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Volumn , Issue , 2006, Pages 605-634

Chromatin simulations

Author keywords

Brownian dynamics; elasticity theory; Monte Carlo models; nucleosome unrolling; persistence length; single molecule stretching; Wormlike polymer chain

Indexed keywords


EID: 84873909965     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-4851-3_24     Document Type: Chapter
Times cited : (5)

References (99)
  • 1
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 å resolution
    • Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389, 251-260.
    • (1997) Nature , vol.389 , pp. 251-260
    • Luger, K.1    Mäder, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5
  • 2
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution
    • Davey, C. A., Sargent, D. F., Luger, K., Maeder, A. W. & Richmond, T. J. (2002). Solvent mediated 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
  • 3
    • 0037992395 scopus 로고    scopus 로고
    • The structure of dna in the nucleosome core
    • Richmond, T. J. & Davey, C. A. (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
  • 4
    • 21844436803 scopus 로고    scopus 로고
    • X-ray structure of a tetranucleosome and its implications for the chromatin fibre
    • Schalch, T., Duda, S., Sargent, D. F. & Richmond, T. J. (2005). X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436, 138-141.
    • (2005) Nature , vol.436 , pp. 138-141
    • Schalch, T.1    Duda, S.2    Sargent, D.F.3    Richmond, T.J.4
  • 5
    • 0000878535 scopus 로고
    • Solenoidal model for superstructure in chromatin
    • Finch, J. T. & Klug, A. (1976). Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA 73, 1897-1901.
    • (1976) Proc Natl Acad Sci USA , vol.73 , pp. 1897-1901
    • Finch, J.T.1    Klug, A.2
  • 6
    • 0018581187 scopus 로고
    • Involvement of histone h1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin
    • Thoma, F., Koller, T. & Klug, A. (1979). Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol 83, 403-427.
    • (1979) J Cell Biol , vol.83 , pp. 403-427
    • Thoma, F.1    Koller, T.2    Klug, A.3
  • 7
    • 0022273023 scopus 로고
    • Structure of the 300a chromatin filament: X-ray diffraction from oriented samples
    • Widom, J. & Klug, A. (1985). Structure of the 300A chromatin filament: X-ray diffraction from oriented samples. Cell 43, 207-213.
    • (1985) Cell , vol.43 , pp. 207-213
    • Widom, J.1    Klug, A.2
  • 8
    • 0027517831 scopus 로고
    • A chromatin folding model that incorporates linker variability generates fibers resembling the native structures
    • Woodcock, C. L., Grigoryev, S. A., Horowitz, R. A. & Whitaker, N. (1993). A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc Natl Acad Sci USA 90, 9021-9025.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 9021-9025
    • Woodcock, C.L.1    Grigoryev, S.A.2    Horowitz, R.A.3    Whitaker, N.4
  • 9
    • 0028221098 scopus 로고
    • The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon
    • Horowitz, R. A., Agard, D. A., Sedat, J. W. & Woodcock, C. L. (1994). The three-dimensional architecture of chromatin in situ: Electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J Cell Biol 125, 1-10.
    • (1994) J Cell Biol , vol.125 , pp. 1-10
    • Horowitz, R.A.1    Agard, D.A.2    Sedat, J.W.3    Woodcock, C.L.4
  • 10
    • 0035313770 scopus 로고    scopus 로고
    • Higher-order structure of chromatin and chromosomes
    • Woodcock, C. L. & Dimitrov, S. (2001). Higher-order structure of chromatin and chromosomes. Curr Opin Genet Dev 11, 130-135.
    • (2001) Curr Opin Genet Dev , vol.11 , pp. 130-135
    • Woodcock, C.L.1    Dimitrov, S.2
  • 11
    • 0027960444 scopus 로고
    • Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy
    • Leuba, S. H., Yang, G., Robert, C., Samori, B., van Holde, K., Zlatanova, J. & Bustamante, C. (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
  • 12
    • 0032564478 scopus 로고    scopus 로고
    • Nucleosomes, linker dna, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin
    • Bednar, J., Horowitz, R. A., Grigoryev, S. A., Carruthers, L. M., Hansen, J. C., Koster, A. J. & Woodcock, C. L. (1998). Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci USA 95, 14173-14178.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 14173-14178
    • Bednar, J.1    Horowitz, R.A.2    Grigoryev, S.A.3    Carruthers, L.M.4    Hansen, J.C.5    Koster, A.J.6    Woodcock, C.L.7
  • 13
    • 0035066656 scopus 로고    scopus 로고
    • DNA folding: Structural and mechanical properties of the two-angle model for chromatin
    • Schiessel, H., Gelbart, W. M. & Bruinsma, R. (2001). DNA folding: Structural and mechanical properties of the two-angle model for chromatin. Biophys J 80, 1940-1956.
