Related references
Note: Only part of the references are listed.H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes
Hisashi Ishida et al.
BIOPHYSICAL JOURNAL (2017)
Histone Acetylation Regulates Chromatin.Accessibility: Role of H4K16 in Inter-nucleosome Interaction
Ruihan Zhang et al.
BIOPHYSICAL JOURNAL (2017)
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions
Alexey K. Shaytan et al.
JOURNAL OF MOLECULAR BIOLOGY (2016)
Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations
Hisashi Ishida et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2016)
Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability
Zhenhai Li et al.
SCIENTIFIC REPORTS (2016)
H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation
Jinzen Ikebe et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
Tension-Dependent Free Energies of Nucleosome Unwrapping
Joshua Lequieu et al.
ACS CENTRAL SCIENCE (2016)
Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers
Alexey K. Shaytan et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2015)
The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects
David Winogradoff et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers
He Meng et al.
NUCLEIC ACIDS RESEARCH (2015)
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations
Hiroo Kenzaki et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Two Arginine Residues Suppress the Flexibility of Nucleosomal DNA in the Canonical Nucleosome Core
Hidetoshi Kono et al.
PLOS ONE (2015)
Characterization of Nucleosome Unwrapping within Chromatin Fibers Using Magnetic Tweezers
Fan-Tso Chien et al.
BIOPHYSICAL JOURNAL (2014)
The Role of Histone Tails in the Nucleosome: A Computational Study
Jochen Erler et al.
BIOPHYSICAL JOURNAL (2014)
Molecular Dynamics Simulations Demonstrate the Regulation of DNA-DNA Attraction by H4 Histone Tail Acetylations and Mutations
Nikolay Korolev et al.
BIOPOLYMERS (2014)
Free-Energy Landscape of Reverse tRNA Translocation through the Ribosome Analyzed by Electron Microscopy Density Maps and Molecular Dynamics Simulations
Hisashi Ishida et al.
PLOS ONE (2014)
Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations
Hisashi Ishida
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2014)
Histone H3 and H4 N-Terminal Tails in Nucleosome Arrays at Cellular Concentrations Probed by Magic Angle Spinning NMR Spectroscopy
Min Gao et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Solution Scattering and FRET Studies on Nucleosomes Reveal DNA Unwrapping Effects of H3 and H4 Tail Removal
Kurt Andresen et al.
PLOS ONE (2013)
Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study
Karine Voltz et al.
BIOPHYSICAL JOURNAL (2012)
Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation
Davit A. Potoyan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Dissecting DNA-Histone Interactions in the Nucleosome by Molecular Dynamics Simulations of DNA Unwrapping
Ramona Ettig et al.
BIOPHYSICAL JOURNAL (2011)
Dynamics of Nucleosome Invasion by DNA Binding Proteins
Hannah S. Tims et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
A quantitative model of nucleosome dynamics
Robert A. Forties et al.
NUCLEIC ACIDS RESEARCH (2011)
Role of Histone Tails in Structural Stability of the Nucleosome
Mithun Biswas et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Charge State of the Globular Histone Core Controls Stability of the Nucleosome
Andrew T. Fenley et al.
BIOPHYSICAL JOURNAL (2010)
spFRET Using Alternating Excitation and FCS Reveals Progressive DNA Unwrapping in Nucleosomes
W. J. A. Koopmans et al.
BIOPHYSICAL JOURNAL (2009)
Structural Variability of Nucleosomes Detected by Single-Pair Forster Resonance Energy Transfer: Histone Acetylation, Sequence Variation, and Salt Effects
Alex Gansen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber
Maarten Kruithof et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome
Michael A. Hall et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)
Adaptively biased molecular dynamics for free energy calculations
Volodymyr Babin et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
In Suk Joung et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Sequence-dependent DNA deformability studied using molecular dynamics simulations
Satoshi Fujii et al.
NUCLEIC ACIDS RESEARCH (2007)
Refinenement of the AMBER force field for nucleic acids:: Improving the description of α/γ conformers
Alberto Perez et al.
BIOPHYSICAL JOURNAL (2007)
Histone tails and the H3 αN helix regulate nucleosome mobility and stability
Helder Ferreira et al.
MOLECULAR AND CELLULAR BIOLOGY (2007)
H3 and H4 histone tails play a central role in the interactions of recombinant NCPs
Aurelie Bertin et al.
BIOPHYSICAL JOURNAL (2007)
Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity
Hernan G. Garcia et al.
BIOPOLYMERS (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Effect of force on mononucleosomal dynamics
Shirley Mihardja et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
P Raiteri et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Molecular dynamics simulations of a nucleosome and free DNA
TC Bishop
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2005)
Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes
B Brower-Toland et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Rapid spontaneous accessibility of nucleosomal DNA
G Li et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2005)
Role of histone tails in the conformation and interactions of nucleosome core particles
A Bertin et al.
BIOCHEMISTRY (2004)
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
XJ Lu et al.
NUCLEIC ACIDS RESEARCH (2003)
Characterization of sequence variability in nucleosome core histone folds
SA Sullivan et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)
Intra- and inter-nucleosomal protein-DNA interactions of the core histone tail domains in a model system
CY Zheng et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 Å resolution
CA Davey et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA
BD Brower-Toland et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Energetics and affinity of the histone octamer for defined DNA sequences
JM Gottesfeld et al.
BIOCHEMISTRY (2001)
Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
M Souaille et al.
COMPUTER PHYSICS COMMUNICATIONS (2001)
Acetylation increases the α-helical content of the histone tails of the nucleosome
XY Wang et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2000)
DNA sequence-dependent contributions of core histone tails to nucleosome stability: Differential effects of acetylation and proteolytic tail removal
HR Widlund et al.
BIOCHEMISTRY (2000)
Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites
JD Anderson et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)