Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations

Journal of Physical Chemistry B

Volumn 116, Issue 29, 2012, Pages 8610-8620

  Predeus, Alexander V ^a   Gul, Seref ^b   Gopal, Srinivasa M ^a   Feig, Michael ^a,b  

^a Michigan State University   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS; NUCLEIC ACIDS;

AQUEOUS SOLVENTS; ATOMISTIC LEVELS; COARSE-GRAINED; CONFORMATIONAL DYNAMICS; CONFORMATIONAL ENSEMBLE; ENTHALPIC EFFECTS; ENTHALPIC INTERACTIONS; IMPLICIT SOLVENTS; MACROMOLECULAR CROWDING; MELITTIN; MULTI-SCALE SIMULATION; MULTISCALE MODELING SCHEMES; PEPTIDE DYNAMICS; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; THREE-COMPONENT; VOLUME EXCLUSION EFFECTS;

PEPTIDES;

EID: 84864254504     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp300129u     Document Type: Article

References (89)

1. Fulton, A. B. Cell 1982, 30, 345-347
2. Minton, A. P. Biopolymers 1981, 20, 2093-2120
3. Ellis, R. J.; Minton, A. P. Nature 2003, 425, 27-28
4. Zhou, H.-X.; Rivas, G.; Minton, A. P. Annu. Rev. Biophys. 2008, 37, 375-397
5. Ping, G.; Yuan, J. M.; Vallieres, M.; Dong, H.; Sun, Z.; Wei, Y.; Li, F. Y.; Lin, S. H. J. Chem. Phys. 2003, 118, 8042-8048
6. Rathore, N.; Knotts, T. A.; de Pablo, J. J. Biophys. J. 2006, 90, 1767-1773
7. Tungtur, S.; Skinner, H.; Zhan, H. L.; Swint-Kruse, L.; Beckett, D. Biophys. Chem. 2011, 159, 142-151
8. Ladbury, J. E.; Williams, M. A. Curr. Opin. Struct. Biol. 2004, 14, 562-569
9. Denesyuk, N. A.; Thirumalai, D. J. Am. Chem. Soc. 2011, 133, 11858-11861
10. Christiansen, A.; Wang, Q.; Samiotakis, A.; Cheung, M. S.; Wittung-Stafshede, P. Biochemistry 2010, 49, 6519-6530
11. Cheung, M. S.; Thirumalai, D. J. Phys. Chem. B 2007, 111, 8250-8257
12. Martin, J.; Hartl, F. U. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 1107-1112
13. Rosgen, J.; Pettitt, B. M.; Bolen, D. W. Biophys. J. 2005, 89, 2988-2997
14. Homouz, D.; Stagg, L.; Wittung-Stafshede, P.; Cheung, M. S. Biophys. J. 2009, 96, 671-680
15. Mittal, J.; Best, R. B. Biophys. J. 2010, 98, 315-320
16. Wang, W.; Xu, W. X.; Levy, Y.; Trizac, E.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5517-5522
17. Kim, Y. C.; Best, R. B.; Mittal, J. J. Chem. Phys. 2010, 133, 205101
18. Rosen, J.; Kim, Y. C.; Mittal, J. J. Phys. Chem. B 2011, 115, 2683-2689
19. McGuffee, S. R.; Elcock, A. H. PLoS Comput. Biol. 2010, 6, e1000694
20. McGuffee, S. R.; Elcock, A. H. J. Am. Chem. Soc. 2006, 128, 12098-12110
21. Magno, A.; Caflisch, A.; Pellarin, R. J. Phys. Chem. Lett. 2010, 1, 3027-3032
22. White, D. A.; Buell, A. K.; Knowles, T. P. J; Welland, M. E.; Dobson, C. M. J. Am. Chem. Soc. 2010, 132, 5170-5175
23. Zhou, H. X. J. Mol. Recognit. 2004, 17, 368-375
24. Mittal, J.; Best, R. B. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 20233-20238
25. Songha, A. K.; Keyes, T. J. Phys. Chem. B 2010, 114, 16908-16917
26. Davis-Searles, P. R.; Saunders, A. J.; Erie, D. A.; Winzor, D. J.; Pielak, G. J. Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 271-306
27. Shah, D.; Tan, A. L.; Ramakrishnan, V.; Jiang, J. W.; Rajagopalan, R. J. Chem. Phys. 2011, 134
28. Zimmerman, S. B.; Minton, A. P. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 27-65
29. Minton, A. P. Biophys. J. 2005, 88, 971-985
30. Zhou, H. X. Acc. Chem. Res. 2004, 37, 123-130
31. Shearwin, K. E.; Winzor, D. J. Eur. J. Biochem. 1990, 190, 523-529
32. Phillip, Y.; Sherman, E.; Haran, G.; Schreiber, G. Biophys. J. 2009, 97, 875-885
33. Crowley, P. B.; Brett, K.; Muldoon, J. ChemBioChem 2008, 9, 685-688
34. Cheung, M. S.; Klimov, D.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 4753-4758
35. Qu, Y. X.; Bolen, C. L.; Bolen, D. W. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 9268-9273
36. Batra, J.; Xu, K.; Qin, S. B.; Zhou, H. X. Biophys. J. 2009, 97, 906-911
37. Homouz, D.; Perham, M.; Samiotakis, A.; Cheung, M. S.; Wittung-Stafshede, P. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11754-11759
38. Tsao, D.; Dokholyan, N. V. Phys. Chem. Chem. Phys. 2010, 12, 3491-3500
39. Cheung, M. S.; Thirumalai, D. J. Mol. Biol. 2006, 357, 632-643
40. Inomata, K.; Ohno, A.; Tochio, H.; Isogai, S.; Tenno, T.; Nakase, I.; Takeuchi, T.; Futaki, S.; Ito, Y.; Hiroaki, H. Nature 2009, 458, 106-109
41. Miklos, A. C.; Sarkar, M.; Wang, Y.; Pielak, G. J. J. Am. Chem. Soc. 2011, 133, 7116-7120