    • (2001) Biophys J , vol.80 , pp. 1940-1956
    • Schiessel, H.1    Gelbart, W.M.2    Bruinsma, R.3
  • 14
    • 0031854165 scopus 로고    scopus 로고
    • Monte carlo simulation of the production of short dna fragments by low-linear energy transfer radiation using higher-order dna models
    • Friedland, W., Jacob, P., Paretzke, H. G. & Stork, T. (1998). Monte Carlo simulation of the production of short DNA fragments by low-linear energy transfer radiation using higher-order DNA models. Radiation Research 150, 170-182.
    • (1998) Radiation Research , vol.150 , pp. 170-182
    • Friedland, W.1    Jacob, P.2    Paretzke, H.G.3    Stork, T.4
  • 15
    • 0032553448 scopus 로고    scopus 로고
    • Chromatin conformation in living cells: Support for a zig-zag model of the 30 nm chromatin fiber
    • Rydberg, B., Holley, W. R., Mian, I. S. & Chatterjee, A. (1998). Chromatin Conformation in Living Cells: Support for a Zig-Zag Model of the 30 nm Chromatin Fiber. J Mol Biol 284, 71-84.
    • (1998) J Mol Biol , vol.284 , pp. 71-84
    • Rydberg, B.1    Holley, W.R.2    Mian, I.S.3    Chatterjee, A.4
  • 16
    • 9444297879 scopus 로고    scopus 로고
    • Nucleosome arrays reveal the two-start organization of the chromatin fiber
    • Dorigo, B., Schalch, T., Kulangara, A., Duda, S., Schroeder, R. R. & Richmond, T. J. (2004). Nucleosome arrays reveal the two-start organization of the chromatin fiber. Science 306, 1571-1573.
    • (2004) Science , vol.306 , pp. 1571-1573
    • Dorigo, B.1    Schalch, T.2    Kulangara, A.3    Duda, S.4    Schroeder, R.R.5    Richmond, T.J.6
  • 17
    • 20444377701 scopus 로고    scopus 로고
    • Electrostatic mechanism of nucleosomal array folding revealed by computer simulation
    • Sun, J., Zhang, Q. & Schlick, T. (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
  • 19
  • 20
    • 0036099317 scopus 로고    scopus 로고
    • Computer simulation of the 30-nanometer chromatin fiber
    • Wedemann, G. & Langowski, J. (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
  • 21
    • 0035093560 scopus 로고    scopus 로고
    • Computational modeling predicts the structure and dynamics of chromatin fiber
    • Beard, D. A. & Schlick, T. (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
  • 22
    • 0034614436 scopus 로고    scopus 로고
    • Pulling chromatin fibers: Computer simulations of direct physical micromanipulations
    • Katritch, V., Bustamante, C. & Olson, V. K. (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, V.K.3
  • 24
    • 0031880233 scopus 로고    scopus 로고
    • A brownian dynamics program for the simulation of linear and circular dna and other wormlike chain polyelectrolytes
    • Klenin, K., Merlitz, H. & Langowski, J. (1998). A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys J 74, 780-788.
    • (1998) Biophys J , vol.74 , pp. 780-788
    • Klenin, K.1    Merlitz, H.2    Langowski, J.3
  • 25
    • 0000579305 scopus 로고    scopus 로고
    • DNA persistence length revisited
    • Lu, Y., Weers, B. & Stellwagen, N. C. (2001). DNA persistence length revisited. Biopolymers 61, 261-275.
    • (2001) Biopolymers , vol.61 , pp. 261-275
    • Lu, Y.1    Weers, B.2    Stellwagen, N.C.3
  • 26
    • 36749121933 scopus 로고
    • Theory of twisting and bending of chain macromolecules: Analysis of the fluorescence depolarization of dna
    • Barkley, M. D. & Zimm, B. H. (1979). Theory of twisting and bending of chain macromolecules: Analysis of the fluorescence depolarization of DNA. J Chem Phys 70, 2991-3007.
