메뉴 건너뛰기




Volumn 6, Issue , 2017, Pages

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CROSS LINKING; CRYOELECTRON MICROSCOPY; DNA BINDING; ENZYME ACTIVITY; GEL ELECTROPHORESIS; MASS SPECTROMETRY; MOLECULAR CLONING; MOLECULAR DYNAMICS; MOLECULAR WEIGHT; MUTAGENESIS; NONHUMAN; PROTEIN EXPRESSION; RADIATION SCATTERING; SIZE EXCLUSION CHROMATOGRAPHY; CHEMISTRY; METABOLISM; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOSOME; PROTEIN CONFORMATION;

EID: 85017511461     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.22510     Document Type: Article
Times cited : (45)

References (83)
  • 1
    • 0028872728 scopus 로고
    • Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative
    • 7862134
    • Adams CC, Workman JL. 1995. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Molecular and Cellular Biology 15:1405–1421. doi: 10.1128/MCB.15.3.1405, PMID: 7862134
    • (1995) Molecular and Cellular Biology , vol.15 , pp. 1405-1421
    • Adams, C.C.1    Workman, J.L.2
  • 2
    • 38349173560 scopus 로고    scopus 로고
    • Single-molecule tracking of mRNA exiting from RNA polymerase II
    • 18162559
    • Andrecka J, Lewis R, Brückner F, Lehmann E, Cramer P, Michaelis J. 2008. Single-molecule tracking of mRNA exiting from RNA polymerase II. PNAS 105:135–140. doi: 10.1073/pnas.0703815105, PMID: 18162559
    • (2008) PNAS , vol.105 , pp. 135-140
    • Andrecka, J.1    Lewis, R.2    Brückner, F.3    Lehmann, E.4    Cramer, P.5    Michaelis, J.6
  • 3
    • 72949099668 scopus 로고    scopus 로고
    • Dynamics of nucleosome remodelling by individual ACF complexes
    • 20033040
    • Blosser TR, Yang JG, Stone MD, Narlikar GJ, Zhuang X. 2009. Dynamics of nucleosome remodelling by individual ACF complexes. Nature 462:1022–1027. doi: 10.1038/nature08627, PMID: 20033040
    • (2009) Nature , vol.462 , pp. 1022-1027
    • Blosser, T.R.1    Yang, J.G.2    Stone, M.D.3    Narlikar, G.J.4    Zhuang, X.5
  • 5
    • 85017501133 scopus 로고    scopus 로고
    • Data from: Coral reef degradation is not correlated with local human population density
    • Bruno JF. 2016. Data from: coral reef degradation is not correlated with local human population density. Dryad Digital Repository. doi: 10.5061/dryad.48r68
    • (2016) Dryad Digital Repository
    • Bruno, J.F.1
  • 7
    • 84871023769 scopus 로고    scopus 로고
    • Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes
    • 23143334
    • Clapier CR, Cairns BR. 2012. Regulation of ISWI involves inhibitory modules antagonized by nucleosomal epitopes. Nature 492:280–284. doi: 10.1038/nature11625, PMID: 23143334
    • (2012) Nature , vol.492 , pp. 280-284
    • Clapier, C.R.1    Cairns, B.R.2
  • 8
    • 67749103813 scopus 로고    scopus 로고
    • On the mechanism of trolox as antiblinking and antibleaching reagent
    • 19301868
    • Cordes T, Vogelsang J, Tinnefeld P. 2009. On the mechanism of trolox as antiblinking and antibleaching reagent. Journal of the American Chemical Society 131:5018–5019. doi: 10.1021/ja809117z, PMID: 19301868
    • (2009) Journal of the American Chemical Society , vol.131 , pp. 5018-5019
    • Cordes, T.1    Vogelsang, J.2    Tinnefeld, P.3
  • 9
    • 36849004886 scopus 로고    scopus 로고
    • Domain architecture of the catalytic subunit in the ISW2-nucleosome complex
    • 17908792
    • Dang W, Bartholomew B. 2007. Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Molecular and Cellular Biology 27:8306–8317. doi: 10.1128/MCB.01351-07, PMID: 17908792
    • (2007) Molecular and Cellular Biology , vol.27 , pp. 8306-8317
