Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile

Journal of Chemical Physics

Volumn 139, Issue 14, 2013, Pages

  Zheng, Wenwei ^a   Vargiu, Attlio Vittorio ^b   Rohrdanz, Mary A ^a   Carloni, Paolo ^c,d   Clementi, Cecilia ^a  

^a RICE UNIVERSITY   (United States)

^b UNIVERSITY OF CAGLIARI   (Italy)

^c German Research School for Simulation Sciences GmbH   (Germany)

^d RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOTHERAPEUTIC AGENTS; COLLECTIVE VARIABLES; FREE ENERGY LANDSCAPE; MACROMOLECULAR SYSTEMS; METADYNAMICS SIMULATIONS; MOLECULAR MECHANISM; NONLINEAR DIMENSIONALITY REDUCTION; REACTION COORDINATES;

DISSOCIATION; FREE ENERGY; LIGANDS; MOLECULAR RECOGNITION; X RAY CRYSTALLOGRAPHY;

DNA;

ANTHRAMYCIN; DNA; LIGAND;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DYNAMICS; X RAY CRYSTALLOGRAPHY;

ANTHRAMYCIN; CRYSTALLOGRAPHY, X-RAY; DNA; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION;

EID: 84886891303     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4824106     Document Type: Article

References (63)

1. J. B. Chaires, A. Randazzo, and J. L. Mergny, Biochimie 93, v (2011). 10.1016/S0300-9084(11)00240-9
2. P. B. Dervan, Bioorg. Med. Chem. 9, 2215 (2001). 10.1016/S0968-0896(01) 00262-0
3. Y. H. Du, J. Huang, X. C. Weng, and X. Zhou, Curr. Med. Chem. 17, 173 (2010). 10.2174/092986710790112648
4. D. Monchaud and M. P. Teulade-Fichou, Org. Biomol. Chem. 6, 627 (2008). 10.1039/b714772b
5. T. C. Jenkins, Curr. Med. Chem. 7, 99 (2000). 10.2174/0929867003375551
6. X. Biarnés, S. Bongarzone, A. V. Vargiu, P. Carloni, and P. Ruggerone, J. Comput.-Aided Mol. Des. 25, 395 (2011). 10.1007/s10822-011-9415-3
7. A. Pérez, F. J. Luque, and M. Orozco, Acc. Chem. Res. 45, 196 (2012). 10.1021/ar2001217
8. M. Zewail-Foote and L. H. Hurley, J. Am. Chem. Soc. 123, 6485 (2001). 10.1021/ja004023p
9. S. Y. Breusegem, F. G. Loontiens, P. Regenfuss, and R. M. Clegg, Methods Enzymol. 340, 212 (2001). 10.1016/S0076-6879(01)40424-1
10. R. Baliga and D. M. Crothers, Proc. Natl. Acad. Sci. U.S.A. 97, 7814 (2000). 10.1073/pnas.97.14.7814
11. R. Baliga, E. E. Baird, D. M. Herman, C. Melander, P. B. Dervan, and D. M. Crothers, Biochemistry 40, 3 (2001). 10.1021/bi0022339
12. R. Baliga and D. M. Crothers, J. Am. Chem. Soc. 122, 11751 (2000). 10.1021/ja002386j
13. A. V. Vargiu, P. Ruggerone, A. Magistrato, and P. Carloni, Nucleic Acids Res. 36, 5910 (2008). 10.1093/nar/gkn561
14. G. G. Holman, M. Zewail-Foote, A. R. Smith, K. A. Johnson, and B. L. Iverson, Nat. Chem. 3, 875 (2011). 10.1038/nchem.1151
15. L. Wolf, Y. Gao, and R. Georgiadis, J. Am. Chem. Soc. 129, 10503 (2007). 10.1021/ja072401l
16. A. V. Vargiu, P. Ruggerone, A. Magistrato, and P. Carloni, Biophys. J. 94, 550 (2008). 10.1529/biophysj.107.113308
17. A. Mukherjee, R. Lavery, B. Bagchi, and J. T. Hynes, J. Am. Chem. Soc. 130, 9747 (2008). 10.1021/ja8001666
18. P. Tummino and R. Copeland, Biochemistry 47, 5481 (2008). 10.1021/bi8002023
19. E. Evans and K. Ritchie, Biophys. J. 72, 1541 (1997). 10.1016/S0006-3495(97)78802-7
20. A. R. Urbach, Nat. Chem. 3, 836 (2011). 10.1038/nchem.1173
21. Y. Okamoto, J. Mol. Graphics Modell. 22, 425 (2004). 10.1016/j.jmgm.2003. 12.009
22. C. Chipot and A. Pohorille, Free Energy Calculations: Theory and Applications in Chemistry and Biology, Springer Series in Chemical Physics Vol. 86 (Springer, 2007).
23. T. Schlick, F1000 Biol Rep 1, 51 (2009). 10.3410/B1-51
24. V. Leone, F. Marinelli, P. Carloni, and M. Parrinello, Curr. Opin. Struct. Biol. 20, 148 (2010). 10.1016/j.sbi.2010.01.011
25. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977). 10.1016/0021-9991(77)90121-8
26. E. Darve and A. Pohorille, J. Chem. Phys. 115, 9169 (2001). 10.1063/1.1410978
27. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002). 10.1073/pnas.202427399
