-
1
-
-
0016221697
-
Chromatin structure: A repeating unit of histones and DNA
-
Kornberg, R. D. 1974. Chromatin structure: a repeating unit of histones and DNA. Science. 184:868-871.
-
(1974)
Science
, vol.184
, pp. 868-871
-
-
Kornberg, R.D.1
-
2
-
-
1842411320
-
Crystal structure of the nucleosome core particle at 2.8 A resolution
-
Luger, K., A. W. Mader, R. K. Richmond, D. F. Sargent, and T. J. Richmond. 1997. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 389:251-260.
-
(1997)
Nature
, vol.389
, pp. 251-260
-
-
Luger, K.1
Mader, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
3
-
-
0034522793
-
Asymmetries in the nucleosome core particle at 2.5 A resolution
-
Harp, J. M., B. L. Hanson, D. E. Timm, and G. J. Bunick. 2000. Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr. D Biol. Crystallogr. 56:1513-1534.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr
, vol.56
, pp. 1513-1534
-
-
Harp, J.M.1
Hanson, B.L.2
Timm, D.E.3
Bunick, G.J.4
-
4
-
-
0036307707
-
Solventmediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
-
Davey, C. A., D. F. Sargent, K. Luger, A. W. Maeder, and T. J. Richmond. 2002. Solventmediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319:1097-1113.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 1097-1113
-
-
Davey, C.A.1
Sargent, D.F.2
Luger, K.3
Maeder, A.W.4
Richmond, T.J.5
-
5
-
-
0035903534
-
Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions
-
White, C. L., R. K. Suto, and K. Luger. 2001. Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J. 20:5207-5218.
-
(2001)
EMBO J
, vol.20
, pp. 5207-5218
-
-
White, C.L.1
Suto, R.K.2
Luger, K.3
-
6
-
-
0035839136
-
Translating the histone code
-
Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science. 293:1074-1080.
-
(2001)
Science
, vol.293
, pp. 1074-1080
-
-
Jenuwein, T.1
Allis, C.D.2
-
7
-
-
0034610814
-
The language of covalent histone modifications
-
Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature. 403:41-45.
-
(2000)
Nature
, vol.403
, pp. 41-45
-
-
Strahl, B.D.1
Allis, C.D.2
-
9
-
-
0034522793
-
Asymmetries in the nucleosome core particle at 2.5 A resolution
-
Harp, J. M., B. L. Hanson, D. E. Timm, and G. J. Bunick. 2000. Asymmetries in the nucleosome core particle at 2.5 A resolution. Acta Crystallogr. D Biol. Crystallogr. 56:1513-1534.
-
(2000)
Acta Crystallogr. D Biol. Crystallogr
, vol.56
, pp. 1513-1534
-
-
Harp, J.M.1
Hanson, B.L.2
Timm, D.E.3
Bunick, G.J.4
-
10
-
-
0036532026
-
Histone modifications in transcriptional regulation
-
Berger, S. L. 2002. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12:142-148.
-
(2002)
Curr. Opin. Genet. Dev
, vol.12
, pp. 142-148
-
-
Berger, S.L.1
-
11
-
-
0033529565
-
Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome
-
Kornberg, R. D., and Y. Lorch. 1999. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell. 98:285-294.
-
(1999)
Cell
, vol.98
, pp. 285-294
-
-
Kornberg, R.D.1
Lorch, Y.2
-
12
-
-
0031968760
-
Chromatin fiber structure: Morphology, molecular determinants, structural transitions
-
Zlatanova, J., S. H. Leuba, and van Holde, K. 1998. Chromatin fiber structure: morphology, molecular determinants, structural transitions. Biophys. J. 74:2554-2566.
-
(1998)
Biophys. J
, vol.74
, pp. 2554-2566
-
-
Zlatanova, J.1
Leuba, S.H.2
van Holde, K.3
-
13
-
-
0029780079
-
What determines the folding of the chromatin fiber?
-
van Holde, K., and J. Zlatanova. 1996. What determines the folding of the chromatin fiber? Proc. Natl. Acad. Sci. USA. 93:10548-10555.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 10548-10555
-
-
van Holde, K.1
Zlatanova, J.2
-
14
-
-
0035883954
-
Transcription regulation by histone methylation: Interplay between different covalent modifications of the core histone tails
-
Zhang, Y., and D. Reinberg. 2001. Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev. 15:2343-2360.