    • Dang, W.1    Bartholomew, B.2
  • 10
    • 84873301476 scopus 로고    scopus 로고
    • ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps
    • 23374341
    • Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X. 2013. ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. Cell 152:442–452. doi: 10.1016/j.cell.2012.12.040, PMID: 23374341
    • (2013) Cell , vol.152 , pp. 442-452
    • Deindl, S.1    Hwang, W.L.2    Hota, S.K.3    Blosser, T.R.4    Prasad, P.5    Bartholomew, B.6    Zhuang, X.7
  • 11
    • 85014409623 scopus 로고    scopus 로고
    • Structural information from Single-molecule FRET experiments using the fast Nano-positioning system
    • 28287526
    • Dörfler T, Eilert T, Röcker C, Nagy J, Michaelis J. 2017. Structural information from Single-molecule FRET experiments using the fast Nano-positioning system. Journal of Visualized Experiments:e54782. doi: 10.3791/54782, PMID: 28287526
    • (2017) Journal of Visualized Experiments
    • Dörfler, T.1    Eilert, T.2    Röcker, C.3    Nagy, J.4    Michaelis, J.5
  • 12
    • 18844457346 scopus 로고    scopus 로고
    • X-ray structures of the sulfolobus solfataricus SWI2/ SNF2 ATPase core and its complex with DNA
    • 15 882619
    • Dürr H, Körner C, Müller M, Hickmann V, Hopfner KP. 2005. X-ray structures of the sulfolobus solfataricus SWI2/ SNF2 ATPase core and its complex with DNA. Cell 121:363–373. doi: 10.1016/j.cell.2005.03.026, PMID: 15 882619
    • (2005) Cell , vol.121 , pp. 363-373
    • Dürr, H.1    Körner, C.2    Müller, M.3    Hickmann, V.4    Hopfner, K.P.5
  • 13
    • 84988378514 scopus 로고    scopus 로고
    • Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing
    • 27106059
    • Fennessy RT, Owen-Hughes T. 2016. Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing. Nucleic Acids Research 44:gkw331. doi: 10.1093/nar/gkw331, PMID: 27106059
    • (2016) Nucleic Acids Research , vol.44
    • Fennessy, R.T.1    Owen-Hughes, T.2
  • 14
    • 33745122231 scopus 로고    scopus 로고
    • Identification of multiple distinct Snf2 subfamilies with conserved structural motifs
    • 16738128
    • Flaus A, Martin DM, Barton GJ, Owen-Hughes T. 2006. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Research 34:2887–2905. doi: 10.1093/nar/gkl295, PMID: 16738128
    • (2006) Nucleic Acids Research , vol.34 , pp. 2887-2905
    • Flaus, A.1    Martin, D.M.2    Barton, G.J.3    Owen-Hughes, T.4
  • 15
    • 80052970429 scopus 로고    scopus 로고
    • Mechanisms for ATP-dependent chromatin remodelling: The means to the end
    • 21810178
    • Flaus A, Owen-Hughes T. 2011. Mechanisms for ATP-dependent chromatin remodelling: the means to the end. FEBS Journal 278:3579–3595. doi: 10.1111/j.1742-4658.2011.08281.x, PMID: 21810178
    • (2011) FEBS Journal , vol.278 , pp. 3579-3595
    • Flaus, A.1    Owen-Hughes, T.2
  • 16
    • 67649668797 scopus 로고    scopus 로고
    • Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2
    • 19595716
    • Gangaraju VK, Prasad P, Srour A, Kagalwala MN, Bartholomew B. 2009. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by ISW2. Molecular Cell 35:58–69. doi: 10. 1016/j.molcel.2009.05.013, PMID: 19595716
    • (2009) Molecular Cell , vol.35 , pp. 58-69
    • Gangaraju, V.K.1    Prasad, P.2    Srour, A.3    Kagalwala, M.N.4    Bartholomew, B.5
  • 18
    • 84979856632 scopus 로고    scopus 로고
    • XVis: A web server for the schematic visualization and interpretation of crosslink-derived spatial restraints
    • 25956653
