Relaxation dynamics of nucleosomal DNA

Physical Chemistry Chemical Physics

Volumn 11, Issue 45, 2009, Pages 10633-10643

  Ponomarev, Sergei Y ^a,c   Putkaradze, Vakhtang ^b   Bishop, Thomas C ^a  

^a TULANE UNIVERSITY   (United States)

^b Veterinary Dentistry and Oral Surgery   (United States)

^c Life Science and Bioengineering Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE;

ARTICLE; CHEMISTRY; MOLECULAR DYNAMICS; NUCLEOSOME;

DNA; HISTONES; MOLECULAR DYNAMICS SIMULATION; NUCLEOSOMES;

EID: 70450225393     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/b910937b     Document Type: Article

References (80)

1. R. M. Levy J. A. Karplus M. McCammon Molecular Dynamics Studies of NMR Relaxation in Proteins Biophys. J. 1980 32 1 628 630
2. A. Bizzarri S. Cannistraro Molecular Dynamics of Water at the Protein-Solvent Interface J. Phys. Chem. B 2002 106 6617 6633
3. L. Nilsson B. Halle Molecular origin of time-dependent fluorescence shifts in proteins Proc. Natl. Acad. Sci. U. S. A. 2005 102 13867 13872 10.1073/pnas.0504181102 (Pubitemid 41377670)
4. A. A. Golosov M. Karplus Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis J. Phys. Chem. B 2007 111 1482 1490 10.1021/jp065493u (Pubitemid 46339079)
5. N. Sengupta S. Jaud D. J. Tobias Hydration dynamics in a partially denatured ensemble of the globular protein human alpha-lactalbumin investigated with molecular dynamics simulations Biophys. J. 2008 95 5257 5267 10.1529/biophysj.108.136531
6. M. Marchi F. Sterpone M. Ceccarelli Water rotational relaxation and diffusion in hydrated lysozyme J. Am. Chem. Soc. 2002 124 6787 6791
7. R. Abseher H. Schreiber O. Steinhauser The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation Proteins: Struct., Funct., Genet. 1996 25 366 378
8. S. Sen N. A. Paraggio L. A. Gearheart E. E. Connor A. Issa R. S. Coleman D. M. Wilson M. D. Wyatt M. A. Berg Effect of protein binding on ultrafast DNA dynamics: characterization of a DNA:APE1 complex Biophys. J. 2005 89 4129 4138 10.1529/biophysj.105.062695 (Pubitemid 41725633)
9. D. Zhong S. K. Pal A. H. Zewail Femtosecond Studies of Protein-DNA Binding and Dynamics: Histone I ChemPhysChem 2001 2 219 227
10. S. Sen D. Andreatta S. Y. Ponomarev D. L. Beveridge M. A. Berg Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments J. Am. Chem. Soc. 2009 131 1724 1735 10.1021/ja805405a
11. M. A. Berg R. S. Coleman C. J. Murphy Nanoscale structure and dynamics of DNA Phys. Chem. Chem. Phys. 2008 10 1229 1242 10.1039/b715272h
12. E. B. Brauns M. L. Madaras R. S. Coleman C. J. Murphy M. A. Berg Complex local dynamics in DNA on the picosecond and nanosecond time scales Phys. Rev. Lett. 2002 88 158101
13. H. Frauenfelder S. G. Sligar P. G. Wolynes The energy landscapes and motions of proteins Science 1991 254 1598 1603
14. C. Angell Formation of Glasses from Liquids and Biopolymers Science 1995 267 1924 1935
15. A. Paciaroni A. Bizzarri S. Cannistraro Molecular Dynamics simulation evidences of a boson peak in protein hydration water Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 1998 57 R6277 R6280
16. A. Paciaroni A. R. Bizzarri S. Cannistraro Neutron scattering evidence of a boson peak in protein hydration water Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 1999 60 R2476 R2479
17. T. Li A. A. Hassanali Y.-T. Kao D. Zhong S. J. Singer Hydration dynamics and time scales of coupled water-protein fluctuations J. Am. Chem. Soc. 2007 129 3376 3382 10.1021/ja0685957 (Pubitemid 46449368)
18. T. Li A. Hassanali S. Singer Origin of Slow Relaxation Following Photoexcitation of W7 in Myoglobin and the Dynamics of Its Hydration Layer J. Phys. Chem. B 2008 112 16121 10.1021/jp803042u
19. S. K. Pal A. H. Zewail Dynamics of water in biological recognition Chem. Rev. 2004 104 2099 2123 10.1021/cr020689l
20. S. Pal J. Peon B. Bagchi A. Zewail Biological water: Femtosecond Dynamics of Macromolecular Hydration J. Phys. Chem. B 2002 106 12376 12395
21. S. Bhattacharyya Z. Wang A. Zewail Dynamics of water near a protein surface J. Phys. Chem. B 2003 107 13218 13228
22. P. Szendro G. Vincze A. Szasz Pink-noise behaviour of biosystems Eur. Biophys. J. 2001 30 227 231