-
(2001)
Genes Dev
, vol.15
, pp. 2343-2360
-
-
Zhang, Y.1
Reinberg, D.2
-
15
-
-
0030798245
-
Histone acetylation in chromatin structure and transcription
-
Grunstein, M. 1997. Histone acetylation in chromatin structure and transcription. Nature. 389:349-352.
-
(1997)
Nature
, vol.389
, pp. 349-352
-
-
Grunstein, M.1
-
16
-
-
0027960444
-
Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy
-
Leuba, S. H., G. Yang, C. Robert, B. Samori, K. van Holde, J. Zlatanova, and C. Bustamante. 1994. Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc. Natl. Acad. Sci. USA. 91:11621-11625.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 11621-11625
-
-
Leuba, S.H.1
Yang, G.2
Robert, C.3
Samori, B.4
van Holde, K.5
Zlatanova, J.6
Bustamante, C.7
-
17
-
-
19544385241
-
Structure alignment via Delaunay tetrahedralization
-
Roach, J., S. Sharma, M. Kapustina, and C. W. Carter, Jr. 2005. Structure alignment via Delaunay tetrahedralization. Proteins. 60:66-81.
-
(2005)
Proteins
, vol.60
, pp. 66-81
-
-
Roach, J.1
Sharma, S.2
Kapustina, M.3
Carter Jr., C.W.4
-
19
-
-
0025048105
-
Molecular dynamics simulations in biology
-
Karplus, M., and G. A. Petsko. 1990. Molecular dynamics simulations in biology. Nature. 347:631-639.
-
(1990)
Nature
, vol.347
, pp. 631-639
-
-
Karplus, M.1
Petsko, G.A.2
-
20
-
-
28844506608
-
Direct observation of protein folding, aggregation, and a prion-like conformational conversion
-
Ding, F., J. J. LaRocque, and N. V. Dokholyan. 2005. Direct observation of protein folding, aggregation, and a prion-like conformational conversion. J. Biol. Chem. 280:40235-40240.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 40235-40240
-
-
Ding, F.1
LaRocque, J.J.2
Dokholyan, N.V.3
-
21
-
-
0032443390
-
Discrete molecular dynamics studies of the folding of a protein-like model
-
Dokholyan, N. V., S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 1998. Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 3:577-587.
-
(1998)
Fold. Des
, vol.3
, pp. 577-587
-
-
Dokholyan, N.V.1
Buldyrev, S.V.2
Stanley, H.E.3
Shakhnovich, E.I.4
-
22
-
-
32344442405
-
Studies of folding and misfolding using simplified models
-
Dokholyan, N. V. 2006. Studies of folding and misfolding using simplified models. Curr. Opin. Struct. Biol. 11:79-85.
-
(2006)
Curr. Opin. Struct. Biol
, vol.11
, pp. 79-85
-
-
Dokholyan, N.V.1
-
23
-
-
0348014438
-
Identifying importance of amino acids for protein folding from crystal structures
-
Dokholyan, N. V., J. M. Borreguero, S. V. Buldyrev, F. Ding, H. E. Stanley, and E. I. Shakhnovich. 2003. Identifying importance of amino acids for protein folding from crystal structures. Methods Enzymol. 374:616-638.
-
(2003)
Methods Enzymol
, vol.374
, pp. 616-638
-
-
Dokholyan, N.V.1
Borreguero, J.M.2
Buldyrev, S.V.3
Ding, F.4
Stanley, H.E.5
Shakhnovich, E.I.6
-
24
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt, M., and A. Warshel. 1975. Computer simulation of protein folding. Nature. 253:694-698.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
25
-
-
0029633186
-
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and freeenergy calculations to simulate the structural and energetic properties of molecules
-
Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and freeenergy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91:1-41.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
26
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
-
Cheatham III, T. E., and M. A. Young. 2000. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers. 56:232-256.
-
(2000)
Biopolymers
, vol.56
, pp. 232-256
-
-
Cheatham III, T.E.1
Young, M.A.2
-
27
-
-
0033654654
-
Molecular dynamics simulation of nucleic acids
-
Cheatham III, T. E., and P. A. Kollman. 2000. Molecular dynamics simulation of nucleic acids. Annu. Rev. Phys. Chem. 51:435-471.
