Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations

References

• Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD. RSC, an essential, abundant chromatin-remodeling complex. Cell 1996; 87:1249-60; PMID:8980231; http://dx.doi.org/10.1016/S0092-8674(00)81820-6
   PubMed Web of Science ®Google Scholar
• Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell 2006; 24:559-68; PMID:17188033
   PubMed Web of Science ®Google Scholar
• Chaban Y, Ezeokonkwo C, Chung WH, Zhang F, Kornberg RD, Maier-Davis B, Lorch Y, Asturias FJ. Structure of a RSC–nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol 2008; 15:1272-1277; http://dx.doi.org/10.1038/nsmb.1524
   PubMed Web of Science ®Google Scholar
• Lavelle C, Praly E, Bensimon D, Le Cam E, Croquette V. Nucleosome-remodelling machines and other molecular motors observed at the single-molecule level. FEBS J 2011; 278:3596-3607; PMID:21810177
   PubMed Web of Science ®Google Scholar
• Shukla MS, Syed SH, Montel F, Faivre-Moskalenko C, Bednar J, Travers A, Angelov D, Dimitrov S. Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer. Proc Natl Acad Sci U S A 2010; 107:1936-41; http://dx.doi.org/10.1073/pnas.0904497107
   PubMed Web of Science ®Google Scholar
• Lowary PT, Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 1998; 276:19-42; http://dx.doi.org/10.1006/jmbi.1997.1494
   PubMed Web of Science ®Google Scholar
• Schiessel H, Widom J, Bruinsma RF, Gelbart WM. Polymer reptation and nucleosome repositioning. Phys Rev Lett 2001; 86:4414-7; PMID:11328188; http://dx.doi.org/10.1103/PhysRevLett.86.4414
   PubMed Web of Science ®Google Scholar
• Kulić IM, Schiessel H. Nucleosome repositioning via loop formation. Biophys J 2003; 84:3197-211; PMID:12719249; http://dx.doi.org/10.1016/S0006-3495(03)70044-7
   PubMed Web of Science ®Google Scholar
• Biswas M, Wocjan T, Langowski J, Smith C. DNA bending potentials for loop-mediated nucleosome repositioning. EPL (Europhysics Letters) 2012; 97:38004; http://dx.doi.org/10.1209/0295-5075/97/38004
   Google Scholar
• Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Structural Biol 2002; 9:788-788
   Google Scholar
• Mackerell AD, Nilsson L. Molecular dynamics simulations of nucleic acid-protein complexes. Curr Opin Struct Biol 2008; 18:194-9; http://dx.doi.org/10.1016/j.sbi.2007.12.012
   PubMed Web of Science ®Google Scholar
• Van Der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ. Biomolecular simulation and modelling: status, progress and prospects. J Royal Soc Interface 2008; 5:173-190; PMID:18611844; http://dx.doi.org/10.1098/rsif.2008.0105.focus
   PubMed Web of Science ®Google Scholar
• Karplus M, Lavery R. Significance of Molecular Dynamics Simulations for Life Sciences. Israel J Chem 2014; 54:1042-1051; http://dx.doi.org/10.1002/ijch.201400074
   Web of Science ®Google Scholar
• Leach A. Molecular modelling principlesand applications. Prentice Hall 2001
   Google Scholar
• Ettig R, Kepper N, Stehr R, Wedemann G, Rippe K. Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping. Biophys J 2011; 101:1999-2008; http://dx.doi.org/10.1016/j.bpj.2011.07.057
   PubMed Web of Science ®Google Scholar
• Biswas M, Langowski J, Bishop TC. Atomistic simulations of nucleosomes. WIREs Comput Mol Sci 2013; 3:378-392; http://dx.doi.org/10.1002/wcms.1139
   Web of Science ®Google Scholar
• Pasi M, Lavery R. Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics. Nucleic Acids Res 2016; 44:5450-6; PMID:27098037
   PubMed Web of Science ®Google Scholar
• Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure ofthe nucleosome core particle at 1.9 a resolution. J Mol Biol 2002; 319:1097-113; PMID:12079350; http://dx.doi.org/10.1016/S0022-2836(02)00386-8
   PubMed Web of Science ®Google Scholar
• Richmond TJ, Davey CA. The structure of DNA in the nucleosome core. Nature 2003; 423:145-50; http://dx.doi.org/10.1038/nature01595
   PubMed Web of Science ®Google Scholar
• Tims HS, Gurunathan K, Levitus M, Widom J. Dynamics of nucleosome invasion by DNA bindingproteins. J Mol Biol 2011; 411:430-448; http://dx.doi.org/10.1016/j.jmb.2011.05.044
   PubMed Web of Science ®Google Scholar
• Kenzaki H, Takada S. Partial unwrapping and histone tail dynamics in nucleosome revealed by coarse-grained molecular simulations. PLoS Comput Biol 2015; 11:e1004443; PMID:26262925; http://dx.doi.org/10.1371/journal.pcbi.1004443
   PubMedGoogle Scholar
• Crick FH, Klug A. Kinky helix. Nature 1975; 25:5530-533
   Google Scholar
• Lankas F, Lavery R, Maddocks JH. Kinking occurs during moleculars dynamics simulations of small DNA minicircles. Structure 2006; 14:1527-34; http://dx.doi.org/10.1016/j.str.2006.08.004
   PubMed Web of Science ®Google Scholar
• Lavery R, Maddocks JH, Pasi M, Zakrzewska K. Analyzing ion distributions around DNA. Nucleic Acids Res 2014; 42:8138-8149; http://dx.doi.org/10.1093/nar/gku504
   PubMed Web of Science ®Google Scholar
• Shukla MS, Syed SH, Goutte-Gattat D, Richard JL, Montel F, Hamiche A, Travers A, Faivre-Moskalenko C, Bednar J, Hayes JJ, et al. The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling. Nucleic Acids Res 2011; 39:2559-70; http://dx.doi.org/10.1093/nar/gkq1174
   PubMed Web of Science ®Google Scholar
• Liu N, Peterson CL, Hayes JJ. SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol 2011; 31:4165-75; PMID:21859889
   PubMed Web of Science ®Google Scholar
• Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 2004; 25:1605-12; http://dx.doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Goddard TD, Huang CC, Ferrin TE. Visualizing density maps with UCSF Chimera. J Struct Biol 2007; 15:7281-7; PMID:16963278
   PubMed Web of Science ®Google Scholar