You have free access to this content

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation

Danilo Roccatano,
Andre Barthel,
Martin Zacharias^*

Article first published online: 24 JAN 2007

DOI: 10.1002/bip.20690

Issue

Biopolymers

Volume 85, Issue 5-6, pages 407–421, 5 - 15 April 2007

Additional Information

How to Cite

Roccatano, D., Barthel, A. and Zacharias, M. (2007), Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation. Biopolymers, 85: 407–421. doi: 10.1002/bip.20690

Author Information

School of Engineering and Science, International University Bremen, Campus Ring 1, D-28759 Bremen, Germany

Email: Martin Zacharias (m.zacharias@iu-bremen.de)

^*School of Engineering and Science, International University Bremen, Campus Ring 1, D-28759 Bremen, Germany

Publication History

Issue published online: 15 MAR 2007
Article first published online: 24 JAN 2007
Manuscript Accepted: 17 JAN 2007
Manuscript Revised: 15 JAN 2007
Manuscript Received: 8 NOV 2006

Funded by

Pacific Northwest National Laboratories, USA. Grant Number: gc9593
VolkswagenStiftung. Grant Number: I/80485

ARTICLE TOOLS

View Full Article with Supporting Information (HTML) Get PDF (652K)

REFERENCES

1
Luger, K.; Maeder, A. W.; Richmond, R. K.; Sargent, D. F.; Richmond, T. J. Nature 1997, 389, 251–259.
2
White, C. L.; Suto, R. K.; Luger, K. EMBO J 2001, 20, 5207–5218.
3
Richmond, T. J.; Davey, C. A. Nature 2003, 423, 145–150.
4
Davey, C. A.; Sargent, D. F.; Luger, K.; Maeder, A. W.; Richard, T. J. J Mol Biol 2003, 319, 1097–1106.
5
Van Holde, K. E. In Chromatin; Springer: New York; 1988; p 288.
6
Fletcher, T. M.; Hansen, J. C. Crit Rev Eukaryot Gene Expr 1996, 6, 149–188.
7
Kornberg, R. D.; Lorch, Y. Cell 1999, 98, 285–294.
8
Richmond, T. J.; Widom, J. Nucleosome and Chromatin Structure; Oxford University Press: Oxford, 2000.
9
Felsenfeld, G.; Groudine, M. Nature 2003, 421, 448–453.
10
Kornberg, R. D.; Lorch, Y. Annu Rev Cell Biol 1992, 8, 563–587.
11
Anderson, J. D.; Thastrom, A.; Widom, J. Mol Cell Biol 2002, 20, 7147–7157.
12
Fazzio, T. G.; Tsukiyama, T. Mol Cell 2003, 12, 1333–1340.
13
Sivolob, A.; Prunell, A. Philos Transact A Math Phys Eng Sci 2004, 362, 1519–1547.
14
Li, G.; Widom, J. Nat Struct Mol Biol 2004, 11, 763–769.
15
Li, G.; Levitus, M.; Bustamante, C.; Widom J. Nat Struct Mol Biol 2005, 12, 46–53.
16
Lachner, M.; O'Sullivan, R. J.; Jenuwein, T. J Cell Sci 2003, 116, 2117–2124.
17
Cosgrove, M. S.; Boeke, J. D.; Wolberger C. Nat Struct Mol Biol 2004, 11, 1037–1043.
18
Khorasanizadeh, S. Cell 2004, 116, 259–272.
19
Turner, B. M. Nat Struct Mol Biol 2005, 12, 110–112.
20
Brower-Toland, B.; Wacker, D. A.; Fulbright, R. M.; Lis, J. T.; Kraus, W. L.; Wang, M. D. J Mol Biol 2005, 346, 135–146.
21
Fan, H. Y.; He, X.; Kingston, R. E.; Narlikar, G. J Mol Cell 2003, 11, 391–403.
- CrossRef,
- Web of Science® Times Cited: 82
22
Widom, J. Q. Rev Biophys 2001, 34, 269–324.
23
Segal, E.; Fondufe-Mittendorf, Y.; Chen, L.; Thaström, A.; Field, Y.; Moore, I. K.; Wang, J. Z.; Widom, J. Nature 2006, 442, 772–778.
24
Cloutier, T. E.; Widom, J. Proc Natl Acad Sci USA 2005, 102, 3645–3650.
25
Lankas, F.; Lavery, R.; Maddocks, J. H. Structure 2006, 10, 1527–1534.
26
Bishop, T. C. J. J Biomol Struct Dyn 2005, 22, 673–685.
27
Ruscio, J. Z.; Onufriev, A. Biophys J 2006, 91, 4121–4132.
28
Mangenot, S.; Leforestier, A.; Vachette, P.; Durand, D.; Livolant, F. Biophys J 2002, 82, 345–356.
29