-
(2000)
Annu. Rev. Phys. Chem
, vol.51
, pp. 435-471
-
-
Cheatham III, T.E.1
Kollman, P.A.2
-
29
-
-
33645314632
-
The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex
-
Schiessel, H. 2006. The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex. Eur. Phys. J. E. 19:251-262.
-
(2006)
Eur. Phys. J. E
, vol.19
, pp. 251-262
-
-
Schiessel, H.1
-
30
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D. A., T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, and R. J. Woods. 2005. The Amber biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
31
-
-
0242443693
-
Force fields for protein simulations
-
Ponder, J. W., and D. A. Case. 2003. Force fields for protein simulations. Adv. Protein Chem. 66:27-85.
-
(2003)
Adv. Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
32
-
-
23944480351
-
Simple but predictive protein models
-
Ding, F., and N. V. Dokholyan. 2005. Simple but predictive protein models. Trends Biotechnol. 23:450-455.
-
(2005)
Trends Biotechnol
, vol.23
, pp. 450-455
-
-
Ding, F.1
Dokholyan, N.V.2
-
33
-
-
0036927818
-
Direct molecular dynamics observation of protein folding transition state ensemble
-
Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 2002. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83:3525-3532.
-
(2002)
Biophys. J
, vol.83
, pp. 3525-3532
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.E.4
Shakhnovich, E.I.5
-
34
-
-
42749108544
-
Discrete molecular dynamics simulations of peptide aggregation
-
Peng, S., F. Ding, B. Urbanc, S. V. Buldyrev, L. Cruz, H. E. Stanley, and N. V. Dokholyan. 2004. Discrete molecular dynamics simulations of peptide aggregation. Phys. Rev. E. 69:041908.
-
(2004)
Phys. Rev. E
, vol.69
, pp. 041908
-
-
Peng, S.1
Ding, F.2
Urbanc, B.3
Buldyrev, S.V.4
Cruz, L.5
Stanley, H.E.6
Dokholyan, N.V.7
-
35
-
-
0141480850
-
Mechanism for the α-helix to β-hairpin transition
-
Ding, F., J. M. Borreguero, S. V. Buldyrey, H. E. Stanley, and N. V. Dokholyan. 2003. Mechanism for the α-helix to β-hairpin transition. Proteins. 53:220-228.
-
(2003)
Proteins
, vol.53
, pp. 220-228
-
-
Ding, F.1
Borreguero, J.M.2
Buldyrey, S.V.3
Stanley, H.E.4
Dokholyan, N.V.5
-
36
-
-
11244291006
-
Folding Trpcage to NMR resolution native structure using a coarse-grained protein model
-
Ding, F., S. V. Buldyrev, and N. V. Dokholyan. 2005. Folding Trpcage to NMR resolution native structure using a coarse-grained protein model. Biophys. J. 88:147-155.
-
(2005)
Biophys. J
, vol.88
, pp. 147-155
-
-
Ding, F.1
Buldyrev, S.V.2
Dokholyan, N.V.3
-
37
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond, T. J., and C. A. Davey. 2003. The structure of DNA in the nucleosome core. Nature. 423:145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
38
-
-
0031475159
-
Folding thermodynamics of a model three-helix-bundle protein
-
Zhou, Y., and M. Karplus. 1997. Folding thermodynamics of a model three-helix-bundle protein. Proc. Natl. Acad. Sci. USA. 94:14429-14432.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 14429-14432
-
-
Zhou, Y.1
Karplus, M.2
-
39
-
-
33750411214
-
iFold: A platform for interactive folding simulations of proteins
-
Sharma, S., F. Ding, H. Nie, D. Watson, A. Unnithan, J. Lopp, D. Pozefsky, and N. V. Dokholyan. 2006. iFold: a platform for interactive folding simulations of proteins. Bioinformatics. 22:2693-2694.
-
(2006)
Bioinformatics
, vol.22
, pp. 2693-2694
-
-
Sharma, S.1
Ding, F.2
Nie, H.3
Watson, D.4
Unnithan, A.5
Lopp, J.6
Pozefsky, D.7
Dokholyan, N.V.8
-
41
-
-
0003474751
-
-
Cambridge University Press, Cambridge, UK
-
Press, W. H., B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. 1988. Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, Cambridge, UK.
-
(1988)
Numerical Recipes in C: The Art of Scientific Computing
-
-
Press, W.H.1
Flannery, B.P.2
Teukolsky, S.A.3
Vetterling, W.T.4
-
42
-
-
33644753038
-
Topological determinants of protein domain swapping
-
Ding, F., K. C. Prutzman, S. L. Campbell, and N. V. Dokholyan. 2006. Topological determinants of protein domain swapping. Structure. 14:5-14.