    • (1979) J Chem Phys , vol.70 , pp. 2991-3007
    • Barkley, M.D.1    Zimm, B.H.2
  • 27
    • 0025366778 scopus 로고
    • Dependence of the torsional rigidity of dna on base composition
    • Fujimoto, B. S. & Schurr, J. M. (1990). Dependence of the torsional rigidity of DNA on base composition. Nature 344, 175-177.
    • (1990) Nature , vol.344 , pp. 175-177
    • Fujimoto, B.S.1    Schurr, J.M.2
  • 28
    • 0000166387 scopus 로고
    • Fluorescence studies of nucleic acids: Dynamics, rigidities and structures
    • Lakowicz, J. R., ed., Plenum Press, New York
    • Schurr, J. M., Fujimoto, B. S., Wu, P. & Song, L. (1992). Fluorescence studies of nucleic acids: Dynamics, rigidities and structures. In Topics in Fluorescence Spectroscopy (Lakowicz, J. R., ed.), Vol. 3, pp. 137-229. Plenum Press, New York.
    • (1992) Topics in Fluorescence Spectroscopy , vol.3 , pp. 137-229
    • Schurr, J.M.1    Fujimoto, B.S.2    Wu, P.3    Song, L.4
  • 29
    • 0021022977 scopus 로고
    • Energetics of dna twisting. i. relation between twist and cyclization probability
    • Shore, D. & Baldwin, R. L. (1983). Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol 179, 957-981.
    • (1983) J Mol Biol , vol.179 , pp. 957-981
    • Shore, D.1    Baldwin, R.L.2
  • 30
    • 0021320555 scopus 로고
    • Torsonal rigidity of dna and length dependence of the free energy of dna supercoiling
    • Horowitz, D. S. & Wang, J. C. (1984). Torsonal Rigidity of DNA and Length Dependence of the Free Energy of DNA Supercoiling. J. Mol. Biol. 173, 75-91.
    • (1984) J. Mol. Biol. , vol.173 , pp. 75-91
    • Horowitz, D.S.1    Wang, J.C.2
  • 31
    • 0025355712 scopus 로고
    • Application of the method of phage t4 dna ligase-catalyzed ring-closure to the study of dna structure i.nacl-dependence of dna flexibility and helical repeat
    • Taylor, W. H. & Hagerman, P. J. (1990). Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure I.NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212, 363-376.
    • (1990) J. Mol. Biol. , vol.212 , pp. 363-376
    • Taylor, W.H.1    Hagerman, P.J.2
  • 33
    • 0030024985 scopus 로고    scopus 로고
    • Overstretching b-dna: The elastic response of individual double-stranded and single-stranded dna molecules
    • Smith, S. B., Cui, Y. & Bustamante, C. (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
  • 34
    • 0034625311 scopus 로고    scopus 로고
    • Sequence-dependent elastic properties of dna
    • Lankaš, F., Šponer, J., Hobza, P. & Langowski, J. (2000). Sequence-dependent Elastic Properties of DNA. J Mol Biol 299, 695-709.
    • (2000) J Mol Biol , vol.299 , pp. 695-709
    • Lankaš, F.1    Šponer, J.2    Hobza, P.3    Langowski, J.4
  • 35
    • 0036225151 scopus 로고    scopus 로고
    • Critical effect of the n2 amino group on structure, dynamics, and elasticity of dna polypurine tracts
    • Lankaš, F., Cheatham, I. T., Spackova, N., Hobza, P., Langowski, J. & Šponer, J. (2002). Critical effect of the n2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts. Biophys J 82, 2592-2609.
    • (2002) Biophys J , vol.82 , pp. 2592-2609
    • Lankaš, F.1    Cheatham, I.T.2    Spackova, N.3    Hobza, P.4    Langowski, J.5    Šponer, J.6
  • 36
    • 0017380736 scopus 로고
    • Electrical double layer, zeta potential, and electrophoretic charge of double-stranded dna
    • Schellman, J. A. & Stigter, D. (1977). Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA. Biopolymers 16, 1415-1434.
    • (1977) Biopolymers , vol.16 , pp. 1415-1434
    • Schellman, J.A.1    Stigter, D.2
  • 37
    • 0028819366 scopus 로고
    • Modulation of intramolecular interactions in superhelical dna by curved sequences: A monte carlo simulation study
    • Klenin, K. V., Frank-Kamenetskii, M. D. & Langowski, J. (1995). Modulation of intramolecular interactions in superhelical DNA by curved sequences: A Monte Carlo simulation study. Biophys J 68, 81-88.