    • Grimm M, Zimniak T, Kahraman A, Herzog F. 2015. xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints. Nucleic Acids Research 43:W362–W369. doi: 10.1093/nar/gkv463, PMID: 25956653
    • (2015) Nucleic Acids Research , vol.43 , pp. W362-W369
    • Grimm, M.1    Zimniak, T.2    Kahraman, A.3    Herzog, F.4
  • 19
    • 0141922979 scopus 로고    scopus 로고
    • Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI
    • 14536084
    • Grüne T, Brzeski J, Eberharter A, Clapier CR, Corona DF, Becker PB, Müller CW. 2003. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Molecular Cell 12:449– 460. doi: 10.1016/S1097-2765(03)00273-9, PMID: 14536084
    • (2003) Molecular Cell , vol.12
    • Grüne, T.1    Brzeski, J.2    Eberharter, A.3    Clapier, C.R.4    Corona, D.F.5    Becker, P.B.6    Müller, C.W.7
  • 20
    • 84982809872 scopus 로고    scopus 로고
    • The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3-H4 tetramers and Asf1-H3-H4 complexes
    • 27036862
    • Hammond CM, Sundaramoorthy R, Larance M, Lamond A, Stevens MA, El-Mkami H, Norman DG, Owen-Hughes T. 2016. The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3-H4 tetramers and Asf1-H3-H4 complexes. Nucleic Acids Research 44:6157–6172. doi: 10. 1093/nar/gkw209, PMID: 27036862
    • (2016) Nucleic Acids Research , vol.44 , pp. 6157-6172
    • Hammond, C.M.1    Sundaramoorthy, R.2    Larance, M.3    Lamond, A.4    Stevens, M.A.5    El-Mkami, H.6    Norman, D.G.7    Owen-Hughes, T.8
  • 21
    • 82955233364 scopus 로고    scopus 로고
    • Structural insights into regulation and action of SWI2/SNF2 ATPases
    • 21996440
    • Hauk G, Bowman GD. 2011. Structural insights into regulation and action of SWI2/SNF2 ATPases. Current Opinion in Structural Biology 21:719–727. doi: 10.1016/j.sbi.2011.09.003, PMID: 21996440
    • (2011) Current Opinion in Structural Biology , vol.21 , pp. 719-727
    • Hauk, G.1    Bowman, G.D.2
  • 22
    • 77956522905 scopus 로고    scopus 로고
    • The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor
    • Hauk G, McKnight JN, Nodelman IM, Bowman GD. 2010. The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Molecular Cell 39:711–723. doi: 10.1016/j.molcel.2010.08.012, PMID: 20832723
    • (2010) Molecular Cell , vol.39 , pp. 711-723
    • Hauk, G.1    McKnight, J.N.2    Nodelman, I.M.3    Bowman, G.D.4
  • 23
    • 0034704235 scopus 로고    scopus 로고
    • Generation of superhelical torsion by ATP-dependent chromatin remodeling activities
    • 11163188
    • Havas K, Flaus A, Phelan M, Kingston R, Wade PA, Lilley DM, Owen-Hughes T. 2000. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 103:1133–1142. doi: 10.1016/S0092-8674(00) 00215-4, PMID: 11163188
    • (2000) Cell , vol.103 , pp. 1133-1142
    • Havas, K.1    Flaus, A.2    Phelan, M.3    Kingston, R.4    Wade, P.A.5    Lilley, D.M.6    Owen-Hughes, T.7
  • 25
    • 84867371116 scopus 로고    scopus 로고
    • A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern
    • 22885008
    • Hughes AL, Jin Y, Rando OJ, Struhl K. 2012. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Molecular Cell 48:5–15. doi: 10.1016/j.molcel.2012.07.003, PMID: 22885008
    • (2012) Molecular Cell , vol.48 , pp. 5-15
    • Hughes, A.L.1    Jin, Y.2    Rando, O.J.3    Struhl, K.4
  • 26
    • 84940862471 scopus 로고    scopus 로고
    • Comparative genomics reveals Chd1 as a determinant of nucleosome spacing in vivo
    • Hughes AL, Rando OJ. 2015. Comparative genomics reveals Chd1 as a determinant of nucleosome spacing in vivo. G3:; Genes|Genomes|Genetics 5:1889–1897. doi: 10.1534/g3.115.020271
    • (2015) Genes|Genomes|Genetics , vol.5 , pp. 1889-1897