-
(2006)
Structure
, vol.14
, pp. 5-14
-
-
Ding, F.1
Prutzman, K.C.2
Campbell, S.L.3
Dokholyan, N.V.4
-
43
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack, R. L., Jr., and F. E. Cohen. 1997. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6:1661-1681.
-
(1997)
Protein Sci
, vol.6
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
44
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
45
-
-
0035704707
-
Role of DNA sequence in nucleosome stability and dynamics
-
Widom, J. 2001. Role of DNA sequence in nucleosome stability and dynamics. Q. Rev. Biophys. 34:269-324.
-
(2001)
Q. Rev. Biophys
, vol.34
, pp. 269-324
-
-
Widom, J.1
-
47
-
-
0037120092
-
Coarse-graining in polymer simulation: From the atomistic to the mesoscopic scale and back
-
Muller-Plathe, F. 2002. Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. ChemPhysChem. 3:755-769.
-
(2002)
ChemPhysChem
, vol.3
, pp. 755-769
-
-
Muller-Plathe, F.1
-
48
-
-
0033527768
-
Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis
-
Zhou, Y., and M. Karplus. 1999. Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis. J. Mol. Biol. 293:917-951.
-
(1999)
J. Mol. Biol
, vol.293
, pp. 917-951
-
-
Zhou, Y.1
Karplus, M.2
-
49
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe, N. M., R. A. Laskowski, and J. M. Thornton. 2001. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29:2860-2874.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
50
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
Luscombe, N. M., and J. M. Thornton. 2002. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol. 320:991-1009.
-
(2002)
J. Mol. Biol
, vol.320
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
51
-
-
33747500567
-
A genomic code for nucleosome positioning
-
Segal, E., Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I. K. Moore, J. P. Wang, and J. Widom. 2006. A genomic code for nucleosome positioning. Nature. 442:772-778.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thastrom, A.4
Field, Y.5
Moore, I.K.6
Wang, J.P.7
Widom, J.8
-
52
-
-
0037126715
-
The effect of salts on the stability of the H2A-H2B histone dimer
-
Gloss, L. M., and B. J. Placek. 2002. The effect of salts on the stability of the H2A-H2B histone dimer. Biochemistry. 41:14951-14959.
-
(2002)
Biochemistry
, vol.41
, pp. 14951-14959
-
-
Gloss, L.M.1
Placek, B.J.2
-
53
-
-
0031707751
-
Alteration of nucleosome structure as a mechanism of transcriptional regulation
-
Workman, J. L., and R. E. Kingston. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545-579.
-
(1998)
Annu. Rev. Biochem
, vol.67
, pp. 545-579
-
-
Workman, J.L.1
Kingston, R.E.2
-
54
-
-
0023660730
-
Spectroscopic studies on histone-DNA interactions. II. Three transitions in nucleosomes resolved by salt-titration
-
Oohara, I., and A. Wada. 1987. Spectroscopic studies on histone-DNA interactions. II. Three transitions in nucleosomes resolved by salt-titration. J. Mol. Biol. 196:399-411.
-
(1987)
J. Mol. Biol
, vol.196
, pp. 399-411
-
-
Oohara, I.1
Wada, A.2
-
55
-
-
0024537375
-
Salt-induced release of DNA from nucleosome core particles
-
Yager, T. D., C. T. McMurray, and K. E. van Holde. 1989. Salt-induced release of DNA from nucleosome core particles. Biochemistry. 28:2271-2281.
-
(1989)
Biochemistry
, vol.28
, pp. 2271-2281
-
-
Yager, T.D.1
McMurray, C.T.2
van Holde, K.E.3
-
56
-
-
0036221883
-
Salt-induced conformation and interaction changes of nucleosome core particles
-
Mangenot, S., A. Leforestier, P. Vachette, D. Durand, and F. Livolant. 2002. Salt-induced conformation and interaction changes of nucleosome core particles. Biophys. J. 82:345-356.
-
(2002)
Biophys. J
, vol.82
, pp. 345-356
-
-
Mangenot, S.1
Leforestier, A.2
Vachette, P.3
Durand, D.4
Livolant, F.5
-
57
-
-
0142185497
-
Phase diagram of nucleosome core particles
-
Mangenot, S., A. Leforestier, D. Durand, and F. Livolant. 2003. Phase diagram of nucleosome core particles. J. Mol. Biol. 333:907-916.
