-
1
-
-
32444434989
-
Histone H4-K16 acetylation controls chromatin structure and protein interactions
-
Shogren-Knaak, M., H. Ishii, ⋯, C. L. Peterson. 2006. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science. 311:844-847.
-
(2006)
Science
, vol.311
, pp. 844-847
-
-
Shogren-Knaak, M.1
Ishii, H.2
Peterson, C.L.3
-
2
-
-
33847076849
-
Chromatin modifications and their function
-
Kouzarides, T. 2007. Chromatin modifications and their function. Cell. 128:693-705.
-
(2007)
Cell
, vol.128
, pp. 693-705
-
-
Kouzarides, T.1
-
3
-
-
34548526743
-
Chromatin remodeling and cancer. Part I: Covalent histone modifications
-
Wang, G. G., C. D. Allis, and P. Chi. 2007. Chromatin remodeling and cancer. Part I: Covalent histone modifications. Trends Mol. Med. 13:363-372.
-
(2007)
Trends Mol. Med
, vol.13
, pp. 363-372
-
-
Wang, G.G.1
Allis, C.D.2
Chi, P.3
-
4
-
-
0022544946
-
Physicochemical studies of the folding of the 100 Å nucleosome filament into the 300 Å filament. Cation dependence
-
Widom, J. 1986. Physicochemical studies of the folding of the 100 Å nucleosome filament into the 300 Å filament. Cation dependence. J. Mol. Biol. 190:411-424.
-
(1986)
J. Mol. Biol
, vol.190
, pp. 411-424
-
-
Widom, J.1
-
5
-
-
0028363760
-
Formation and stability of higher order chromatin structures. Contributions of the histone octamer
-
Schwarz, P. M., and J. C. Hansen. 1994. Formation and stability of higher order chromatin structures. Contributions of the histone octamer. J. Biol. Chem. 269:16284-16289.
-
(1994)
J. Biol. Chem
, vol.269
, pp. 16284-16289
-
-
Schwarz, P.M.1
Hansen, J.C.2
-
6
-
-
33745829766
-
Highly compact folding of chromatin induced by cellular cation concentrations. Evidence from atomic force microscopy studies in aqueous solution
-
Cano, S., J. M. Caravaca, ⋯, J. R. Daban. 2006. Highly compact folding of chromatin induced by cellular cation concentrations. Evidence from atomic force microscopy studies in aqueous solution. Eur. Biophys. J. 35:495-501.
-
(2006)
Eur. Biophys. J
, vol.35
, pp. 495-501
-
-
Cano, S.1
Caravaca, J.M.2
Daban, J.R.3
-
7
-
-
0029882454
-
Reversible oligonucleosome self-association: Dependence on divalent cations and core histone tail domains
-
Schwarz, P. M., A. Felthauser, ⋯, J. C. Hansen. 1996. Reversible oligonucleosome self-association: Dependence on divalent cations and core histone tail domains. Biochemistry. 35:4009-4015.
-
(1996)
Biochemistry
, vol.35
, pp. 4009-4015
-
-
Schwarz, P.M.1
Felthauser, A.2
Hansen, J.C.3
-
8
-
-
0034901554
-
Aggregation of nucleosomes by divalent cations
-
de Frutos, M., E. Raspaud, ⋯, F. Livolant. 2001. Aggregation of nucleosomes by divalent cations. Biophys. J. 81:1127-1132.
-
(2001)
Biophys. J
, vol.81
, pp. 1127-1132
-
-
De Frutos, M.1
Raspaud, E.2
Livolant, F.3
-
9
-
-
33744800781
-
Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails
-
Korolev, N., A. P. Lyubartsev, and L. Nordenskiold. 2006. Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails. Biophys. J. 90:4305-4316.
-
(2006)
Biophys. J
, vol.90
, pp. 4305-4316
-
-
Korolev, N.1
Lyubartsev, A.P.2
Nordenskiold, L.3
-
10
-
-
65249149694
-
Brownian dynamics simulation of DNA unrolling from the nucleosome
-
Wocjan, T., K. Klenin, and J. Langowski. 2009. Brownian dynamics simulation of DNA unrolling from the nucleosome. J. Phys. Chem. B. 113:2639-2646.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2639-2646
-
-
Wocjan, T.1
Klenin, K.2
Langowski, J.3
-
11
-
-
56049111628
-
The effect of internucleosomal interaction on folding of the chromatin fiber
-
Stehr, R., N. Kepper, ⋯, G. Wedemann. 2008. The effect of internucleosomal interaction on folding of the chromatin fiber. Biophys. J. 95:3677-3691.
-
(2008)
Biophys. J
, vol.95
, pp. 3677-3691
-
-
Stehr, R.1
Kepper, N.2
Wedemann, G.3
-
13
-
-
44449099745
-
Coarse-grained force field for the nucleosome from self-consistent multiscaling
-
Voltz, K., J. Trylska, ⋯, J. Smith. 2008. Coarse-grained force field for the nucleosome from self-consistent multiscaling. J. Comput. Chem. 29:1429-1439.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1429-1439
-
-
Voltz, K.1
Trylska, J.2
Smith, J.3
-
14
-
-
66149136864
-
Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles
-
Yang, Y., A. P. Lyubartsev, ⋯, L. Nordenskiold. 2009. Computer modeling reveals that modifications of the histone tail charges define salt-dependent interaction of the nucleosome core particles. Biophys. J. 96:2082-2094.
