Theoretical studies of the base pair fidelity of selenium-modified DNA

Journal of Physical Chemistry B

Volumn 115, Issue 33, 2011, Pages 10041-10048

  Christofferson, Andrew ^a   Zhao, Lifeng ^a   Sun, Hanzi ^a   Huang, Zhen ^b   Huang, Niu ^a  

^a NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^b GEORGIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DNA; FREE ENERGY; MOLECULAR DYNAMICS; QUANTUM THEORY; SELENIUM; STABILITY;

FORCE FIELD PARAMETERS; FREE ENERGY PERTURBATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR DYNAMICS TRAJECTORIES; PROTEIN-DNA COMPLEXES; RELATIVE FREE ENERGY; RELATIVE STABILITIES; WATER INTERACTIONS;

DNA SEQUENCES;

EID: 84860418457     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp204204x     Document Type: Article

References (44)

1. Srinivasan, A. R.; Sauers, R. R.; Fenley, M. O.; Boschitsch, A. H.; Matsumoto, A.; Colasanti, A. V.; Olson, W. K. Biophys. Rev. 2009, 1, 13
2. Schlick, T. Topics in Nucleic Acids Structure: DNA Interactions and Folding. In Molecular Modeling and Simulation: An Interdisciplinary Guide; Marsden, J. E.; Sirovich, L.; Wiggins, S., Eds.; Springer: New York, 2010; Vol. 21, p 163.
3. Rambo, R. P.; Tainer, J. A. Curr. Opin. Struct. Biol. 2010, 20, 128
4. Klug, A. Annu. Rev. Biochem. 2010, 79, 1
5. Deacon, A. M.; Ealick, S. E. Structure 1999, 7, R161
6. Hendrickson, W. A. Trends Biochem. Sci. 2001, 25, 637
7. Jiang, J.; Sweet, R. M. J. Synchrotron Radiat. 2004, 11, 319
8. Sheng, J.; Huang, Z. Chem. Biodiversity 2010, 7, 753
9. Jiang, J.; Sheng, J.; Carrasco, N.; Huang, Z. Nucleic Acids Res. 2007, 35, 477
10. Hassan, A. E. A.; Sheng, J.; Zhang, W.; Huang, Z. J. Am. Chem. Soc. 2010, 132, 2120
11. Vazquez-Mayagoitia, A.; Huertas, O.; Brancolini, G.; Migliore, A.; Sumpter, B. G.; Orozco, M.; Luque, F. J.; Felice, R. D.; Fuentes-Cabrera, M. J. Phys. Chem. B 2009, 113, 14465
12. Karplus, M.; McCammon, J. A. Nat. Struct. Biol. 2002, 9, 646
13. MacKerell, A. D.; Banavali, N.; Foloppe, N. Biopolymers 2000, 56, 257
14. Cheatham, T. E.; Young, M. A. Biopolymers 2000, 56, 232
15. MacKerell, A. D.; Nilsson, L. Curr. Opin. Struct. Biol. 2008, 18, 194
16. Huang, N.; Banavali, N. K.; MacKerell, A. D. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 68
17. Garcia-Nieto, R.; Manzanares, I.; Cuevas, C.; Gago, F. J. Am. Chem. Soc. 2000, 122, 7172
18. Florian, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B 2000, 104, 10092
19. Steinbach, P. J.; Brooks, B. R. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 9135
20. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Kosecki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347
21. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 533
22. Riley, K. E.; Pitonak, M.; Cerny, J.; Hobza, P. J. Chem. Theory Comput. 2010, 6, 66
23. Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. Phys. Chem. Chem. Phys. 2006, 8, 1985
24. Thota, N.; Li, X. H.; Bingman, C.; Sundaralingam, M. Acta Crystallogr., Sect. D 1993, 49, 282
25. Foloppe, N.; MacKerell, A. D. J. Comput. Chem. 2000, 21, 86
26. Mackerell, A. D. J. Comput. Chem. 2004, 25, 1584
27. Sarzyńska, J.; Kuliński, T. Comput. Methods Sci. Technol. 2005, 11, 49
28. Feng, B.; Stone, M. P. Chem. Res. Toxicol. 1995, 8, 821
29. 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
30. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Biol. Chem. 1983, 79, 926
31. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
32. Darden, T.; Perera, L.; Li, L. P.; Pedersen, L. Struct. Fold. Des. 1999, 7, R55
33. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327
34. Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. J. Am. Chem. Soc. 2008, 130, 2817
35. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420
36. Boresch, S.; Karplus, M. J. Phys. Chem. B 1999, 103, 103
37. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011
38. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1339
39. Roux, B. Comput. Phys. Commun. 1995, 91, 275
40. Souaille, M.; Roux, B. Comput. Phys. Commun. 2001, 135, 40
41. Boresch, S.; Archontis, G.; Karplus, M. Proteins: Struct., Funct., Genet. 1994, 20, 25
42. Alvarez-Salgado, F.; Desvaux, H.; Boulard, Y. Magn. Reson. Chem. 2006, 44, 1081
43. Boulard, Y.; Cognet, J. A.; Fazakerley, G. V. J. Mol. Biol. 1997, 268, 331
44. Lian, C.; Robinson, H.; Wang, A. H.-J. J. Am. Chem. Soc. 1996, 118, 8791