    • (1995) Biophys J , vol.68 , pp. 81-88
    • Klenin, K.V.1    Frank-Kamenetskii, M.D.2    Langowski, J.3
  • 38
    • 0031555013 scopus 로고    scopus 로고
    • Comparison of hard-cylinder and screened coulomb interactions in the modeling of supercoiled dnas
    • Delrow, J. J., Gebe, J. A. & Schurr, J. M. (1997). Comparison of hard-cylinder and screened Coulomb interactions in the modeling of supercoiled DNAs. Biopolymers 42, 455-470.
    • (1997) Biopolymers , vol.42 , pp. 455-470
    • Delrow, J.J.1    Gebe, J.A.2    Schurr, J.M.3
  • 39
    • 0031793539 scopus 로고    scopus 로고
    • Salt-dependent dna superhelix diameter studied by small angle neutron scattering measurements and monte carlo simulations
    • Hammermann, M., Brun, N., Klenin, K. V., May, R., Toth, K. & Langowski, J. (1998). Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations. Biophys J 75, 3057-3063
    • (1998) Biophys J , vol.75 , pp. 3057-3063
    • Hammermann, M.1    Brun, N.2    Klenin, K.V.3    May, R.4    Toth, K.5    Langowski, J.6
  • 40
    • 0027279063 scopus 로고
    • Probability of dna knotting and the effective diameter of the dna double helix
    • Rybenkov, V. V., Cozzarelli, N. R. & Vologodskii, A. V. (1993). Probability of DNA knotting and the effective diameter of the DNA double helix. Proc Natl Acad Sci USA 90, 5307-5311
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 5307-5311
    • Rybenkov, V.V.1    Cozzarelli, N.R.2    Vologodskii, A.V.3
  • 41
    • 0030740986 scopus 로고    scopus 로고
    • The effect of ionic conditions on dna helical repeat, effective diameter and free energy of supercoiling
    • Rybenkov, V. V., Vologodskii, A. V. & Cozzarelli, N. R. (1997). The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucl Acids Res 25, 1412-1418.
    • (1997) Nucl Acids Res , vol.25 , pp. 1412-1418
    • Rybenkov, V.V.1    Vologodskii, A.V.2    Cozzarelli, N.R.3
  • 42
    • 0030844210 scopus 로고    scopus 로고
    • Salt effects on the structure and internal dynamics of superhelical dnas studied by light scattering and brownian dynamics
    • Hammermann, M., Steinmaier, C., Merlitz, H., Kapp, U., Waldeck, W., Chirico, G. & Langowski, J. (1997). Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics. Biophys J 73, 2674-2687.
    • (1997) Biophys J , vol.73 , pp. 2674-2687
    • Hammermann, M.1    Steinmaier, C.2    Merlitz, H.3    Kapp, U.4    Waldeck, W.5    Chirico, G.6    Langowski, J.7
  • 43
    • 0031880930 scopus 로고    scopus 로고
    • Looping dynamics of linear dna molecules and the effect of dna curvature: A study by brownian dynamics simulation
    • Merlitz, H., Rippe, K., Klenin, K. V. & Langowski, J. (1998). Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation. Biophys J 74, 773-779.
    • (1998) Biophys J , vol.74 , pp. 773-779
    • Merlitz, H.1    Rippe, K.2    Klenin, K.V.3    Langowski, J.4
  • 46
    • 33645324903 scopus 로고
    • Monte-carlo simulation of circular dnas-1st transition in writhe and twist energy parameters
    • Gebe, J. A. & Schurr, J. M. (1994). Monte-Carlo Simulation of Circular DNAs-1st Transition in Writhe and Twist Energy Parameters. Biophys J 66, A156-A156.
    • (1994) Biophys J , vol.66
    • Gebe, J.A.1    Schurr, J.M.2
  • 47
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak, D. L. & McCammon, J. A. (1978). Brownian dynamics with hydrodynamic interactions. J Chem Phys 69, 1352-1359.
    • (1978) J Chem Phys , vol.69 , pp. 1352-1359
    • Ermak, D.L.1    McCammon, J.A.2
  • 48
    • 0001329681 scopus 로고
    • Brownian dynamics simulation of wormlike chains. fluorescence depolarization and depolarized light scattering
    • Allison, S. A. (1986). Brownian dynamics simulation of wormlike chains. Fluorescence depolarization and depolarized light scattering. Macromolecules 19, 118-124.