    • Hughes, A.L.1    Rando, O.J.2
  • 27
    • 84906267703 scopus 로고    scopus 로고
    • Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA
    • 25043036
    • Hwang WL, Deindl S, Harada BT, Zhuang X. 2014. Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA. Nature 512:213–217. doi: 10.1038/nature13380, PMID: 25043036
    • (2014) Nature , vol.512 , pp. 213-217
    • Hwang, W.L.1    Deindl, S.2    Harada, B.T.3    Zhuang, X.4
  • 28
    • 34147218123 scopus 로고    scopus 로고
    • Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance
    • 17431518
    • Jeschke G, Polyhach Y. 2007. Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. Physical Chemistry Chemical Physics 9:1895–1910. doi: 10.1039/b614920k, PMID: 17431518
    • (2007) Physical Chemistry Chemical Physics , vol.9 , pp. 1895-1910
    • Jeschke, G.1    Polyhach, Y.2
  • 29
    • 2942561969 scopus 로고    scopus 로고
    • Topography of the ISW2-nucleosome complex: Insights into nucleosome spacing and chromatin remodeling
    • 15131696
    • Kagalwala MN, Glaus BJ, Dang W, Zofall M, Bartholomew B. 2004. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. The EMBO Journal 23:2092–2104. doi: 10.1038/sj.emboj.7600220, PMID: 15131696
    • (2004) The EMBO Journal , vol.23 , pp. 2092-2104
    • Kagalwala, M.N.1    Glaus, B.J.2    Dang, W.3    Zofall, M.4    Bartholomew, B.5
  • 32
    • 84952639674 scopus 로고    scopus 로고
    • Crosslinking and mass spectrometry: An integrated technology to understand the structure and function of molecular machines
    • 26654279
    • Leitner A, Faini M, Stengel F, Aebersold R. 2016. Crosslinking and mass spectrometry: an integrated technology to understand the structure and function of molecular machines. Trends in Biochemical Sciences 41:20–32. doi: 10.1016/j.tibs.2015.10.008, PMID: 26654279
    • (2016) Trends in Biochemical Sciences , vol.41 , pp. 20-32
    • Leitner, A.1    Faini, M.2    Stengel, F.3    Aebersold, R.4
  • 33
    • 84924041052 scopus 로고    scopus 로고
    • A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler
    • 25684208
    • Leonard JD, Narlikar GJ. 2015. A nucleotide-driven switch regulates flanking DNA length sensing by a dimeric chromatin remodeler. Molecular Cell 57:850–859. doi: 10.1016/j.molcel.2015.01.008, PMID: 25684208
    • (2015) Molecular Cell , vol.57 , pp. 850-859
    • Leonard, J.D.1    Narlikar, G.J.2
  • 34
    • 41849142342 scopus 로고    scopus 로고
    • Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle
    • 18267970
    • Lewis R, Dürr H, Hopfner KP, Michaelis J. 2008. Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle. Nucleic Acids Research 36:1881–1890. doi: 10.1093/nar/gkn040, PMID: 18267970
    • (2008) Nucleic Acids Research , vol.36 , pp. 1881-1890
    • Lewis, R.1    Dürr, H.2    Hopfner, K.P.3    Michaelis, J.4
  • 36
    • 84920522426 scopus 로고    scopus 로고
    • Human CHD2 is a chromatin assembly ATPase regulated by its chromo-and DNA-binding domains
    • 25384982
    • Liu JC, Ferreira CG, Yusufzai T. 2015. Human CHD2 is a chromatin assembly ATPase regulated by its chromo-and DNA-binding domains. Journal of Biological Chemistry 290:25–34. doi: 10.1074/jbc.M114.609156, PMID: 25384982
    • (2015) Journal of Biological Chemistry , vol.290 , pp. 25-34
    • Liu, J.C.1    Ferreira, C.G.2    Yusufzai, T.3
  • 37
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • 9514715
    • Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology 276:19–42. doi: 10.1006/jmbi.1997.1494, PMID: 9514715