-
(2003)
J. Mol. Biol
, vol.333
, pp. 907-916
-
-
Mangenot, S.1
Leforestier, A.2
Durand, D.3
Livolant, F.4
-
58
-
-
0030606239
-
The transcriptional coactivators p300 and CBP are histone acetyltransferases
-
Ogryzko, V. V., R. L. Schiltz, V. Russanova, B. H. Howard, and Y. Nakatani. 1996. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell. 87:953-959.
-
(1996)
Cell
, vol.87
, pp. 953-959
-
-
Ogryzko, V.V.1
Schiltz, R.L.2
Russanova, V.3
Howard, B.H.4
Nakatani, Y.5
-
59
-
-
0034644473
-
Signaling to chromatin through histone modifications
-
Cheung, P., C. D. Allis, and P. Sassone-Corsi. 2000. Signaling to chromatin through histone modifications. Cell. 103:263-271.
-
(2000)
Cell
, vol.103
, pp. 263-271
-
-
Cheung, P.1
Allis, C.D.2
Sassone-Corsi, P.3
-
60
-
-
0024573304
-
Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome
-
Ausio, J., F. Dong, and K. E. van Holde. 1989. Use of selectively trypsinized nucleosome core particles to analyze the role of the histone "tails" in the stabilization of the nucleosome. J. Mol. Biol. 206:451-463.
-
(1989)
J. Mol. Biol
, vol.206
, pp. 451-463
-
-
Ausio, J.1
Dong, F.2
van Holde, K.E.3
-
61
-
-
35949036748
-
Some problems of statistical physics of polymer-chains with volume interaction
-
Lifshitz, I. M., A. Y. Grosberg, and A. R. Khokhlov. 1978. Some problems of statistical physics of polymer-chains with volume interaction. Rev. Mod. Phys. 50:683-713.
-
(1978)
Rev. Mod. Phys
, vol.50
, pp. 683-713
-
-
Lifshitz, I.M.1
Grosberg, A.Y.2
Khokhlov, A.R.3
-
62
-
-
0038605538
-
Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system
-
Zheng, C., and J. J. Hayes. 2003. Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system. J. Biol. Chem. 278:24217-24224.
-
(2003)
J. Biol. Chem
, vol.278
, pp. 24217-24224
-
-
Zheng, C.1
Hayes, J.J.2
-
63
-
-
1642453556
-
Probing core histone tail-DNA interactions in a model dinucleosome system
-
Zheng, C., and J. J. Hayes. 2004. Probing core histone tail-DNA interactions in a model dinucleosome system. Methods Enzymol. 375:179-193.
-
(2004)
Methods Enzymol
, vol.375
, pp. 179-193
-
-
Zheng, C.1
Hayes, J.J.2
-
64
-
-
25844484588
-
Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array
-
Zheng, C., X. Lu, J. C. Hansen, and J. J. Hayes. 2005. Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array. J. Biol. Chem. 280:33552-33557.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 33552-33557
-
-
Zheng, C.1
Lu, X.2
Hansen, J.C.3
Hayes, J.J.4
-
65
-
-
0036923039
-
Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism
-
Ding, F., N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 2002. Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. J. Mol. Biol. 324:851-857.
-
(2002)
J. Mol. Biol
, vol.324
, pp. 851-857
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.E.4
Shakhnovich, E.I.5
-
66
-
-
10644242867
-
Molecular dynamics simulation of amyloid beta dimer formation
-
Urbanc, B., L. Cruz, F. Ding, D. Sammond, S. Khare, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan. 2004. Molecular dynamics simulation of amyloid beta dimer formation. Biophys. J. 87:2310-2321.
-
(2004)
Biophys. J
, vol.87
, pp. 2310-2321
-
-
Urbanc, B.1
Cruz, L.2
Ding, F.3
Sammond, D.4
Khare, S.5
Buldyrev, S.V.6
Stanley, H.E.7
Dokholyan, N.V.8
-
67
-
-
3042857533
-
Multiple folding pathways of the SH3 domain
-
Borreguero, J. M., F. Ding, S. V. Buldyrev, H. E. Stanley, and N. V. Dokholyan. 2004. Multiple folding pathways of the SH3 domain. Biophys. J. 87:521-533.