23. A. Bizzarri S. Cannistraro Flickering noise in the potential energy fluctuations of proteins as investigated by MD simulation Phys. Lett. A 1997 236 596 601
24. A. Bizzarri S. Cannistraro Molecular dynamics simulation of plastocyanin potential energy fluctuations: 1/f noise Phys. A 1999 267 257 270
25. T. G. Dewey J. G. Bann Protein dynamics and 1/f noise Biophys. J. 1992 63 594 598
26. S. K. Pal L. Zhao T. Xia A. H. Zewail Site- and sequence-selective ultrafast hydration of DNA Proc. Natl. Acad. Sci. U. S. A. 2003 100 13746 13751 10.1073/pnas.2336222100 (Pubitemid 37499137)
27. S. Pal P. K. Maiti B. Bagchi J. T. Hynes Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, cross-correlations J. Phys. Chem. B 2006 110 26396 26402 10.1021/jp065690t (Pubitemid 46133362)
28. S. Y. Ponomarev K. M. Thayer D. L. Beveridge Ion motions in molecular dynamics simulations on DNA Proc. Natl. Acad. Sci. U. S. A. 2004 101 14771 14775 10.1073/pnas.0406435101 (Pubitemid 39410750)
29. A. P. Sokolov H. Grimm A. Kisliuk A. Dianoux Slow Relaxation Process in DNA J. Biol. Phys. 2001 27 313 327
30. M. E. Hogan O. Jardetzky Internal motions in deoxyribonucleic acid II Biochemistry 1980 19 3460 3468
31. 1H nuclear magnetic resonance investigation of flexibility in DNA Proc. Natl. Acad. Sci. U. S. A. 1979 76 4165 4169
32. K. Luger Dynamic nucleosomes Chromosome Res. 2006 14 5 16 10.1007/s10577-005-1026-1 (Pubitemid 43315775)
33. K. Luger Structure and dynamic behavior of nucleosomes Curr. Opin. Genet. Dev. 2003 13 127 135
34. B. Dorigo T. Schalch A. Kulangara S. Duda R. R. Schroeder T. J. Richmond Nucleosome arrays reveal the two-start organization of the chromatin fiber Science 2004 306 1571 1573 10.1126/science.1103124 (Pubitemid 39564956)
35. D. Roccatano A. Barthel M. Zacharias Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation Biopolymers 2007 85 407 421 10.1002/bip.20690 (Pubitemid 46649822)
36. S. Sharma F. Ding N. V. Dokholyan Multiscale modeling of nucleosome dynamics Biophys. J. 2007 92 1457 1470 10.1529/biophysj.106.094805 (Pubitemid 46393459)
37. T. C. Bishop Molecular dynamics simulations of a nucleosome and free DNA J. Biomol. Struct. Dyn. 2005 22 673 685
38. K. Voltz J. Trylska V. Tozzini V. Kurkal-Siebert J. Langowski J. Smith Coarse-grained force field for the nucleosome from self-consistent multiscaling J. Comput. Chem. 2008 29 1429 1439 10.1002/jcc.20902 (Pubitemid 351757766)
39. J. Z. Ruscio A. Onufriev A computational study of nucleosomal DNA flexibility Biophys. J. 2006 91 4121 4132 10.1529/biophysj.106.082099 (Pubitemid 44887272)
40. T. C. Bishop Geometry of the nucleosomal DNA superhelix Biophys. J. 2008 95 1007 1017 10.1529/biophysj.107.122853
41. C. L. White R. K. Suto K. Luger Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions EMBO J. 2001 20 5207 5218 10.1093/emboj/20.18.5207 (Pubitemid 32910915)
42. J. C. Simó J. E. Marsden P. S. Krishnaprasad The Hamiltonian structure of nonlinear elasticity: The material and convective representations of solids, rods, plates Arch. Rat. Mech. Anal. 1988 104 125 183
43. T. C. Bishop R. Cortez O. O. Zhmudsky Investigation of bend and shear waves in a geometrically exact elastic rod model J. Comput. Phys. 2004 193 642 665
44. D. Dichmann, Y. Li and J. Maddocks, Hamiltonian formulations and symmetries in rod mechanics, in Mathematical Approaches to Biomolecular Structure and Dynamics (Minneapolis, MN, 1994), Springer, New York, 1996, vol. 82 of IMA Vol. Math. Appl., pp. 71-113
45. D. D. Holm V. Putkaradze Nonlocal orientation-dependent dynamics of molecular strands C. R. Acad. Sci. Paris 2008
46. D. Ellis D. D. Holm F. Gay-Balmaz V. Putkaradze T. Ratiu Geometric mechanics of flexible strands of charged molecules Arch. Rat. Mach. Anal. 2008
47. R. Kohlrausch Ueber das Dellmann'sche Elektrometer Ann. Phys. 1847 72 353
48. G. Williams D. Watts Non-symmetrical Dielectric Relaxation Behavior Arising from a Simple Empirical Decay Function Trans. Faraday Soc. 1970 66 80 85
49. B. K. Oksendal, Stochastic Differential Equations: An Introduction with Applications, Springer, Berlin-Heidelberg-New York, 5th edn, 2002
50. Y. L. Klimontovich J.-P. Boon Natural Flicker Noise (1/f Noise) in Music Europhys. Lett. 1987 3 395 399