    • (1998) Journal of Molecular Biology , vol.276 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 38
    • 0033039285 scopus 로고    scopus 로고
    • Preparation of nucleosome core particle from recombinant histones
    • 10372352
    • Luger K, Rechsteiner TJ, Richmond TJ. 1999. Preparation of nucleosome core particle from recombinant histones. Methods in Enzymology 304:3–19. doi: 10.1016/s0076-6879(99)04003-3, PMID: 10372352
    • (1999) Methods in Enzymology , vol.304 , pp. 3-19
    • Luger, K.1    Rechsteiner, T.J.2    Richmond, T.J.3
  • 39
    • 15544369061 scopus 로고    scopus 로고
    • Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly
    • 15643425
    • Lusser A, Urwin DL, Kadonaga JT. 2005. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nature Structural and Molecular Biology 12:160–166. doi: 10.1038/nsmb884, PMID: 15643425
    • (2005) Nature Structural and Molecular Biology , vol.12 , pp. 160-166
    • Lusser, A.1    Urwin, D.L.2    Kadonaga, J.T.3
  • 42
    • 84991706628 scopus 로고    scopus 로고
    • The chromatin remodelling protein CHD1 contains a previously unrecognised C-Terminal helical domain
    • 27591891
    • Mohanty B, Helder S, Silva AP, Mackay JP, Ryan DP. 2016. The chromatin remodelling protein CHD1 contains a previously unrecognised C-Terminal helical domain. Journal of Molecular Biology 428:4298–4314. doi: 10.1016/j.jmb.2016.08.028, PMID: 27591891
    • (2016) Journal of Molecular Biology , vol.428 , pp. 4298-4314
    • Mohanty, B.1    Helder, S.2    Silva, A.P.3    Mackay, J.P.4    Ryan, D.P.5
  • 45
    • 85009804160 scopus 로고    scopus 로고
    • Interdomain communication of the Chd1 chromatin remodeler across the DNA gyres of the nucleosome
    • 28111016
    • Nodelman IM, Bleichert F, Patel A, Ren R, Horvath KC, Berger JM, Bowman GD. 2017. Interdomain communication of the Chd1 chromatin remodeler across the DNA gyres of the nucleosome. Molecular Cell 65: 447–459. doi: 10.1016/j.molcel.2016.12.011, PMID: 28111016
    • (2017) Molecular Cell , vol.65 , pp. 447-459
    • Nodelman, I.M.1    Bleichert, F.2    Patel, A.3    Ren, R.4    Horvath, K.C.5    Berger, J.M.6    Bowman, G.D.7
  • 46
    • 84973460206 scopus 로고    scopus 로고
    • The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo
    • 26861626
    • Ocampo J, Chereji RV, Eriksson PR, Clark DJ. 2016. The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo. Nucleic Acids Research 44:4625–4635. doi: 10.1093/nar/gkw068, PMID: 26861626
    • (2016) Nucleic Acids Research , vol.44 , pp. 4625-4635
    • Ocampo, J.1    Chereji, R.V.2    Eriksson, P.R.3    Clark, D.J.4
  • 47
    • 0034132251 scopus 로고    scopus 로고
    • Dead-time free measurement of dipole-dipole interactions between electron spins
    • 10648151
    • Pannier M, Veit S, Godt A, Jeschke G, Spiess HW. 2000. Dead-time free measurement of dipole-dipole interactions between electron spins. Journal of Magnetic Resonance 142:331–340. doi: 10.1006/jmre.1999. 1944, PMID: 10648151
    • (2000) Journal of Magnetic Resonance , vol.142 , pp. 331-340
    • Pannier, M.1    Veit, S.2    Godt, A.3    Jeschke, G.4    Spiess, H.W.5
  • 48
    • 84873643234 scopus 로고    scopus 로고
    • Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler
    • 23275572
    • Patel A, Chakravarthy S, Morrone S, Nodelman IM, McKnight JN, Bowman GD. 2013. Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler. Nucleic Acids Research 41:1637–1648. doi: 10.1093/nar/gks1440, PMID: 23275572
    • (2013) Nucleic Acids Research , vol.41 , pp. 1637-1648