Beard, D. A.; Schlick, T. Biophys J 2001, 9, 105–114.
30
Wedemann, G.; Langowski, J. Biophys J 2002, 2, 2847–2859.
31
Bharath, M. M. S.; Chandra, N. R.; Rao, M. R. S. Nucleic Acids Res 2003, 31, 4264–4274.
32
Mergell, B.; Everaes, R.; Schiessel H. Phys Rev E Stat Nonlin Soft Matter Phys 2004, 70, 011915.
- CrossRef,
- PubMed
33
Sun, J.; Zhang, Q.; Schlick, T. Proc Natl Acad Sci USA 2005, 102, 8180–8185.
34
Arya, G.; Zhang, Q.; Schlick, T. Biophys J 2006, 91, 133–150.
35
Sharma, S.; Ding, F.; Dokhalyan, N. V. Biophys J 2007, 92, 1457–1470.
36
Doublie, S.; Tabor, S.; Long, A. M.; Richardson, C. C.; Ellenberger, T. Nature 1998, 391, 251–258.
37
Cramer, P.; Bushnell, D. A.; Fu, J.; Gnatt, A. L.; Maier-Davis, B.; Thompson, N. E.; Burgess, R. R.; Edwards, A. M.; David, P. R.; Kornberg, R. D. Science 2000, 288, 640–649.
38
Case, D.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E.,III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. Amber 8, University of California, San Francisco, 2003.
39
Jorgensen, W.; Chandrasekhar J.; Madura J.; Impey R.; Klein M. J Chem Phys 1983, 79, 926–935.
40
Duan, Y.; Wu A.; Chowdhury, C. S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman P. J Comput Chem 2003, 24, 1999–2012.
Direct Link:
41
Miyamoto, S.; Kollman, P. A. J Comput Chem 1992, 13, 952–962.
Direct Link:
42
Darden, T. A.; York, D. M.; Pedersen L. J Chem Phys 1993, 98, 10089–10092.
43
Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen H. J. E. J Comput Chem 2005, 26, 1701–1718.
Direct Link:
44
Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graph 1996, 14, 33–38.
45
Lavery, R.; Sklenar, H. J Biomol Struct Dyn 1988, 6, 63–91.
46
Rosenberg, J. M.; Seeman, N. C.; Day, R. O.; Rich A. Biochem Biophys Res Commun 1976, 69, 979–987.
47
Packer, M. J.; Hunter C. A. J Mol Biol 1998, 280, 407–420.
48
Dixit S. B.; Beveridge, D. L.; Case, D. A.; Cheatham, T. E.,III; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Sklenar, H.; Thayer, K. M.; Varnai, P. Biophys J 2005, 89, 3721–3740.
49
Barone, F.; Lankas, F.; Spackova, N.; Sponer, J.; Karran, P.; Bignami, M.; Mazzei, F. Biophys Chem 2005, 118, 31–41.
50
Suto, R. K.; Edayathumangalam, R. S.; White, C. L.; Melander, C.; Gottesfeld, J. M.; Dervan, P. B.; Luger, K. J Mol Biol 2003, 326, 371–380.
51
Tolstorukov, M. Y.; Colasanti, A. V.; McCandlish, D.; Olson, W. K.; Zhurkin, V. B. J Biomol Struct Dyn 2005, 22, 854–855.
52
Ramaswamy, A.; Bahar, I.; Ioshikhes, I. Proteins 2005, 58, 683–696.
Direct Link:
53
Hünenberger, P. H.; McCammon, J. A. Biophys Chem 1999, 78, 69–80.
54
Kastenholz, M. A.; Hünenberger, P. H. J Chem Phys 2006, 124, 124108.
55
Bertin, A.; Leforestier, A.; Durand, D.; Livolant, F. Biochem 2004, 43, 4773–4780.

View Full Article with Supporting Information (HTML) Get PDF (652K)

JOURNAL TOOLS

JOURNAL MENU

FIND ISSUES

FIND ARTICLES

GET ACCESS

FOR CONTRIBUTORS

ABOUT THIS JOURNAL

SPECIAL FEATURES

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation

Biopolymers

How to Cite

Author Information

Publication History

Funded by

ARTICLE TOOLS

REFERENCES

More content like this

JOURNAL TOOLS

JOURNAL MENU

FIND ISSUES

FIND ARTICLES

GET ACCESS

FOR CONTRIBUTORS

ABOUT THIS JOURNAL

SPECIAL FEATURES

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation

Biopolymers

How to Cite

Author Information

Publication History

Funded by

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

REFERENCES

More content like this