51. R. Voss J. Clark 1/f noise in music and speech Nature 1975 258 317 318
52. B. Pilgram D. T. Kaplan Nonstationarity and 1/f noise characteristics in heart rate Am. J. Physiol. 1999 276 R1 R9
53. A. van der Ziel Unified Presentation of 1/f Noise in Electronic Devices: Fundamental 1/f Noise Sources Proc. IEEE 1988 76 3 233 258
54. P. G. Collins M. Fuhrer A. Zettl 1/f noise in carbon nanotubes Appl. Phys. Lett. 2000 76 894 896
55. J. M. Halley Ecology, evolution and 1/f-noise Trends Ecol. Evol. 1996 11 33 37
56. Y. Liu P. Gopikrishnan P. Cizeau M. Meyer C. K. Peng H. E. Stanley Statistical properties of the volatility of price fluctuations Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 1999 60 1390 1400
57. W. Press Flicker noises in astronomy and elsewhere Comments Mod. Phys. 1978 7 103 119
58. R. Voss Evolution of long-range fractal correlations and 1/f noise in DNA base sequences Phys. Rev. Lett. 1992 68 3805 3808
59. P. Bak C. Tang K. Wiesenfeld Self-organized criticality: An explanation of the 1/f noise Phys. Rev. Lett. 1987 59 381 384
60. M. Joyeux S. Buyukdagli M. Sanrey 1/f fluctuations of DNA temperature at thermal denaturation Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2007 75 061914
61. J. C. Phillips R. Braun W. Wang J. Gumbart E. Tajkhorshid E. Villa C. Chipot R. D. Skeel L. Kal K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 2005 26 1781 1802 10.1002/jcc.20289 (Pubitemid 43078511)
62. T. E. Cheatham P. Cieplak P. A. Kollman A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 1999 16 845 862
63. D. Case, T. Darden, I. T. E. Cheatham, 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, P. B. G. Cui, C. Schafmeister, J. Caldwell, W. Ross and P. Kollman, AMBER 8, University of California, San Francisco, 2004
64. A. Perez I. Marchan D. Svozil J. Sponer T. E. Cheatham C. A. Laughton M. Orozco Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers Biophys. J. 2007 92 3817 3829 10.1529/biophysj.106.097782 (Pubitemid 46910569)
65. J. Aqvist Ion-water interaction potentials derived from free energy perturbation simulations J. Phys. Chem. 1990 94 8021 8024
66. T. Fox P. A. Kollman Application of the RESP Methodology in the Parametrization of Organic Solvents J. Phys. Chem. B 1998 102 8070 8079
67. X.-J. Lu W. K. Olson 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures Nat. Protoc. 2008 3 1213 1227 10.1038/nprot.2008.104
68. S. Arnott D. W. Hukins Optimised parameters for A-DNA and B-DNA Biochem. Biophys. Res. Commun. 1972 47 1504 1509
69. R. E. Dickerson Definitions and nomenclature of nucleic acid structure parameters J. Biomol. Struct. Dyn. 1989 6 627 634
70. W. K. Olson M. Bansal S. K. Burley R. E. Dickerson M. Gerstein S. C. Harvey U. Heinemann X. J. Lu S. Neidle Z. Shakked H. Sklenar M. Suzuki C. S. Tung E. Westhof C. Wolberger H. M. Berman A standard reference frame for the description of nucleic acid base-pair geometry J. Mol. Biol. 2001 313 229 237 10.1006/jmbi.2001.4987 (Pubitemid 33001177)
71. R. Lavery H. Sklenar The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids J. Biomol. Struct. Dyn. 1988 6 63 91
72. P. K. Mehrotra D. L. Beveridge Structural analysis of molecular solutions based on quasi-component distribution functions. Application to [H2CO]aq at 25 °C J. Am. Chem. Soc. 1980 102 4287 4294
73. Mathematica, Version 6.0, Wolfram Research, Inc., Champaign, IL, 2008
74. Microcal Origin 7.5, Microcal Software, Inc., Northampton, MA, 2003
75. T. C. Bishop Virtual DNA: A Tool for Investigating the Structure, Flexibility and Dynamics of DNA and Other Fibers Bioinformatics 2009
76. K. Luger T. J. Richmond DNA binding within the nucleosome core Curr. Opin. Struct. Biol. 1998 8 33 40
77. S. K. Pal L. Zhao A. H. Zewail Water at DNA surfaces: ultrafast dynamics in minor groove recognition Proc. Natl. Acad. Sci. U. S. A. 2003 100 8113 8118 10.1073/pnas.1433066100 (Pubitemid 36842507)
78. I. Ohmine Liquid Water Dynamics: Collective Motions, Fluctuation, Relaxation J. Phys. Chem. 1995 99 6767 6776
79. P. Bak C. Tang K. Wiesenfeld Self-organized criticality Phys. Rev. A: At., Mol., Opt. Phys. 1988 38 364 374
80. P. Bak C. Tang K. Wiesenfeld Comment on "Relaxation at the angle of repose" Phys. Rev. Lett. 1989 62 110