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J Mol Biol
2016 Jan 16;4281:221-237. doi: 10.1016/j.jmb.2015.12.004.
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Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.
Shaytan AK
,
Armeev GA
,
Goncearenco A
,
Zhurkin VB
,
Landsman D
,
Panchenko AR
.
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An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.
Angelov,
Preferential interaction of the core histone tail domains with linker DNA.
2001, Pubmed
Angelov,
Preferential interaction of the core histone tail domains with linker DNA.
2001,
Pubmed
Arya,
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model.
2006,
Pubmed
Baxevanis,
A variety of DNA-binding and multimeric proteins contain the histone fold motif.
1995,
Pubmed
Best,
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.
2012,
Pubmed
Biswas,
Role of histone tails in structural stability of the nucleosome.
2011,
Pubmed
Brogaard,
A map of nucleosome positions in yeast at base-pair resolution.
2012,
Pubmed
Brower-Toland,
Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.
2002,
Pubmed
Choy,
Structural dynamics of nucleosomes at single-molecule resolution.
2012,
Pubmed
Collepardo-Guevara,
Chromatin fiber polymorphism triggered by variations of DNA linker lengths.
2014,
Pubmed
Collepardo-Guevara,
Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.
2015,
Pubmed
Davey,
Does the nucleosome break its own rules?
2013,
Pubmed
Davey,
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.
2002,
Pubmed
,
Xenbase
Dehghani,
Organization of chromatin in the interphase mammalian cell.
2005,
Pubmed
Dorigo,
Chromatin fiber folding: requirement for the histone H4 N-terminal tail.
2003,
Pubmed
,
Xenbase
Dyer,
Reconstitution of nucleosome core particles from recombinant histones and DNA.
2004,
Pubmed
Edayathumangalam,
Nucleosomes in solution exist as a mixture of twist-defect states.
2005,
Pubmed
,
Xenbase
Erler,
The role of histone tails in the nucleosome: a computational study.
2014,
Pubmed
Fenley,
Charge state of the globular histone core controls stability of the nucleosome.
2010,
Pubmed
Galindo-Murillo,
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).
2015,
Pubmed
Gansen,
Nucleosome disassembly intermediates characterized by single-molecule FRET.
2009,
Pubmed
Gao,
Histone H3 and H4 N-terminal tails in nucleosome arrays at cellular concentrations probed by magic angle spinning NMR spectroscopy.
2013,
Pubmed
Hall,
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome.
2009,
Pubmed
Hart,
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.
2012,
Pubmed
Henikoff,
Nucleosome destabilization in the epigenetic regulation of gene expression.
2008,
Pubmed
Humphrey,
VMD: visual molecular dynamics.
1996,
Pubmed
Hwang,
Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA.
2014,
Pubmed
Iwaki,
How are small ions involved in the compaction of DNA molecules?
2007,
Pubmed
Jin,
Synergistic action of RNA polymerases in overcoming the nucleosomal barrier.
2010,
Pubmed
Kato,
Characterization of the N-terminal tail domain of histone H3 in condensed nucleosome arrays by hydrogen exchange and NMR.
2009,
Pubmed
Korolev,
Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations.
2007,
Pubmed
Korolev,
H4 histone tail mediated DNA-DNA interaction and effects on DNA structure, flexibility, and counterion binding: a molecular dynamics study.
,
Pubmed
Korolev,
Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations.
2014,
Pubmed
Lee,
Linker DNA and H1-dependent reorganization of histone-DNA interactions within the nucleosome.
1998,
Pubmed
,
Xenbase
Lee,
The N-terminal tail of histone H2A binds to two distinct sites within the nucleosome core.
1997,
Pubmed
,
Xenbase
Lenz,
The influence of DNA shape fluctuations on fluorescence resonance energy transfer efficiency measurements in nucleosomes.
2015,
Pubmed
Li,
Rapid spontaneous accessibility of nucleosomal DNA.
2005,
Pubmed
Lindorff-Larsen,
Systematic validation of protein force fields against experimental data.
2012,
Pubmed
Lu,
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
2008,
Pubmed
Luger,
Crystal structure of the nucleosome core particle at 2.8 A resolution.