    • (1986) Macromolecules , vol.19 , pp. 118-124
    • Allison, S.A.1
  • 49
    • 0025383092 scopus 로고
    • Brownian dynamics simulations of wormlike chains: Dynamic light scattering from a 2311 base pair dna fragment
    • Allison, S. A., Sorlie, S. S. & Pecora, R. (1990). Brownian dynamics simulations of wormlike chains: Dynamic light scattering from a 2311 base pair DNA fragment. Macromolecules 23, 1110-1118.
    • (1990) Macromolecules , vol.23 , pp. 1110-1118
    • Allison, S.A.1    Sorlie, S.S.2    Pecora, R.3
  • 50
    • 0026632050 scopus 로고
    • Calculating hydrodynamic properties of dna through a second-order brownian dynamics algorithm
    • Chirico, G. & Langowski, J. (1992). Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm. Macromolecules 25, 769-775.
    • (1992) Macromolecules , vol.25 , pp. 769-775
    • Chirico, G.1    Langowski, J.2
  • 51
    • 0000598304 scopus 로고
    • 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., Austin, R. & Hogan, M. (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
  • 52
    • 0028184699 scopus 로고
    • Kinetics of dna supercoiling studied by brownian dynamics simulation
    • Chirico, G. & Langowski, J. (1994). Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers 34, 415-433.
    • (1994) Biopolymers , vol.34 , pp. 415-433
    • Chirico, G.1    Langowski, J.2
  • 53
    • 0032160958 scopus 로고    scopus 로고
    • Kinetics of structural changes in superhelical dna
    • Wedemann, G., Munkel, C., Schoppe, G. & Langowski, J. (1998). Kinetics of structural changes in superhelical DNA. Phys Rev E 58, 3537-3546.
    • (1998) Phys Rev e , vol.58 , pp. 3537-3546
    • Wedemann, G.1    Munkel, C.2    Schoppe, G.3    Langowski, J.4
  • 54
    • 0036392202 scopus 로고    scopus 로고
    • Kinetics of site-site interactions in supercoiled dna with bent sequences
    • Bussiek, M., Klenin, K. & Langowski, J. (2002). Kinetics of site-site interactions in supercoiled DNA with bent sequences. J Mol Biol 322, 707-718.
    • (2002) J Mol Biol , vol.322 , pp. 707-718
    • Bussiek, M.1    Klenin, K.2    Langowski, J.3
  • 55
    • 4544353147 scopus 로고    scopus 로고
    • Modeling of intramolecular reactions of polymers: An efficient method based on brownian dynamics simulations
    • Klenin, K. V. & Langowski, J. (2004). Modeling of intramolecular reactions of polymers: An efficient method based on Brownian dynamics simulations. J Chem Phys 121, 4951-4960.
    • (2004) J Chem Phys , vol.121 , pp. 4951-4960
    • Klenin, K.V.1    Langowski, J.2
  • 56
    • 0035134518 scopus 로고    scopus 로고
    • Diffusion-controlled intrachain reactions of supercoiled dna: Brownian dynamics simulations
    • Klenin, K. V. & Langowski, J. (2001). Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations. Biophys J 80, 69-74.
    • (2001) Biophys J , vol.80 , pp. 69-74
    • Klenin, K.V.1    Langowski, J.2
  • 57
    • 0035868623 scopus 로고    scopus 로고
    • Kinetics of intrachain reactions of supercoiled dna: Theory and numerical modeling
    • Klenin, K. V. & Langowski, J. (2001). Kinetics of intrachain reactions of supercoiled DNA: Theory and numerical modeling. J Chem Phys 114, 5049-5060.
    • (2001) J Chem Phys , vol.114 , pp. 5049-5060
    • Klenin, K.V.1    Langowski, J.2
  • 58
    • 0034815621 scopus 로고    scopus 로고
    • Intrachain reactions of supercoiled dna simulated by brownian dynamics
    • Klenin, K. V. & Langowski, J. (2001). Intrachain Reactions of Supercoiled DNA Simulated by Brownian Dynamics. Biophys J 81, 1924-1929.
    • (2001) Biophys J , vol.81 , pp. 1924-1929
    • Klenin, K.V.1    Langowski, J.2
  • 60
    • 84933517499 scopus 로고
    • Variational treatment of hydrodynamic interaction in polymers
    • Rotne, J. & Prager, S. (1969). Variational treatment of hydrodynamic interaction in polymers. J Chem Phys 50, 4831-4837.
