A computational study of nucleosomal DNA flexibility

Biophysical Journal

Volumn 91, Issue 11, 2006, Pages 4121-4132

  Ruscio, Jory Z ^a   Onufriev, Alexey ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BASE;

ARTICLE; DNA ISOLATION; DNA SEQUENCE; ENERGY ABSORPTION; ENERGY COST; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NUCLEOSOME; SIMULATION; VALIDATION PROCESS; WHOLE CELL; X RAY ANALYSIS;

EID: 33845365528     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.082099     Document Type: Article

References (53)

1. Kornberg, R., and Y. Lorch. 1995. Interplay between chromatin structure and transcription. Curr. Opin. Cell Biol. 7:371-375.
2. Kornberg, R., and Y. Lorch. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell. 98:285-294.
3. Workman, J., and R. Kingston. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545-579.
4. Wolffe, A., and D. Guschin. 2000. Chromatin structural features and targets that regulate transcription. J. Struct. Biol. 129:102-122.
5. Gottesfeld, J., J. Belitsky, C. Melander, P. Dervan, and K. Luger. 2002. Blocking transcription through a nucleosome with synthetic DNA ligands. J. Mol. Biol. 321:249-263.
6. Thåström, A., J. Gottesfeld, K. Luger, and J. Widom. 2004. Histone-DNA binding free energy cannot be measured in dilution-driven dissociation experiments. Biochemistry. 43:736-741.
7. Anderson, J., A. Thåström, and J. Widom. 2002. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Mol. Cell. Biol. 22:7147-7157.
8. Polach, K., and J. Widom. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254:130-149.
9. Shore, D., J. Langowski, and R. Baldwin. 1981. DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. USA. 78:4833-4837.
10. Crothers, D., J. Drak, J. Kahn, and S. Levene. 1992. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol. 212:3-29.
11. Vologodskaia, M., and A. Vologodskii. 2002. Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317:205-213.
12. Hayes, J., T. Tullius, and A. Wolffe. 1990. The structure of DNA in a nucleosome. Proc. Natl. Acad. Sci. USA. 87:7405-7409.
13. Hayes, J., J. Bashkin, T. Tullius, and A. Wolffe. 1991. The histone core exerts a dominant constraint on the structure of DNA in a nucleosome. Biochemistry. 30:8434-8440.
14. Richmond, T., and C. Davey. 2003. The structure of DNA in the nucleosome core. Nature. 423:145-150.
15. Hogan, M., T. Rooney, and R. Austin. 1987. Evidence for kinks in DNA folding in the nucleosome. Nature. 328:554-557.
16. Pruss, D., F. Bushman, and A. Wolffe. 1994. Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc. Natl. Acad. Sci. USA. 91:5913-5917.
17. Fitzgerald, D., and J. Anderson. 1999. DNA distortion as a factor in nucleosome positioning. J. Mol. Biol. 293:477-491.
18. Cloutier, T., and J. Widom. 2004. Spontaneous sharp bending of double-stranded DNA. Mol. Cell. 14:355-362.
19. Cloutier, T., and J. Widom. 2005. DNA twisting flexibility and the formation of sharply looped protein-DNA complexes. Proc. Natl. Acad. Sci. USA. 102:3645-3650.
20. Du, Q., C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii. 2005. Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. USA. 102:5397-5402.
21. Yan, J., and J. Marko. 2004. Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93:108108.
22. Shroff, H., B. M. Reinhard, M. Siu, H. Agarwal, A. Spakowitz, and J. Liphardt. 2005. Biocompatible force sensor with optical readout and dimensions of 6 NM3. Nano Lett. 5:1509-1514.
23. Reference deleted in proof.
24. Tsui, V., and D. Case. 2001. Theory and applications of the Generalized Born solvation model in macromolecular simulations. Biopolymers. 56:275-291.
25. Onufriev, A., D. Bashford, and D. Case. 2004. Exploring protein native states and large-scale conformational changes with a modified Generalized Born model. Proteins. 55:383-394.
26. Kuhlman, B., G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, and D. Baker. 2003. Design of a novel globular protein fold with atomiclevel accuracy. Science. 302:1364-1368.
27. Simmerling, C., B. Strockbine, and A. E. Roitberg. 2002. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124:11258-11259.
28. Davey, C., D. Sargent, K. Luger, A. Maeder, and T. Richmond. 2002. Solvent-mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution. J. Mol. Biol. 319:1097-1113.
29. Macke, T., and D. Case. 1998. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. American Chemical Society, Washington, DC. 379-393.
30. Lu, X.-J., and W. K. Olson. 2003. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucl. Acids Res. 31:5108-5121.
31. Case, D., T. Darden, T. Cheatham, H. Gohlke, K. Merz, A. Onufriev, R. Luo, and R. Woods. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
32. Case, D., T. Darden, T. Cheatham III, C. Simmerling, J. Wang, R. Duke, R. Luo, K. Merz, B. Wang, D. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. Caldwell, W. Ross, and P. Kollman. 2004. AMBER 8. University of California, San Francisco, CA.
33. El Hassan, M., and C. Calladine. 1998. Two distinct modes of protein-induced bending in DNA. J. Mol. Biol. 282:331-343.
34. Lavery, R., and H. Sklenar. 1988. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6:63-91.
35. Schlick, T. 2002. Molecular Modeling and Simulation. Springer, Berlin.
36. Cornell, W., P. Cieplak, C. Bayly, I. Gould, K. Merz, D. Ferguson, D. Spellmeyer, T. Fox, J. Caldwell, and P. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
37. Srinivasan, J., M. Trevathan, P. Beroza, and D. Case. 1999. Application of a pairwise Generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor. Chem. Acc. 101:426-434.
38. Tsui, V., and D. Case. 2000. Molecular dynamics simulations of nucleic acids with a Generalized Born solvation model. J. Am. Chem. Soc. 122:2489-2498.
39. Xia, B., V. Tsui, D. Case, H. Dyson, and P. Wright. 2002. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a Generalized Born model, and with explicit water. J. Biomol. NMR. 22:317-331.
40. Cheatham, T. 2004. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 14:360-367.
41. Cheatham, T., and M. Young. 2001. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers. 56:232-256.
42. Shimado, J., and H. Yamakawa. 1984. Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules. 17:689-698.
43. Zhang, Y., and D. Crothers. 2003. Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophys. J. 84:136-153.
44. Flory, P. 1969. Statistical Mechanics of Chain Molecules. Interscience Publishers, New York.
45. Doi, M., and S. Edwards. 1985. Theory of Polymer Dynamics. Oxford Press, New York.
46. Kollman, P., I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D. Case, and T. I. Cheatham. 2000. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33:889-897.
47. Srinivasan, J., T. Cheatham, P. Cieplak, P. Kollman, and D. Case. 1998. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120:9401-9409.
48. Wiggins, P. A., and P. C. Nelson. 2006. Generalized theory of semi-flexible polymers. Phys. Rev. E. 73:031906.
49. Landau, L. D., and E. M. Lifshitz. 1986. Theory of Elasticity. Pergamon, New York.
50. Onufriev, A., D. Case, and D. Bashford. 2003. Structural details, pathways, and energetics of unfolding apomyoglobin. J. Mol. Biol. 325:555-567.
51. Beard, D., and T. Schlick. 2001. Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome. Biopolymers. 58:106-115.
52. Sun, J., Q. Zhang, and T. Schlick. 2005. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc. Natl. Acad. Sci. USA. 102:8180-8185.
53. Bishop, T. 2005. Molecular dynamics simulations of a nucleosome and free DNA. J. Biomol. Struct. Dyn. 22:673-685.