    • Patel, A.1    Chakravarthy, S.2    Morrone, S.3    Nodelman, I.M.4    McKnight, J.N.5    Bowman, G.D.6
  • 49
    • 23244455562 scopus 로고    scopus 로고
    • Global rigid body modeling of macromolecular complexes against small-angle scattering data
    • 15923225
    • Petoukhov MV, Svergun DI. 2005. Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophysical Journal 89:1237–1250. doi: 10.1529/biophysj.105.064154, PMID: 15923225
    • (2005) Biophysical Journal , vol.89 , pp. 1237-1250
    • Petoukhov, M.V.1    Svergun, D.I.2
  • 51
    • 0029875865 scopus 로고    scopus 로고
    • A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites
    • 8637011
    • Polach KJ, Widom J. 1996. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. Journal of Molecular Biology 258:800–812. doi: 10.1006/jmbi.1996.0288, PMID: 8637011
    • (1996) Journal of Molecular Biology , vol.258 , pp. 800-812
    • Polach, K.J.1    Widom, J.2
  • 54
    • 80052033059 scopus 로고    scopus 로고
    • CrossWork: Software-assisted identification of cross-linked peptides
    • 21600323
    • Rasmussen MI, Refsgaard JC, Peng L, Houen G, Højrup P. 2011. CrossWork: software-assisted identification of cross-linked peptides. Journal of Proteomics 74:1871–1883. doi: 10.1016/j.jprot.2011.04.019, PMID: 21600323
    • (2011) Journal of Proteomics , vol.74 , pp. 1871-1883
    • Rasmussen, M.I.1    Refsgaard, J.C.2    Peng, L.3    Houen, G.4    Højrup, P.5
  • 55
    • 33750295496 scopus 로고    scopus 로고
    • Nonblinking and long-lasting single-molecule fluorescence imaging
    • 17013382
    • Rasnik I, McKinney SA, Ha T. 2006. Nonblinking and long-lasting single-molecule fluorescence imaging. Nature Methods 3:891–893. doi: 10.1038/nmeth934, PMID: 17013382
    • (2006) Nature Methods , vol.3 , pp. 891-893
    • Rasnik, I.1    McKinney, S.A.2    Ha, T.3
  • 57
    • 84963958060 scopus 로고    scopus 로고
    • Methods to account for movement and flexibility in cryo-EM data processing
    • 27016144
    • Rawson S, Iadanza MG, Ranson NA, Muench SP. 2016. Methods to account for movement and flexibility in cryo-EM data processing. Methods 100:35–41. doi: 10.1016/j.ymeth.2016.03.011, PMID: 27016144
    • (2016) Methods , vol.100 , pp. 35-41
    • Rawson, S.1    Iadanza, M.G.2    Ranson, N.A.3    Muench, S.P.4
  • 58
    • 84946488108 scopus 로고    scopus 로고
    • CTFFIND4: Fast and accurate defocus estimation from electron micrographs
    • 26278980
    • Rohou A, Grigorieff N. 2015. CTFFIND4: fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology 192:216–221. doi: 10.1016/j.jsb.2015.08.008, PMID: 26278980
    • (2015) Journal of Structural Biology , vol.192 , pp. 216-221
    • Rohou, A.1    Grigorieff, N.2
  • 59
    • 84946473054 scopus 로고    scopus 로고
    • Alignment of cryo-EM movies of individual particles by optimization of image translations
    • 26296328
    • Rubinstein JL, Brubaker MA. 2015. Alignment of cryo-EM movies of individual particles by optimization of image translations. Journal of Structural Biology 192:188–195. doi: 10.1016/j.jsb.2015.08.007, PMID: 26296328
    • (2015) Journal of Structural Biology , vol.192 , pp. 188-195
    • Rubinstein, J.L.1    Brubaker, M.A.2
  • 60
    • 79960065933 scopus 로고    scopus 로고
    • The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains
    • 21623345
    • Ryan DP, Sundaramoorthy R, Martin D, Singh V, Owen-Hughes T. 2011. The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. The EMBO Journal 30:2596–2609. doi: 10.1038/emboj.2011.166, PMID: 21623345
    • (2011) The EMBO Journal , vol.30 , pp. 2596-2609