    • (1969) J Chem Phys , vol.50 , pp. 4831-4837
    • Rotne, J.1    Prager, S.2
  • 61
    • 0029776063 scopus 로고    scopus 로고
    • Brownian dynamics simulations of supercoiled dna with bent sequences
    • Chirico, G. & Langowski, J. (1996). Brownian dynamics simulations of supercoiled DNA with bent sequences. Biophys J 71, 955-971.
    • (1996) Biophys J , vol.71 , pp. 955-971
    • Chirico, G.1    Langowski, J.2
  • 62
    • 0029875865 scopus 로고    scopus 로고
    • A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites
    • Polach, K. J. & Widom, J. (1996). A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J Mol Biol 258, 800-812.
    • (1996) J Mol Biol , vol.258 , pp. 800-812
    • Polach, K.J.1    Widom, J.2
  • 63
    • 0034598944 scopus 로고    scopus 로고
    • Sequence and position-dependence of the equilibrium accessibility of nucleosomal dna target sites
    • Anderson, J. D. & Widom, J. (2000). Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol 296, 979-987.
    • (2000) J Mol Biol , vol.296 , pp. 979-987
    • Anderson, J.D.1    Widom, J.2
  • 64
    • 0037604739 scopus 로고    scopus 로고
    • The physics of chromatin
    • Schiessel, H. (2003). The physics of chromatin. J Phys Cond Mat 15, R699-R774.
    • (2003) J Phys Cond Mat , vol.15
    • Schiessel, H.1
  • 65
  • 66
    • 3042834082 scopus 로고    scopus 로고
    • DNA spools under tension
    • Kulic, I. M. & Schiessel, H. (2004). DNA Spools under Tension. Phys Rev Lett 92, 228101-228104.
    • (2004) Phys Rev Lett , vol.92 , pp. 228101-228104
    • Kulic, I.M.1    Schiessel, H.2
  • 67
    • 0034602688 scopus 로고    scopus 로고
    • Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure
    • Cui, Y. & Bustamante, C. (2000). Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc Natl Acad Sci USA 97, 127-132.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 127-132
    • Cui, Y.1    Bustamante, C.2
  • 68
    • 0035849539 scopus 로고    scopus 로고
    • Trajectory of nucleosomal linker dna studied by fluorescence resonance energy transfer
    • Tóth, K., Brun, N. & Langowski, J. (2001). Trajectory of nucleosomal linker DNA studied by fluorescence resonance energy transfer. Biochemistry 40, 6921-6928.
    • (2001) Biochemistry , vol.40 , pp. 6921-6928
    • Tóth, K.1    Brun, N.2    Langowski, J.3
  • 69
    • 12344284012 scopus 로고    scopus 로고
    • Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes
    • Brower-Toland, B., Wacker, D. A., Fulbright, R. M., Lis, J. T., Kraus, W. L. & Wang, M. D. (2005). Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol 346, 135-146.
    • (2005) J Mol Biol , vol.346 , pp. 135-146
    • Brower-Toland, B.1    Wacker, D.A.2    Fulbright, R.M.3    Lis, J.T.4    Kraus, W.L.5    Wang, M.D.6
  • 71
    • 14744270719 scopus 로고    scopus 로고
    • Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer
    • Tomschik, M., Zheng, H., van Holde, K., Zlatanova, J. & Leuba, S. H. (2005). Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc Natl Acad Sci USA 102, 3278-3283.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 3278-3283
    • Tomschik, M.1    Zheng, H.2    Van Holde, K.3    Zlatanova, J.4    Leuba, S.H.5
  • 72
    • 0030866748 scopus 로고    scopus 로고
    • Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: Evidence for a discotic columnar hexagonal phase
    • Leforestier, A. & Livolant, F. (1997). Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: Evidence for a discotic columnar hexagonal phase. Biophys J 73, 1771-1776.
    • (1997) Biophys J , vol.73 , pp. 1771-1776
    • Leforestier, A.1    Livolant, F.2
  • 73
    • 0034080775 scopus 로고    scopus 로고
    • Chiral discotic columnar germs of nucleosome core particles
    • Livolant, F. & Leforestier, A. (2000). Chiral discotic columnar germs of nucleosome core particles. Biophys J 78, 2716-2729.
    • (2000) Biophys J , vol.78 , pp. 2716-2729
    • Livolant, F.1    Leforestier, A.2
  • 74
    • 0034816185 scopus 로고    scopus 로고
    • Bilayers of nucleosome core particles
    • Leforestier, A., Dubochet, J. & Livolant, F. (2001). Bilayers of nucleosome core particles. Biophys J 81, 2414-2421.