-
(2004)
Biophys. J
, vol.87
, pp. 521-533
-
-
Borreguero, J.M.1
Ding, F.2
Buldyrev, S.V.3
Stanley, H.E.4
Dokholyan, N.V.5
-
68
-
-
21744448828
-
Scaling behavior and structure of denatured proteins
-
Ding, F., R. K. Jha, and N. V. Dokholyan. 2005. Scaling behavior and structure of denatured proteins. Structure. 13:1047-1054.
-
(2005)
Structure
, vol.13
, pp. 1047-1054
-
-
Ding, F.1
Jha, R.K.2
Dokholyan, N.V.3
-
69
-
-
0242662235
-
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis
-
Khare, S. D., F. Ding, and N. V. Dokholyan. 2003. Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J. Mol. Biol. 334:515-525.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 515-525
-
-
Khare, S.D.1
Ding, F.2
Dokholyan, N.V.3
-
70
-
-
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
-
71
-
-
11444262202
-
Rapid spontaneous accessibility of nucleosomal DNA
-
Li, G., M. Levitus, C. Bustamante, and J. Widom. 2005. Rapid spontaneous accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol. 12:46-53.
-
(2005)
Nat. Struct. Mol. Biol
, vol.12
, pp. 46-53
-
-
Li, G.1
Levitus, M.2
Bustamante, C.3
Widom, J.4
-
72
-
-
0030999604
-
Histone octamer function in vivo: Mutations in the dimertetramer interfaces disrupt both gene activation and repression
-
Santisteban, M. S., G. Arents, E. N. Moudrianakis, and M. M. Smith. 1997. Histone octamer function in vivo: mutations in the dimertetramer interfaces disrupt both gene activation and repression. EMBO J. 16:2493-2506.
-
(1997)
EMBO J
, vol.16
, pp. 2493-2506
-
-
Santisteban, M.S.1
Arents, G.2
Moudrianakis, E.N.3
Smith, M.M.4
-
73
-
-
33744472502
-
High-resolution structure of the native histone octamer
-
Wood, C. M., J. M. Nicholson, S. J. Lambert, L. Chantalat, C. D. Reynolds, and J. P. Baldwin. 2005. High-resolution structure of the native histone octamer. Acta Crystallogr. F. 61:541-545.
-
(2005)
Acta Crystallogr. F
, vol.61
, pp. 541-545
-
-
Wood, C.M.1
Nicholson, J.M.2
Lambert, S.J.3
Chantalat, L.4
Reynolds, C.D.5
Baldwin, J.P.6
-
74
-
-
0347914548
-
Redefinition of the cleavage sites of DNase I on the nucleosome core particle
-
Cousins, D. J., S. A. Islam, M. R. Sanderson, Y. G. Proykova, C. Crane-Robinson, and D. Z. Staynov. 2004. Redefinition of the cleavage sites of DNase I on the nucleosome core particle. J. Mol. Biol. 335:1199-1211.
-
(2004)
J. Mol. Biol
, vol.335
, pp. 1199-1211
-
-
Cousins, D.J.1
Islam, S.A.2
Sanderson, M.R.3
Proykova, Y.G.4
Crane-Robinson, C.5
Staynov, D.Z.6
-
75
-
-
0031741231
-
Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding
-
Mutskov, V., D. Gerber, D. Angelov, J. Ausio, J. Workman, and S. Dimitrov. 1998. Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding. Mol. Cell. Biol. 18:6293-6304.
-
(1998)
Mol. Cell. Biol
, vol.18
, pp. 6293-6304
-
-
Mutskov, V.1
Gerber, D.2
Angelov, D.3
Ausio, J.4
Workman, J.5
Dimitrov, S.6
-
76
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
-
Solomon, M. J., P. L. Larsen, and A. Varshavsky. 1988. Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell. 53:937-947.
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
Larsen, P.L.2
Varshavsky, A.3
-
77
-
-
0033388858
-
In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment
-
Kuo, M. H., and C. D. Allis. 1999. In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods. 19:425-433.