    • Ryan, D.P.1    Sundaramoorthy, R.2    Martin, D.3    Singh, V.4    Owen-Hughes, T.5
  • 61
    • 26944461283 scopus 로고    scopus 로고
    • Chromatin remodeling through directional DNA translocation from an internal nucleosomal site
    • 16086025
    • Saha A, Wittmeyer J, Cairns BR. 2005. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nature Structural and Molecular Biology 12:747–755. doi: 10.1038/nsmb973, PMID: 16086025
    • (2005) Nature Structural and Molecular Biology , vol.12 , pp. 747-755
    • Saha, A.1    Wittmeyer, J.2    Cairns, B.R.3
  • 62
    • 84868444740 scopus 로고    scopus 로고
    • RELION: Implementation of a bayesian approach to cryo-EM structure determination
    • 23000701
    • Scheres SH. 2012. RELION: implementation of a bayesian approach to cryo-EM structure determination. Journal of Structural Biology 180:519–530. doi: 10.1016/j.jsb.2012.09.006, PMID: 23000701
    • (2012) Journal of Structural Biology , vol.180 , pp. 519-530
    • Scheres, S.H.1
  • 64
    • 33646017369 scopus 로고    scopus 로고
    • Structural basis for RNA unwinding by the DEAD-box protein Drosophila vasa
    • 16630817
    • Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S. 2006. Structural basis for RNA unwinding by the DEAD-box protein Drosophila vasa. Cell 125:287–300. doi: 10.1016/j.cell.2006.01.054, PMID: 16630817
    • (2006) Cell , vol.125 , pp. 287-300
    • Sengoku, T.1    Nureki, O.2    Nakamura, A.3    Kobayashi, S.4    Yokoyama, S.5
  • 65
    • 82755183623 scopus 로고    scopus 로고
    • Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA
    • 22033927
    • Sharma A, Jenkins KR, Héroux A, Bowman GD. 2011. Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. Journal of Biological Chemistry 286: 42099–42104. doi: 10.1074/jbc.C111.294462, PMID: 22033927
    • (2011) Journal of Biological Chemistry , vol.286 , pp. 42099-42104
    • Sharma, A.1    Jenkins, K.R.2    Héroux, A.3    Bowman, G.D.4
  • 66
    • 84878617377 scopus 로고    scopus 로고
    • Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET
    • 23624933
    • Sikor M, Mapa K, von Voithenberg LV, Mokranjac D, Lamb DC. 2013. Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET. The EMBO Journal 32:1639–1649. doi: 10.1038/emboj.2013.89, PMID: 23624933
    • (2013) The EMBO Journal , vol.32 , pp. 1639-1649
    • Sikor, M.1    Mapa, K.2    Von Voithenberg, L.V.3    Mokranjac, D.4    Lamb, D.C.5
  • 67
    • 84882671972 scopus 로고    scopus 로고
    • TagDock: An efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning
    • 23875708
    • Smith JA, Edwards SJ, Moth CW, Lybrand TP. 2013. TagDock: an efficient rigid body docking algorithm for oligomeric protein complex model construction and experiment planning. Biochemistry 52:5577–5584. doi: 10. 1021/bi400158k, PMID: 23875708
    • (2013) Biochemistry , vol.52 , pp. 5577-5584
    • Smith, J.A.1    Edwards, S.J.2    Moth, C.W.3    Lybrand, T.P.4
  • 69
    • 0034387984 scopus 로고    scopus 로고
    • One- and three-dimensional pathways for proteins to reach specific DNA sites
    • 11101527
    • Stanford NP, Szczelkun MD, Marko JF, Halford SE. 2000. One- and three-dimensional pathways for proteins to reach specific DNA sites. The EMBO Journal 19:6546–6557. doi: 10.1093/emboj/19.23.6546, PMID: 11101527
    • (2000) The EMBO Journal , vol.19 , pp. 6546-6557
    • Stanford, N.P.1    Szczelkun, M.D.2    Marko, J.F.3    Halford, S.E.4
  • 70
    • 0029185933 scopus 로고
    • CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