    • (2001) Biophys J , vol.81 , pp. 2414-2421
    • Leforestier, A.1    Dubochet, J.2    Livolant, F.3
  • 75
    • 0037379723 scopus 로고    scopus 로고
    • X-ray diffraction characterization of the dense phases formed by nucleosome core particles
    • Mangenot, S., Leforestier, A., Durand, D. & Livolant, F. (2003). X-ray diffraction characterization of the dense phases formed by nucleosome core particles. Biophys J 84, 2570-2584.
    • (2003) Biophys J , vol.84 , pp. 2570-2584
    • Mangenot, S.1    Leforestier, A.2    Durand, D.3    Livolant, F.4
  • 76
    • 0036525256 scopus 로고    scopus 로고
    • Interactions between isolated nucleosome core particles: A tail-bridging effect?
    • Mangenot, S., Raspaud, E., Tribet, C., Belloni, L. & Livolant, F. (2002). Interactions between isolated nucleosome core particles: A tail-bridging effect? Eur Phys J E 7, 221-231.
    • (2002) Eur Phys J e , vol.7 , pp. 221-231
    • Mangenot, S.1    Raspaud, E.2    Tribet, C.3    Belloni, L.4    Livolant, F.5
  • 77
    • 0036221883 scopus 로고    scopus 로고
    • Salt-induced conformation and interaction changes of nucleosome core particles
    • Mangenot, S., Leforestier, A., Vachette, P., Durand, D. & Livolant, F. (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
  • 78
    • 0035156429 scopus 로고    scopus 로고
    • Modeling salt-mediated electrostatics of macromolecules: The discrete surface charge optimization algorithm and its application to the nucleosome
    • Beard, D. A. & Schlick, T. (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
  • 79
    • 84889999693 scopus 로고    scopus 로고
    • Controlled dna compaction within chromatin: The tail-bridging effect
    • in press
    • Muehlbacher, F., Holm, C. & Schiessel, H. (2005). Controlled DNA compaction within chromatin: The tail-bridging effect. Europhysics Letters, in press.
    • (2005) Europhysics Letters
    • Muehlbacher, F.1    Holm, C.2    Schiessel, H.3
  • 80
    • 0006188311 scopus 로고
    • Measurement of the elasticity of single chromatin fibers: The effect of histone h1
    • PhD Thesis
    • Castro, C. (1994). Measurement of the elasticity of single chromatin fibers: The effect of histone H1. PhD Thesis, University of Oregon, Eugene.
    • (1994) University of Oregon, Eugene
    • Castro, C.1
  • 81
    • 2142855641 scopus 로고    scopus 로고
    • Polylysine-coated mica can be used to observe systematic changes in the supercoiled dna conformation by scanning force microscopy in solution
    • Bussiek, M., Mucke, N. & Langowski, J. (2003). Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution. Nucleic Acids Res 31, e137.
    • (2003) Nucleic Acids Res , vol.31
    • Bussiek, M.1    Mucke, N.2    Langowski, J.3
  • 82
    • 0033485539 scopus 로고    scopus 로고
    • Quantitative comparison of dna looping in vitro and in vivo: Chromatin increases effective dna flexibility at short distances
    • Ringrose, L., Chabanis, S., Angrand, P. O., Woodroofe, C. & Stewart, A. F. (1999). Quantitative comparison of DNA looping in vitro and in vivo: Chromatin increases effective DNA flexibility at short distances. EMBO J 18, 6630-6641.
    • (1999) EMBO J , vol.18 , pp. 6630-6641
    • Ringrose, L.1    Chabanis, S.2    Angrand, P.O.3    Woodroofe, C.4    Stewart, A.F.5
  • 83
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. (2002). Capturing Chromosome Conformation. Science 295, 1306-1311.
    • (2002) Science , vol.295 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 84
    • 0026737923 scopus 로고
    • Estimating genomic distance from dna sequence location in cell nuclei by a random walk model
    • van den Engh, G., Sachs, R. & Trask, B. J. (1992). Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model. Science 257, 1410-1412.
    • (1992) Science , vol.257 , pp. 1410-1412
    • Van Den Engh, G.1    Sachs, R.2    Trask, B.J.3
  • 86
    • 0029129565 scopus 로고
    • Evidence for the organization of chromatin in megabase pair-sized loops arranged along a
    • random walk path in the human G0/G1 interphase nucleus
    • Yokota, H., van den Engh, G., Hearst, J., Sachs, R. K. & Trask, B. J. (1995). Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus. J Cell Biol 130, 1239-1249.