42. Feig, M.; Sugita, Y. J. Phys. Chem. B 2012, 116, 599-605
43. Ignatova, Z.; Krishnan, B.; Bombardier, J. P.; Marcelino, A. M. C.; Hong, J.; Gierasch, L. M. Biopolymers 2007, 88, 157-163
44. Ghaemmaghami, S.; Oas, T. G. Nat. Struct. Biol. 2001, 8, 879-882
45. Despa, F.; Fernandez, A.; Berry, R. S. Phys. Rev. Lett. 2004, 93, 228104
46. Tanizaki, S.; Clifford, J. W.; Connelly, B. D.; Feig, M. Biophys. J. 2008, 94, 747-759
47. Ellis, R. J. Curr. Opin. Struct. Biol. 2001, 11, 114-119
48. Schutz, C. N.; Warshel, A. Proteins 2001, 44, 400-417
49. Gilson, M. K.; Honig, B. H. Biopolymers 1986, 25, 2097-2119
50. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. Biochemistry 1996, 35, 7819-7833
51. Dwyer, J. J.; Gittis, A. G.; Karp, D. A.; Lattman, E. E.; Spencer, D. S.; Stites, W. E.; Garcia-Moreno, B. Biophys. J. 2000, 79, 1610-1620
52. Warshel, A.; Papazyan, A. Curr. Opin. Struct. Biol. 1998, 8, 211-217
53. Akhadov, Y. Y. Dielectric Properties of Binary Solutions; Pergamon Press: Oxford, U.K., 1981.
54. Zhao, J. H.; Liu, H. L. Chem. Phys. Lett. 2006, 420, 235-240
55. Bello, J. Biopolymers 1993, 33, 491-495
56. Liu, H. L.; Hsu, C. M. Chem. Phys. Lett. 2003, 375, 119-125
57. Dwyer, D. S. Biopolymers 1999, 49, 635-645
58. Hirota, N.; Mizuno, K.; Goto, Y. J. Mol. Biol. 1998, 275, 365-378
59. Hong, D.; Hoshino, M.; Kuboi, R.; Goto, Y. J. Am. Chem. Soc. 1999, 121, 8427-8433
60. Bhattacharjya, S.; Venkatraman, J.; Balaram, P.; Kumar, A. J. Peptide Res. 1999, 54, 100-111
61. Tomar, R.; Dubey, V. K.; Jagannadham, M. V. Biochimie 2009, 91, 951-960
62. Shibata, A.; Yamamoto, M.; Yamashita, T.; Chiou, J. S.; Kamaya, H.; Ueda, I. Biochemistry 1992, 31, 5728-5733
63. Perham, M.; Liao, J.; Wittung-Stafshede, P. Biochemistry 2006, 45, 7740-7749
64. Feig, M.; Brooks, C. L., III. Curr. Opin. Struct. Biol. 2004, 14, 217-224
65. Feig, M.; Im, W.; Brooks, C. L., III. J. Chem. Phys. 2004, 120
66. Gopal, S. M.; Mukherjee, S.; Cheng, Y.-M.; Feig, M. Proteins 2010, 78, 1266-1281
67. Feig, M.; Gopal, S. M.; Vadivel, K.; Stumpff-Kane, A. W. Conformational sampling in structure prediction and refinement with atomistic and coarse-grained models. In Multiscale approaches to protein modeling: Structure prediction, dynamics, thermodynamics and macromolecular assemblies; Kolinski, A., Ed.; Springer: New York, 2010.
68. Terwilliger, T. C.; Eisenberg, D. J. Biol. Chem. 1982, 257, 6016-6022
69. Neidigh, J. W.; Fesinmeyer, R. M.; Andersen, N. H. Nat. Struct. Biol. 2002, 9, 425-430
70. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, J. D.; Evanseck, M. J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. J. Phys. Chem. B 1998, 102, 3586-3616
71. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J. Comput. Chem. 2004, 25, 1400-1415
72. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. J. Am. Chem. Soc. 2004, 126, 698-699
73. Wesson, L.; Eisenberg, D. Protein Sci. 1992, 1, 227-235
74. Chocholousova, J.; Feig, M. J. Comput. Chem. 2006, 27, 719-729
75. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. J. Comput. Chem. 2003, 24, 1348-1356
76. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988
77. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341
78. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151
79. 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. J. Comput. Chem. 2009, 30, 1545-1614
80. Feig, M.; Karanicolas, J.; Brooks, C. L., III. J. Mol. Graphics Modell. 2004, 22, 377-395
81. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33.
82. Zhou, R. H. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13280-13285
83. Juraszek, J.; Bolhuis, P. G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 15859-15864
84. Paschek, D.; Hempel, S.; Garcia, A. E. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 17754-17759
85. Day, R.; Paschek, D.; Garcia, A. E. Proteins 2010, 78, 1889-1899
86. Heyda, J.; Kozisek, M.; Bednarova, L.; Thompson, G.; Konvalinka, J.; Vondrasek, J.; Jungwirth, P. J. Phys. Chem. B 2011, 115, 8910-8924
87. Lee, M. S.; Olson, M. A. J. Chem. Theory Comput. 2010, 6, 2477-2487
88. Ota, M.; Ikeguchi, M.; Kidera, A. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17658-17663
89. Sheinerman, F. B.; Brooks, C. L. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1562-1567