    • Svergun D, Barberato C, Koch MHJ. 1995. CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates. Journal of Applied Crystallography 28:768–773. doi: 10. 1107/S0021889895007047
    • (1995) Journal of Applied Crystallography , vol.28 , pp. 768-773
    • Svergun, D.1    Barberato, C.2    Koch, M.H.J.3
  • 71
    • 0035010533 scopus 로고    scopus 로고
    • Determination of domain structure of proteins from X-ray solution scattering
    • 11371467
    • Svergun DI, Petoukhov MV, Koch MH. 2001. Determination of domain structure of proteins from X-ray solution scattering. Biophysical Journal 80:2946–2953. doi: 10.1016/S0006-3495(01)76260-1, PMID: 11371467
    • (2001) Biophysical Journal , vol.80 , pp. 2946-2953
    • Svergun, D.I.1    Petoukhov, M.V.2    Koch, M.H.3
  • 74
    • 84936847118 scopus 로고    scopus 로고
    • Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering
    • 25866658
    • Tria G, Mertens HD, Kachala M, Svergun DI. 2015. Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering. IUCrJ 2:207–217. doi: 10.1107/S205225251500202X, PMID: 25866658
    • (2015) Iucrj , vol.2 , pp. 207-217
    • Tria, G.1    Mertens, H.D.2    Kachala, M.3    Svergun, D.I.4
  • 75
    • 77955045449 scopus 로고    scopus 로고
    • The role of nucleosome positioning in the evolution of gene regulation
    • 20625544
    • Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. 2010. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biology 8:e1000414. doi: 10.1371/journal.pbio.1000414, PMID: 20625544
    • (2010) Plos Biology , vol.8
    • Tsankov, A.M.1    Thompson, D.A.2    Socha, A.3    Regev, A.4    Rando, O.J.5
  • 76
    • 0003903126 scopus 로고
    • New York: Springer-Verlag
    • Van Holde KE. 1988. Chromatin. New York: Springer-Verlag.
    • (1988) Chromatin
    • Van Holde, K.E.1
  • 78
    • 84978164240 scopus 로고    scopus 로고
    • Structure of chromatin remodeler Swi2/Snf2 in the resting state
    • 27399259
    • Xia X, Liu X, Li T, Fang X, Chen Z. 2016. Structure of chromatin remodeler Swi2/Snf2 in the resting state. Nature Structural and Molecular Biology 23:722–729. doi: 10.1038/nsmb.3259, PMID: 27399259
    • (2016) Nature Structural and Molecular Biology , vol.23 , pp. 722-729
    • Xia, X.1    Liu, X.2    Li, T.3    Fang, X.4    Chen, Z.5
  • 80
    • 84862643713 scopus 로고    scopus 로고
    • Genome-wide nucleosome specificity and directionality of chromatin remodelers
    • 22726434
    • Yen K, Vinayachandran V, Batta K, Koerber RT, Pugh BF. 2012. Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell 149:1461–1473. doi: 10.1016/j.cell.2012.04.036, PMID: 22726434
    • (2012) Cell , vol.149 , pp. 1461-1473
    • Yen, K.1    Vinayachandran, V.2    Batta, K.3    Koerber, R.T.4    Pugh, B.F.5
  • 82
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • 21596991
    • Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332:977–980. doi: 10.1126/science.1200508, PMID: 21596991
    • (2011) Science , vol.332 , pp. 977-980
    • Zhang, Z.1    Wippo, C.J.2    Wal, M.3    Ward, E.4    Korber, P.5    Pugh, B.F.6
  • 83
    • 33744916194 scopus 로고    scopus 로고
    • Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome
    • 16518397
    • Zofall M, Persinger J, Kassabov SR, Bartholomew B. 2006. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nature Structural and Molecular Biology 13:339–346. doi: 10.1038/nsmb1071, PMID: 16518397
    • (2006) Nature Structural and Molecular Biology , vol.13 , pp. 339-346
    • Zofall, M.1    Persinger, J.2    Kassabov, S.R.3    Bartholomew, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.