1997,
Pubmed
Madej,
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
2014,
Pubmed
Mangenot,
Salt-induced conformation and interaction changes of nucleosome core particles.
2002,
Pubmed
Mariño-Ramírez,
The Histone Database: an integrated resource for histones and histone fold-containing proteins.
2011,
Pubmed
Materese,
Counterion atmosphere and hydration patterns near a nucleosome core particle.
2009,
Pubmed
McGhee,
Nucleosome structure.
1980,
Pubmed
Mirny,
Nucleosome-mediated cooperativity between transcription factors.
2010,
Pubmed
Mueller-Planitz,
Nucleosome sliding mechanisms: new twists in a looped history.
2013,
Pubmed
Nishi,
Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites.
2015,
Pubmed
Norouzi,
Topological polymorphism of the two-start chromatin fiber.
2015,
Pubmed
Nurse,
Clipping of flexible tails of histones H3 and H4 affects the structure and dynamics of the nucleosome.
2013,
Pubmed
,
Xenbase
Obri,
ANP32E is a histone chaperone that removes H2A.Z from chromatin.
2014,
Pubmed
Olson,
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.
1998,
Pubmed
Pachov,
On the structure and dynamics of the complex of the nucleosome and the linker histone.
2011,
Pubmed
Pepenella,
Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure.
2014,
Pubmed
Pérez,
Frontiers in molecular dynamics simulations of DNA.
2012,
Pubmed
Petty,
Balancing chromatin remodeling and histone modifications in transcription.
2013,
Pubmed
Phillips,
Scalable molecular dynamics with NAMD.
2005,
Pubmed
Pilotto,
Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation.
2015,
Pubmed
Potoyan,
Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation.
2012,
Pubmed
Potoyan,
Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics.
2011,
Pubmed
Racki,
The histone H4 tail regulates the conformation of the ATP-binding pocket in the SNF2h chromatin remodeling enzyme.
2014,
Pubmed
Rando,
Combinatorial complexity in chromatin structure and function: revisiting the histone code.
2012,
Pubmed
Rhee,
Subnucleosomal structures and nucleosome asymmetry across a genome.
2014,
Pubmed
Roccatano,
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation.
,
Pubmed
Rohs,
The role of DNA shape in protein-DNA recognition.
2009,
Pubmed
Ruscio,
A computational study of nucleosomal DNA flexibility.
2006,
Pubmed
Ruthenburg,
Multivalent engagement of chromatin modifications by linked binding modules.
2007,
Pubmed
Shaytan,
Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.
2016,
Pubmed
Shaytan,
Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers.
2015,
Pubmed
Shogren-Knaak,
Histone H4-K16 acetylation controls chromatin structure and protein interactions.
2006,
Pubmed
Shukla,
The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling.
2011,
Pubmed
Stefanovsky VYu,
Laser-induced crosslinking of histones to DNA in chromatin and core particles: implications in studying histone-DNA interactions.
1989,
Pubmed
Studitsky,
Mechanism of transcription through the nucleosome by eukaryotic RNA polymerase.
1997,
Pubmed
Suto,
Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
2000,
Pubmed
,
Xenbase
Tan,
Nucleosome structural studies.
2011,
Pubmed
Tolstorukov,
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning.
2007,
Pubmed
Tomschik,
Nucleosome dynamics as studied by single-pair fluorescence resonance energy transfer: a reevaluation.
2009,
Pubmed
Tóth,
Chromatin compaction at the mononucleosome level.
2006,
Pubmed
Wang,
Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA.
2013,
Pubmed
,
Xenbase
Weng,
Probing interactions between lysine residues in histone tails and nucleosomal DNA via product and kinetic analysis.
2015,
Pubmed
Wilhelm,
Reconstitution of chromatin: assembly of the nucleosome.
1978,
Pubmed
Yang,
Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes.
2011,
Pubmed
Yang,
The core histone tail domains contribute to sequence-dependent nucleosome positioning.
2007,
Pubmed
,
Xenbase
Zhou,
Histone H4 K16Q mutation, an acetylation mimic, causes structural disorder of its N-terminal basic patch in the nucleosome.
2012,
Pubmed
Zlatanova,
The nucleosome family: dynamic and growing.
2009,
Pubmed
