 1992, 68, 9 - 12
62. Lee, J. Phys. Rev. Lett. 1993, 71, 211 - 214
63. Hao, M.; Scheraga, H. A. J. Phys. Chem. 1994, 98, 4940 - 4948
64. Marinari, E.; Parisi, G. Europhys. Lett. 1992, 19, 451 - 458
65. Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V.; Vorontsov-Velyaminov, P. N. J. Chem. Phys. 1992, 96, 1776 - 1783
66. Swendsen, R. H.; Wang, J. S. Phys. Rev. Lett. 1986, 57, 2607 - 2609
67. Hukushima, K.; Nemoto, K. J. Phys. Soc. Jpn. 1996, 65, 1604 - 1608
68. Hansmann, U. H. E. Chem. Phys. Lett. 1997, 281, 140 - 150
69. Geyer, C. Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface; Keramidas, E. M., Ed.; Interface Foundation: Fairfax Station, VA, 1991; pp 156 - 163.
70. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011 - 1021
71. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 2000, 329, 261 - 270
72. Mitsutake, A.; Okamoto, Y. Chem. Phys. Lett. 2000, 332, 131 - 138
73. Nanias, M.; Czaplewski, C.; Scheraga, H. A. J. Chem. Theory Comput. 2006, 3, 513 - 528
74. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 1-2, 141 - 151
75. Rhee, Y. M.; Pande, V. S. Biophys. J. 2003, 2, 775 - 786
76. Czaplewski, C.; Kalinowski, S.; Liwo, A.; Scheraga, H. A. J. Chem. Theory Comput. 2009, 5, 627 - 640
77. Murtagh, F. Multidimensional clustering algorithms; Physica-Verlag: Vienna, Austria, 1985.
78. Murtagh, F.; Heck, A. MultiVariate data analysis; Kluwer Academic: Dordrecht, Holland, 1987.
79. Frauenfelder, H.; Sligar, S. G.; Wolynes, P. G. Science 1991, 254, 1598 - 1603
80. Brooks, C. L. III.; Onuchic, J. N.; Wales, D. J. Science 2001, 293, 612 - 613
81. Wales, D. J. Energy Landscapes; Cambridge University Press: Cambridge, 2003.
82. Gruebele, M. Annu. Rev. Phys. Chem. 1999, 50, 485 - 516
83. Myers, J. K.; Oas, T. G. Annu. Rev. Biochem. 2002, 71, 783 - 815
84. Yang, W. Y.; Gruebele, M. Nature 2003, 423, 193 - 197
85. Karplus, M.; McCammon, J. A. Nat. Struct. Biol. 2002, 9, 646 - 652
86. Brooks, C. L. III. Acc. Chem. Res. 2002, 35, 447 - 454
87. Granakaran, S.; Nymeyer, H.; Portman, J. J.; Sanbonmatsu, K. Y.; Garcia, A. E. Curr. Opin. Struct. Biol. 2003, 13, 168 - 174
88. Boczko, E. M.; Brooks, C. L., III. Science 1995, 269, 393 - 396
89. Bursulaya, B. D.; Brooks, C. L., III. J. Am. Chem. Soc. 1999, 121, 9947 - 9951
90. Jolliffe, I. T. Principal component analysis; Springer: New York, 2002.
91. Doruker, P.; Atilgan, A. R.; Bahar, I. Proteins: Struct,. Funct., Genet. 2000, 40, 520 - 524
92. Ozkan, S. B.; Dill, K. A.; Bahar, I. Protein Sci. 2002, 11, 1958 - 1970
93. Balsera, M. A.; Wriggers, W.; Oono, Y.; Schulten, K. J. Phys. Chem. 1996, 100, 2567 - 2572
94. Hess, B. Phys. Rev. E 2000, 62, 8438 - 8448
95. Maisuradze, G. G.; Leitner, D. M. Proteins 2007, 67, 569 - 578
96. Hess, B. Phys. Rev. E 2002, 65, 031910-1 - 031910-10
97. Mu, Y.; Nguyen, P. H.; Stock, G. Proteins 2005, 58, 45 - 52
98. Altis, A.; Nguyen, P. H.; Hegger, R.; Stock, G. J. Chem. Phys. 2007, 126, 244111-1 - 244111-10
99. Krivov, S. V.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14766 - 14770
100. Altis, A.; Otten, M.; Nguyen, P. H.; Hegger, R.; Stock. J. Chem. Phys. 2008, 128, 245102-1 - 245102-11
101. Kitao, A.; Hayward, S.; Goï, N. Proteins 1998, 33, 496 - 517
102. Hegger, R.; Altis, A.; Nguyen, P. H.; Stock, G. Phys. Rev. Lett. 2007, 98, 028102-1 - 028102-4
103. Nguyen, H.; Jäger, M.; Moretto, A.; Gruebele, M.; Kelly, J. W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3948 - 3953
104. Ansari, A. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 5000 - 5004
105. Frauenfelder, H. F.; Parak, F.; Young, R. D. Annu. Rev. Biophys. Chem. 1988, 17, 451 - 479
106. Nishikawa, K.; Momany, F. A.; Scheraga, H. A. Macromolecules 1974, 7, 797 - 806
107. Senet, P.; Maisuradze, G. G.; Foulie, C.; Delarue, P.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 19708 - 19713
108. Karanicolas, J.; Brooks, C. L., III. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3954 - 3959