28. F. Marinelli, F. Pietrucci, A. Laio, and S. Piana, PLoS Comput. Biol. 5, e1000452 (2009). 10.1371/journal.pcbi.1000452
29. M. Ceccarelli, A. V. Vargiu, and P. Ruggerone, J. Phys. Condens. Matter 24, 104012 (2012). 10.1088/0953-8984/24/10/104012
30. R. Du, V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. S. Shakhnovich, J. Chem. Phys. 108, 334 (1998). 10.1063/1.475393
31. A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005). 10.1021/jp045546c
32. R. B. Best and G. Hummer, Proc. Natl. Acad. Sci. U.S.A. 102, 6732 (2005). 10.1073/pnas.0408098102
33. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002). 10.1103/PhysRevB.66.052301
34. E. Weinan, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005). 10.1021/jp0455430
35. A. K. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004). 10.1063/1.1738640
36. I. T. Jolliffe, Principal Components Analysis (Springer-Verlag, 1986).
37. Y. Mu, P. H. Nguyen, and G. Stock, Proteins 58, 45 (2005). 10.1002/prot.20310
38. S. T. Roweis and L. K. Saul, Science 290, 2323 (2000). 10.1126/science.290.5500.2323
39. J. B. Tenenbaum, V. De Silva, and J. C. Langford, Science 290, 2319 (2000). 10.1126/science.290.5500.2319
40. P. Das, M. Moll, H. Stamati, L. E. Kavraki, and C. Clementi, Proc. Natl. Acad. Sci. U.S.A. 103, 9885 (2006). 10.1073/pnas.0603553103
41. M. A. Rohrdanz, W. Zheng, M. Maggioni, and C. Clementi, J. Chem. Phys. 134, 124116 (2011). 10.1063/1.3569857
42. M. Ceriotti, G. Tribello, and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 108, 13023 (2011). 10.1073/pnas.1108486108
43. R. R. Coifman, I. G. Kevrekidis, S. Lafon, M. Maggioni, and B. Nadler, Multiscale Model. Simul. 7, 842 (2008). 10.1137/070696325
44. W. Zheng, M. A. Rohrdanz, M. Maggioni, and C. Clementi, J. Chem. Phys. 134, 144109 (2011). 10.1063/1.3575245
45. W. Zheng, B. Qi, M. A. Rohrdanz, A. Caflisch, A. R. Dinner, and C. Clementi, J. Phys. Chem. B 115, 13065 (2011). 10.1021/jp2076935
46. S. V. Krivov and M. Karplus, J. Phys. Chem. B 110, 12689 (2006). 10.1021/jp060039b
47. S. Muff and A. Caflisch, Proteins 70, 1185 (2008). 10.1002/prot.21565
48. S. V. Krivov and M. Karplus, J. Chem. Phys. 117, 10894 (2002). 10.1063/1.1517606
49. B. Qi, S. Muff, A. Caflisch, and A. R. Dinner, J. Phys. Chem. B 114, 6979 (2010). 10.1021/jp101476g
50. S. V. Krivov, S. Muff, A. Caflisch, and M. Karplus, J. Phys. Chem. B 112, 8701 (2008). 10.1021/jp711864r
51. A. V. Vargiu, P. Ruggerone, A. Magistrato, and P. Carloni, J. Phys. Chem. B 110, 24687 (2006). 10.1021/jp063155n
52. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995). 10.1021/ja00124a002
53. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, and D. A. Case, J. Comput. Chem. 25, 1157 (2004). 10.1002/jcc.20035
54. D. A. Case, T. E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K. M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods, J. Comput. Chem. 26, 1668 (2005). 10.1002/jcc.20290
55. M. J. Frisch, G. W. Trucks, H. B. Schlegel, Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford, CT, 2004.
56. C. I. Bayly, P. Cieplak, W. Cornell, and P. A. Kollman, J. Phys. Chem. 97, 10269 (1993). 10.1021/j100142a004
57. J. Aaqvist, J. Phys. Chem. 94, 8021 (1990). 10.1021/j100384a009
58. W. L. Jorgensen, J. Am. Chem. Soc. 103, 335 (1981). 10.1021/ja00392a016
59. See supplementary material at http://dx.doi.org/10.1063/1.4824106 E-JCPSA6-139-002339 for more details.
60. H. Berendsen, D. van der Spoel, and R. Van Drunen, Comput. Phys. Commun. 91, 43 (1995). 10.1016/0010-4655(95)00042-E
61. E. Lindahl, B. Hess, and D. van der Spoel, J. Mol. Model. 7, 306 (2001). 10.1007/s008940100045
62. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. Mark, and H. Berendsen, J. Comput. Chem. 26, 1701 (2005). 10.1002/jcc.20291
63. A. L. Ferguson, A. Z. Panagiotopoulos, P. G. Debenedetti, and I. G. Kevrekidis, J. Chem. Phys. 134, 135103 (2011). 10.1063/1.3574394