-
(1999)
Methods
, vol.19
, pp. 425-433
-
-
Kuo, M.H.1
Allis, C.D.2
-
78
-
-
0028341116
-
Rearrangement of the histone H2A C-terminal domain in the nucleosome
-
Usachenko, S. I., S. G. Bavykin, I. M. Gavin, and E. M. Bradbury. 1994. Rearrangement of the histone H2A C-terminal domain in the nucleosome. Proc. Natl. Acad. Sci. USA. 91:6845-6849.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 6845-6849
-
-
Usachenko, S.I.1
Bavykin, S.G.2
Gavin, I.M.3
Bradbury, E.M.4
-
79
-
-
0034634558
-
Acetylation increases the α-helical content of the histone tails of the nucleosome
-
Wang, X., S. C. Moore, M. Laszckzak, and J. Ausio. 2000. Acetylation increases the α-helical content of the histone tails of the nucleosome. J. Biol. Chem. 275:35013-35020.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 35013-35020
-
-
Wang, X.1
Moore, S.C.2
Laszckzak, M.3
Ausio, J.4
-
80
-
-
0026495432
-
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
-
Smith, S. B., L. Finzi, and C. Bustamante. 1992. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science. 258:1122-1126.
-
(1992)
Science
, vol.258
, pp. 1122-1126
-
-
Smith, S.B.1
Finzi, L.2
Bustamante, C.3
-
81
-
-
0030024985
-
Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
82
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
Cloutier, T. E., and J. Widom. 2004. Spontaneous sharp bending of double-stranded DNA. Mol. Cell. 14:355-362.
-
(2004)
Mol. Cell
, vol.14
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
83
-
-
41349115456
-
Phase diagram for unzipping DNA with long-range interactions
-
Mukamel, E. A., and E. I. Shakhnovich. 2002. Phase diagram for unzipping DNA with long-range interactions. Phys. Rev. E. 66:032901.
-
(2002)
Phys. Rev. E
, vol.66
, pp. 032901
-
-
Mukamel, E.A.1
Shakhnovich, E.I.2
-
85
-
-
0000420829
-
Stretching DNA: Role of electrostatic interactions
-
Lee, N., and D. Thirumalai. 1999. Stretching DNA: role of electrostatic interactions. Eur. Phys. J. B. 12:599-605.
-
(1999)
Eur. Phys. J. B
, vol.12
, pp. 599-605
-
-
Lee, N.1
Thirumalai, D.2
-
86
-
-
2142753980
-
Pulling-speed-dependent force-extension profiles for semiflexible chains
-
Lee, N. K., and D. Thirumalai. 2004. Pulling-speed-dependent force-extension profiles for semiflexible chains. Biophys. J. 86:2641-2649.
-
(2004)
Biophys. J
, vol.86
, pp. 2641-2649
-
-
Lee, N.K.1
Thirumalai, D.2
-
88
-
-
0030798605
-
Clues and consequences of DNA bending in transcription
-
Perez-Martin, J., and V. de Lorenzo. 1997. Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol. 51:593-628.
-
(1997)
Annu. Rev. Microbiol
, vol.51
, pp. 593-628
-
-
Perez-Martin, J.1
de Lorenzo, V.2
-
90
-
-
0032522139
-
DNA bending: The prevalence of kinkiness and the virtues of normality
-
Dickerson, R. E. 1998. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26:1906-1926.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1906-1926
-
-
Dickerson, R.E.1
-
91
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson, W. K., A. A. Gorin, X. J. Lu, L. M. Hock, and V. B. Zhurkin. 1998. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA. 95:11163-11168.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
92
-
-
0032698634
-
Transcription activation by catabolite activator protein (CAP)
-
Busby, S., and R. H. Ebright. 1999. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:199-213.
-
(1999)
J. Mol. Biol
, vol.293
, pp. 199-213
-
-
Busby, S.1
Ebright, R.H.2
-
93
-
-
0033548524
-
Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability
-
Anselmi, C., G. Bocchinfuso, S. P. De, M. Savino, and A. Scipioni. 1999. Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability. J. Mol. Biol. 286:1293-1301.
-
(1999)
J. Mol. Biol
, vol.286
, pp. 1293-1301
-
-
Anselmi, C.1
Bocchinfuso, G.2
De, S.P.3
Savino, M.4
Scipioni, A.5
-
94
-
-
3542998667
-
Nucleosomes facilitate their own invasion
-
Li, G., and J. Widom. 2004. Nucleosomes facilitate their own invasion. Nat. Struct. Mol. Biol. 11:763-769.