-
(2009)
Biophys. J
, vol.96
, pp. 2082-2094
-
-
Yang, Y.1
Lyubartsev, A.P.2
Nordenskiold, L.3
-
15
-
-
0035156429
-
Modeling salt-mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome
-
Beard, D. A., 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.
-
(2001)
Biopolymers
, vol.58
, pp. 106-115
-
-
Beard, D.A.1
Schlick, T.2
-
16
-
-
0042940030
-
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DiSCO) algorithm
-
Zhang, Q., D. A. Beard, and T. Schlick. 2003. Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the Discrete Surface Charge Optimization (DiSCO) algorithm. J. Comput. Chem. 24:2063-2074.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 2063-2074
-
-
Zhang, Q.1
Beard, D.A.2
Schlick, T.3
-
17
-
-
20444377701
-
Electrostatic mechanism of nucleosomal array folding revealed by computer simulation
-
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.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 8180-8185
-
-
Sun, J.1
Zhang, Q.2
Schlick, T.3
-
18
-
-
33745738426
-
Flexible histone tails in a new mesoscopic oligonucleosome model
-
Arya, G., Q. Zhang, and T. Schlick. 2006. Flexible histone tails in a new mesoscopic oligonucleosome model. Biophys. J. 91:133-150.
-
(2006)
Biophys. J
, vol.91
, pp. 133-150
-
-
Arya, G.1
Zhang, Q.2
Schlick, T.3
-
19
-
-
33750807408
-
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model
-
Arya, G., and T. Schlick. 2006. Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proc. Natl. Acad. Sci. USA. 103:16236-16241.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 16236-16241
-
-
Arya, G.1
Schlick, T.2
-
20
-
-
70450257681
-
Mesoscale simulations of two nucleosome- repeat length oligonucleosomes
-
Schlick, T., and O. Perisic. 2009. Mesoscale simulations of two nucleosome- repeat length oligonucleosomes. Phys. Chem. Chem. Phys. 11:10729-10737.
-
(2009)
Phys. Chem. Chem. Phys
, vol.11
, pp. 10729-10737
-
-
Schlick, T.1
Perisic, O.2
-
21
-
-
77958480124
-
Modeling studies of chromatin fiber structure as a function of DNA linker length
-
In Press, DOI:10.1016/j.jmb.2010.07.057
-
Perisic, O., R. Collepardo, and T. Schlick. 2010. Modeling studies of chromatin fiber structure as a function of DNA linker length. J. Mol. Biol. In Press, DOI:10.1016/j.jmb.2010.07.057.
-
(2010)
J. Mol. Biol
-
-
Perisic, O.1
Collepardo, R.2
Schlick, T.3
-
22
-
-
0036099317
-
Computer simulation of the 30-nanometer chromatin fiber
-
Wedemann, G., and J. Langowski. 2002. Computer simulation of the 30-nanometer chromatin fiber. Biophys. J. 82:2847-2859.
-
(2002)
Biophys. J
, vol.82
, pp. 2847-2859
-
-
Wedemann, G.1
Langowski, J.2
-
23
-
-
69449098842
-
Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions
-
Grigoryev, S. A., G. Arya, ⋯, T. Schlick. 2009. Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions. Proc. Natl. Acad. Sci. USA. 106:13317-13322.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 13317-13322
-
-
Grigoryev, S.A.1
Arya, G.2
Schlick, T.3
-
25
-
-
0345055328
-
DNA bending by small, mobile multivalent cations
-
Rouzina, I., and V. A. Bloomfield. 1998. DNA bending by small, mobile multivalent cations. Biophys. J. 74:3152-3164.
-
(1998)
Biophys. J
, vol.74
, pp. 3152-3164
-
-
Rouzina, I.1
Bloomfield, V.A.2
-
26
-
-
70350065991
-
Counterion atmosphere and hydration patterns near a nucleosome core particle
-
Materese, C. K., A. Savelyev, and G. A. Papoian. 2009. Counterion atmosphere and hydration patterns near a nucleosome core particle. J. Am. Chem. Soc. 131:15005-15013.
-
(2009)
J. Am. Chem. Soc
, vol.131
, pp. 15005-15013
-
-
Materese, C.K.1
Savelyev, A.2
Papoian, G.A.3
-
28
-
-
36048952831
-
Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
-
Chu, V. B., Y. Bai, ⋯, S. Doniach. 2007. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophys. J. 93:3202-3209.
-
(2007)
Biophys. J
, vol.93
, pp. 3202-3209
-
-
Chu, V.B.1
Bai, Y.2
Doniach, S.3
-
29
-
-
0000065196
-
The statistical-mechanics of the electrical double-layer
-
Carnie, S. L., and G. M. Torrie. 1984. The statistical-mechanics of the electrical double-layer. Adv. Chem. Phys. 56:141-253.