    • (1995) J Cell Biol , vol.130 , pp. 1239-1249
    • Yokota, H.1    Van Den Engh, G.2    Hearst, J.3    Sachs, R.K.4    Trask, B.J.5
  • 87
    • 9344239339 scopus 로고    scopus 로고
    • Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques
    • Bystricky, K., Heun, P., Gehlen, L., Langowski, J. & Gasser, S. M. (2004). Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. Proc Natl Acad Sci USA 101, 16495-16500.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 16495-16500
    • Bystricky, K.1    Heun, P.2    Gehlen, L.3    Langowski, J.4    Gasser, S.M.5
  • 88
    • 0034958378 scopus 로고    scopus 로고
    • Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers
    • Bennink, M. L., Leuba, S. H., Leno, G. H., Zlatanova, J., de Grooth, B. G. & Greve, J. (2001). Unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers. Nat Struct Biol 8, 606-610.
    • (2001) Nat Struct Biol , vol.8 , pp. 606-610
    • Bennink, M.L.1    Leuba, S.H.2    Leno, G.H.3    Zlatanova, J.4    De Grooth, B.G.5    Greve, J.6
  • 90
    • 21244444606 scopus 로고    scopus 로고
    • Histone octamer instability under single molecule experiment conditions
    • Claudet, C., Angelov, D., Bouvet, P., Dimitrov, S. & Bednar, J. (2005). Histone octamer instability under single molecule experiment conditions. J Biol Chem 280, 19958-19965.
    • (2005) J Biol Chem , vol.280 , pp. 19958-19965
    • Claudet, C.1    Angelov, D.2    Bouvet, P.3    Dimitrov, S.4    Bednar, J.5
  • 91
    • 1942502793 scopus 로고    scopus 로고
    • Role of histone tails in the conformation and interactions of nucleosome core particles
    • Bertin, A., Leforestier, A., Durand, D. & Livolant, F. (2004). Role of histone tails in the conformation and interactions of nucleosome core particles. Biochemistry 43, 4773-4780.
    • (2004) Biochemistry , vol.43 , pp. 4773-4780
    • Bertin, A.1    Leforestier, A.2    Durand, D.3    Livolant, F.4
  • 92
    • 0031876314 scopus 로고    scopus 로고
    • Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by rna polymerase iii
    • Tse, C., Sera, T., Wolffe, A. P. & Hansen, J. C. (1998). Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III Mol Cell Biol 18, 4629-4638.
    • (1998) Mol Cell Biol , vol.18 , pp. 4629-4638
    • Tse, C.1    Sera, T.2    Wolffe, A.P.3    Hansen, J.C.4
  • 93
    • 0033605391 scopus 로고    scopus 로고
    • MENT, a heterochromatin protein that mediates higher order chromatin folding, is a new serpin family member
    • Grigoryev, S. A., Bednar, J. & Woodcock, C. L. (1999). MENT, a heterochromatin protein that mediates higher order chromatin folding, is a new serpin family member. J Biol Chem 274, 5626-5636.
    • (1999) J Biol Chem , vol.274 , pp. 5626-5636
    • Grigoryev, S.A.1    Bednar, J.2    Woodcock, C.L.3
  • 96
    • 42749101777 scopus 로고    scopus 로고
    • Nucleosome interactions in chromatin: Fiber stiffening and hairpin formation
    • Mergell, B., Everaers, R. & Schiessel, H. (2004). Nucleosome interactions in chromatin: Fiber stiffening and hairpin formation. Phys Rev E 70, 011915.
    • (2004) Phys Rev e , vol.70 , pp. 011915
    • Mergell, B.1    Everaers, R.2    Schiessel, H.3
  • 99
    • 33645304637 scopus 로고    scopus 로고
    • Spatially confined polymer chains: Implication of chromatin fiber flexibility and peripheral anchoring on telomere-telomere interaction
    • in press
    • Gehlen, L. R., Rosa, A., Klenin, K., Langowski, J., Gasser, S. & Bystricky, K. (2005). Spatially confined polymer chains: Implication of chromatin fiber flexibility and peripheral anchoring on telomere-telomere interaction. J Phys Cond Matter, in press.
    • (2005) J Phys Cond Matter
    • Gehlen, L.R.1    Rosa, A.2    Klenin, K.3    Langowski, J.4    Gasser, S.5    Bystricky, K.6


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