-
(2004)
Nat. Struct. Mol. Biol
, vol.11
, pp. 763-769
-
-
Li, G.1
Widom, J.2
-
95
-
-
0026006495
-
Progression of the cell cycle through mitosis leads to abortion of nascent transcripts
-
Shermoen, A. W., and P. H. O'Farrell. 1991. Progression of the cell cycle through mitosis leads to abortion of nascent transcripts. Cell. 67:303-310.
-
(1991)
Cell
, vol.67
, pp. 303-310
-
-
Shermoen, A.W.1
O'Farrell, P.H.2
-
96
-
-
0037042149
-
A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions
-
Fukunaga, H., J. Takimoto, and M. Doi. 2002. A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions. J. Chem. Phys. 116:8183-8190.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 8183-8190
-
-
Fukunaga, H.1
Takimoto, J.2
Doi, M.3
-
97
-
-
0242407193
-
Phylogenomics of the nucleosome
-
Malik, H. S., and S. Henikoff. 2003. Phylogenomics of the nucleosome. Nat. Struct. Biol. 10:882-891.
-
(2003)
Nat. Struct. Biol
, vol.10
, pp. 882-891
-
-
Malik, H.S.1
Henikoff, S.2
-
98
-
-
8844281536
-
H2A.Z alters the nucleosome surface to promote HP1α-mediated chromatin fiber folding
-
Fan, J. Y., D. Rangasamy, K. Luger, and D. J. Tremethick. 2004. H2A.Z alters the nucleosome surface to promote HP1α-mediated chromatin fiber folding. Mol. Cell. 16:655-661.
-
(2004)
Mol. Cell
, vol.16
, pp. 655-661
-
-
Fan, J.Y.1
Rangasamy, D.2
Luger, K.3
Tremethick, D.J.4
-
99
-
-
0037058948
-
Histone H3 variants specify modes of chromatin assembly
-
Ahmad, K., and S. Henikoff. 2002. Histone H3 variants specify modes of chromatin assembly. Proc. Natl. Acad. Sci. USA. 99(Suppl. 4):16477-16484.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, Issue.SUPPL. 4
, pp. 16477-16484
-
-
Ahmad, K.1
Henikoff, S.2
-
100
-
-
0036299092
-
The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly
-
Ahmad, K., and S. Henikoff. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell. 9:1191-1200.
-
(2002)
Mol. Cell
, vol.9
, pp. 1191-1200
-
-
Ahmad, K.1
Henikoff, S.2
-
101
-
-
0035918170
-
Effects of histone acetylation on the solubility and folding of the chromatin fiber
-
Wang, X., C. He, S. C. Moore, and J. Ausio. 2001. Effects of histone acetylation on the solubility and folding of the chromatin fiber. J. Biol. Chem. 276:12764-12768.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 12764-12768
-
-
Wang, X.1
He, C.2
Moore, S.C.3
Ausio, J.4
-
102
-
-
0029780079
-
What determines the folding of the chromatin fiber?
-
van Holde, K., and J. Zlatanova. 1996. What determines the folding of the chromatin fiber? Proc. Natl. Acad. Sci. USA. 93:10548-10555.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 10548-10555
-
-
van Holde, K.1
Zlatanova, J.2
-
103
-
-
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
-
104
-
-
0034614436
-
Pulling chromatin fibers: Computer simulations of direct physical micromanipulations
-
Katritch, V., C. Bustamante, and W. K. Olson. 2000. Pulling chromatin fibers: computer simulations of direct physical micromanipulations. J. Mol. Biol. 295:29-40.
-
(2000)
J. Mol. Biol
, vol.295
, pp. 29-40
-
-
Katritch, V.1
Bustamante, C.2
Olson, W.K.3
-
105
-
-
0036253737
-
Mechanical model of the nucleosome and chromatin
-
Bishop, T. C., and O. O. Zhmudsky. 2002. Mechanical model of the nucleosome and chromatin. J. Biomol. Struct. Dyn. 19:877-887.
-
(2002)
J. Biomol. Struct. Dyn
, vol.19
, pp. 877-887
-
-
Bishop, T.C.1
Zhmudsky, O.O.2
-
106
-
-
18844427832
-
Molecular dynamics simulations of a nucleosome and free DNA
-
Bishop, T. C. 2005. Molecular dynamics simulations of a nucleosome and free DNA. J. Biomol. Struct. Dyn. 22:673-686.
-
(2005)
J. Biomol. Struct. Dyn
, vol.22
, pp. 673-686
-
-
Bishop, T.C.1
|