-
(1984)
Adv. Chem. Phys
, vol.56
, pp. 141-253
-
-
Carnie, S.L.1
Torrie, G.M.2
-
30
-
-
47549101415
-
The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
-
Gruziel, M., P. Grochowski, and J. Trylska. 2008. The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff. J. Comput. Chem. 29:1970-1981.
-
(2008)
J. Comput. Chem
, vol.29
, pp. 1970-1981
-
-
Gruziel, M.1
Grochowski, P.2
Trylska, J.3
-
31
-
-
0035093560
-
Computational modeling predicts the structure and dynamics of chromatin fiber
-
Beard, D. A., and T. Schlick. 2001. Computational modeling predicts the structure and dynamics of chromatin fiber. Structure. 9:105-114.
-
(2001)
Structure
, vol.9
, pp. 105-114
-
-
Beard, D.A.1
Schlick, T.2
-
32
-
-
65649099698
-
A tale of tails: How histone tails mediate chromatin compaction in different salt and linker histone environments
-
Arya, G., and T. Schlick. 2009. A tale of tails: How histone tails mediate chromatin compaction in different salt and linker histone environments. J. Phys. Chem. A. 113:4045-4059.
-
(2009)
J. Phys. Chem. A
, vol.113
, pp. 4045-4059
-
-
Arya, G.1
Schlick, T.2
-
33
-
-
0000598304
-
Bending and twisting dynamics of short linear DNAs: Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation
-
Allison, S. A., R. Austin, and M. Hogan. 1989. Bending and twisting dynamics of short linear DNAs: Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation. J. Chem. Phys. 90:3843-3854.
-
(1989)
J. Chem. Phys
, vol.90
, pp. 3843-3854
-
-
Allison, S.A.1
Austin, R.2
Hogan, M.3
-
34
-
-
0030572145
-
Comparison of analytical theory with Brownian dynamics simulations for small linear and circular DNAs
-
Heath, P. J., J. A. Gebe, ⋯, J. M. Schurr. 1996. Comparison of analytical theory with Brownian dynamics simulations for small linear and circular DNAs. Macromolecules. 29:3583-3596.
-
(1996)
Macromolecules
, vol.29
, pp. 3583-3596
-
-
Heath, P.J.1
Gebe, J.A.2
Schurr, J.M.3
-
35
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia, W., E. Alexov, and B. Honig. 2001. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J. Phys. Chem. B. 105:6507-6514.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
36
-
-
1642464809
-
Poisson-Boltzmann methods for biomolecular electrostatics
-
Baker, N. A. 2004. Poisson-Boltzmann methods for biomolecular electrostatics. Methods Enzymol. 383:94-118.
-
(2004)
Methods Enzymol
, vol.383
, pp. 94-118
-
-
Baker, N.A.1
-
37
-
-
0041375848
-
Ionic effects beyond Poisson-Boltzmann theory
-
Vlachy, V. 1999. Ionic effects beyond Poisson-Boltzmann theory. Annu. Rev. Phys. Chem. 50:145-165.
-
(1999)
Annu. Rev. Phys. Chem
, vol.50
, pp. 145-165
-
-
Vlachy, V.1
-
39
-
-
0037143629
-
DNA-dependent divalent cation binding in the nucleosome core particle
-
Davey, C. A., and T. J. Richmond. 2002. DNA-dependent divalent cation binding in the nucleosome core particle. Proc. Natl. Acad. Sci. USA. 99:11169-11174.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11169-11174
-
-
Davey, C.A.1
Richmond, T.J.2
-
40
-
-
0037436410
-
Chromatin fiber folding: Requirement for the histone H4 N-terminal tail
-
Dorigo, B., T. Schalch, ⋯, T. J. Richmond. 2003. Chromatin fiber folding: Requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327:85-96.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 85-96
-
-
Dorigo, B.1
Schalch, T.2
Richmond, T.J.3
-
41
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
Sharp, K. A., and B. Honig. 1990. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 94:7684-7692.
-
(1990)
J. Phys. Chem
, vol.94
, pp. 7684-7692
-
-
Sharp, K.A.1
Honig, B.2
-
42
-
-
0001354663
-
Effective interactions between electric double layers
-
Hansen, J. P., and H. Lowen. 2000. Effective interactions between electric double layers. Annu. Rev. Phys. Chem. 51:209-242.
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 209-242
-
-
Hansen, J.P.1
Lowen, H.2
-
43
-
-
0345447138
-
Monte Carlo simulation of the mean force between two like-charged macroions with simple 1:3 salt added
-
Angelescu, D. G., and P. Linse. 2003. Monte Carlo simulation of the mean force between two like-charged macroions with simple 1:3 salt added. Langmuir. 19:9661-9668.
-
(2003)
Langmuir
, vol.19
, pp. 9661-9668
-
-
Angelescu, D.G.1
Linse, P.2
|