Modeling DNA-bending in the nucleosome: Role of AA periodicity

Journal of Physical Chemistry B

Volumn 115, Issue 26, 2011, Pages 8638-8644

  Prytkova, Tatiana R ^a,b   Zhu, Xiao ^b   Widom, Jonathan ^b   Schatz, George C ^b,c  

^a CHAPMAN UNIVERSITY   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c Northwestern University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POTENTIAL ENERGY;

AMBER FORCE-FIELD; BENDING ENERGIES; BENDING POTENTIAL; BENDING PROPERTIES; BENT STRUCTURE; DNA SEGMENTS; LOOP STRUCTURE; LOW ENERGIES; MINIMUM-ENERGY STRUCTURES; MINOR GROOVES; NARROW DISTRIBUTION; NUCLEOSOME STRUCTURE; NUCLEOSOMES; POTENTIAL ENERGY LANDSCAPES; RADIUS OF CURVATURE; RANDOM SEQUENCE;

DNA;

EID: 79959986230     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp203564q     Document Type: Article

References (49)

1. Segal, E.; Widom, J. Trends in Genetics 2009, 25, 335
2. Field, Y.; Kaplan, N.; Fondufe-Mittendorf, Y.; Moore, I. K.; Sharon, E.; Lubling, Y.; Widom, J.; Segal, E. PLoS Comput. Biol. 2008, 4, e1000216
3. Kaplan, N.; Moore, I. K.; Fondufe-Mittendorf, Y.; Gossett, A. J.; Tillo, D.; Field, Y.; LeProust, E. M.; Hughes, T. R.; Lieb, J. D.; Widom, J.; Segal, E. Nature 2009, 458, 362
4. Garcia, H. G.; Grayson, P.; Han, L.; Inamdar, M.; Kondev, J.; Nelson, P. C.; Phillips, R.; Widom, J.; Wiggins, P. A. Biopolymers 2007, 85, 115
5. Wang, J.-P.; Fondufe-Mittendorf, Y.; Xi, L.; Tsai, G.-F.; Segal, E.; Widom, J. PLoS Comput. Biol. 2008, 4, e1000175
6. Segal, E.; Fondufe-Mittendorf, Y.; Chen, L. Y.; Thastrom, A.; Field, Y.; Moore, I. K.; Wang, J. P. Z.; Widom, J. Nature 2006, 442, 772
7. Segal, E.; Widom, J. Curr. Opin. Struct. Biol. 2009, 19, 65
8. Anderson, J. D.; Widom, J. Mol. Cell. Biol. 2001, 21, 3830
9. Segal, E.; Widom, J. Nat. Rev. Gen. 2009, 10, 443
10. Rohs, R.; West, S. M.; Sosinsky, A.; Liu, P.; Mann, R. S.; Honig, B. Nature 2009, 461, 1248
11. West, S. M.; Rohs, R.; Mann, R. S.; Honig, B. J. Biomol. Struct. Dyn. 2010, 27, 861
12. Olson, W. K.; Zhurkin, V. B. Curr. Opin. Struct. Biol. 2000, 10, 286
13. Benham, C. J.; Mielke, S. P. Annu. Rev. Biomed. Eng. 2005, 7, 21
14. Podgornik, R. Nat. Nanotechnol. 2006, 1, 100
15. Tu, Z. C.; Ou-Yang, Z. C. J. Comput. Theor. Nanosci. 2008, 5, 422
16. Tkachenko, A. V. Phys. A (Amsterdam, Neth.) 2007, 384, 133
17. Wiggins, P. A.; Van Der Heijden, T.; Moreno-Herrero, F.; Spakowitz, A.; Phillips, R.; Widom, J.; Dekker, C.; Nelson, P. C. Nat. Nanotechnol. 2006, 1, 137
18. Zuccheri, G.; Scipioni, A.; Cavaliere, V.; Gargiulo, G.; De Santis, P.; Samori, B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 3074
19. Anselmi, C.; DeSantis, P.; Scipioni, A. Biophys. Chem. 2005, 113, 209
20. Coleman, B. D.; Olson, W. K.; Swigon, D. J. Chem. Phys. 2003, 118, 7127
21. Zhurkin, V. B.;; Tolstorukov, M. Y.; Xu, F.; Colasanti, A. V.; Olson, W. K. In DNA Conformation and Transcription; Landes Bioscience/Eurekah.com: Georgetown, TX, 2005; p 18.
22. Tolstorukov, M. Y.; Choudhary, V.; Olson, W. K.; Zhurkin, V. B.; Park, P. J. Bioinformatics 2008, 24, 1456
23. Morozov, A. V.; Fortney, K.; Gaykalova, D. A.; Studitsky, V. M.; Widom, J.; Siggia, E. D. Nucleic Acids Res. 2009, 37, 4707
24. Bomble, Y. J.; Case, D. A. Biopolymers 2008, 89, 722
25. Mazur, A. K. Biophys. J. 2006, 91, 4507
26. Mazur, A. K. J. Phys. Chem. B 2009, 113, 2077
27. Bishop, T. C. J. Biomol. Struct. Dyn. 2005, 22, 673
28. Ruscio, J. Z.; Onufriev, A. Biophys. J. 2006, 91, 4121
29. Lavery, R.; Zakrzewska, K.; Sklenar, H. Comput. Phys. Commun. 1995, 91, 135
30. Sanghani, S. R.; Zakrzewska, K.; Harvey, S. C.; Lavery, R. Nucleic Acids Res. 1996, 24, 1632
31. Zakrzewska, K.; Bouvier, B.; Michon, A.; Blanchet, C.; Lavery, R. Phys. Chem. Chem. Phys. 2009, 11, 10712
32. Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049
33. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817
34. 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
35. Thastrom, A.; Bingham, L. M.; Widom, J. J. Mol. Biol. 2004, 338, 695
36. Lowary, P. T.; Widom, J. J. Mol. Biol. 1998, 276, 19
37. Ulanovsky, L. E.; Trifonov, E. N. Cell Biochem. Biophys. 1983, 5, 281
38. Tolstorukov, M. Y.; Colasanti, A. V.; McCandlish, D. M.; Olson, W. K.; Zhurkin, V. B. J. Mol. Biol. 2007, 371, 725
39. Lu, X. J.; Olson, W. K. Nucleic Acids Res. 2003, 31, 5108
40. Young, M. A.; Ravishanker, G.; Beveridge, D. L.; Berman, H. M. Biophys. J. 1995, 68, 2454
41. El Hassan, M. A.; Calladine, C. R. J. Mol. Biol. 1998, 282, 331
42. Ramstein, J.; Lavery, R. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7231
43. Nakanishi, M.; Mitane, Y.; Tsuboi, M. Biochim. Biophys. Acta 1984, 798, 46
44. Wu, B.; Mohideen, K.; Vasudevan, D.; Davey, C. A. Structure 2010, 18, 528
45. Tachiwana, H.; Kagawa, W.; Osakabe, A.; Kawaguchi, K.; Shiga, T.; Hayashi-Takanaka, Y.; Kimura, H.; Kurumizaka, H. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 10454
46. Davey, C. A.; Sargent, D. F.; Luger, K.; Maeder, A. W.; Richmond, T. J. J. Mol. Biol. 2002, 319, 1097
47. Gabb, H. A.; Lavery, R.; Prevost, C. J. Comput. Chem. 1995, 16, 667
48. Sklenar, H.; Wustner, D.; Rohs, R. J. Comput. Chem. 2006, 27, 309
49. Ulyanov, N. B.; Schmitz, U.; James, T. L. J. Biomol. NMR 1993, 3, 547