Related references
Note: Only part of the references are listed.Biophysics of Chromatin Remodeling
Ilana M. Nodelman et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 50, 2021 (2021)
Effects of H2A.B incorporation on nucleosome structures and dynamics
Havva Kohestani et al.
BIOPHYSICAL JOURNAL (2021)
Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA
Hisashi Ishida et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)
Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome
Rina Hirano et al.
COMMUNICATIONS BIOLOGY (2021)
Structural basis of nucleosome transcription mediated by Chd1 and FACT
Lucas Farnung et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)
Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
Grigoriy A. Armeev et al.
NATURE COMMUNICATIONS (2021)
The dark side of histones: genomic organization and role of oncohistones in cancer
Stefano Amatori et al.
CLINICAL EPIGENETICS (2021)
Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics
Sergio Cruz-Leon et al.
LANGMUIR (2020)
Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding
Anna S. Kamenik et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
The expanding landscape of 'oncohistone' mutations in human cancers
Benjamin A. Nacev et al.
NATURE (2019)
The Oligomerization Landscape of Histones
Haiqing Zhao et al.
BIOPHYSICAL JOURNAL (2019)
A Mutation in Histone H2B Represents a New Class of Oncogenic Driver
Richard L. Bennett et al.
CANCER DISCOVERY (2019)
Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome
Hidetoshi Kono et al.
BIOPHYSICS AND PHYSICOBIOLOGY (2019)
Functions of FACT in Breaking the Nucleosome and Maintaining Its Integrity at the Single-Nucleosome Level
Ping Chen et al.
MOLECULAR CELL (2018)
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
Jejoong Yoo et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2018)
Developing a molecular dynamics force field for both folded and disordered protein states
Paul Robustelli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
Hidetoshi Kono et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA
Jessica Winger et al.
ELIFE (2018)
Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function
Rajbir Singh et al.
NUCLEIC ACIDS RESEARCH (2018)
Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations
Louis G. Smith et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Structure and dynamics of the yeast SWR1-nucleosome complex
Oliver Willhoft et al.
SCIENCE (2018)
High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes
Alexander Gansen et al.
NATURE COMMUNICATIONS (2018)
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA
Giovanni B. Brandani et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes
Cedric R. Clapier et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Histone chaperone networks shaping chromatin function
Colin M. Hammond et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Dual function of Swc5 in SWR remodeling ATPase activation and histone H2A eviction
Lu Sun et al.
NUCLEIC ACIDS RESEARCH (2017)
Histone isoform H2A1H promotes attainment of distinct physiological states by altering chromatin dynamics
Saikat Bhattacharya et al.
EPIGENETICS & CHROMATIN (2017)
Effects of charge-modifying mutations in histone H2A α3-domain on nucleosome stability assessed by single-pair FRET and MD simulations
Kathrin Lehmann et al.
SCIENTIFIC REPORTS (2017)
H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes
Hisashi Ishida et al.
BIOPHYSICAL JOURNAL (2017)
Single-Molecule Investigations on Histone H2A-H2B Dynamics in the Nucleosome
Jaehyoun Lee et al.
BIOCHEMISTRY (2017)
Parmbsc1: a refined force field for DNA simulations
Ivan Ivani et al.
NATURE METHODS (2016)
Integrated molecular mechanism directing nucleosome reorganization by human FACT
Yasuo Tsunaka et al.
GENES & DEVELOPMENT (2016)
Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones
Haiqing Zhao et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
Exploring the Free Energy Landscape of Nucleosomes
Bin Zhang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (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)
The Abundant Histone Chaperones Spt6 and FACT Collaborate to Assemble, Inspect, and Maintain Chromatin Structure in Saccharomyces cerevisiae
Laura McCullough et al.
GENETICS (2015)
Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment
Joao Henriques et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
Stefano Piana et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Histone exchange, chromatin structure and the regulation of transcription
Swaminathan Venkatesh et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)
Nucleosomes undergo slow spontaneous gaping
Thuy T. M. Ngo et al.
NUCLEIC ACIDS RESEARCH (2015)
Generation of a synthetic GlcNAcylated nucleosome reveals regulation of stability by H2A-Thr101 GlcNAcylation
Lukas Lercher et al.
NATURE COMMUNICATIONS (2015)
H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast
Anand Ranjan et al.
ELIFE (2015)
Histone H3 Ser57 and Thr58 phosphorylation in the brain of 5XFAD mice
Kyle W. Anderson et al.
FEBS OPEN BIO (2015)
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)
Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations
Anita de Ruiter et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Histone chaperone FACT action during transcription through chromatin by RNA polymerase II
Fu-Kai Hsieh et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme
Shinya Watanabe et al.
SCIENCE (2013)
Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss
Maxim Y. Sheinin et al.
NATURE COMMUNICATIONS (2013)
The conformational flexibility of the C-terminus of histone H4 promotes histone octamer and nucleosome stability and yeast viability
Myrriah S. Chavez et al.
EPIGENETICS & CHROMATIN (2012)
A Conserved Patch near the C Terminus of Histone H4 Is Required for Genome Stability in Budding Yeast
Yao Yu et al.
MOLECULAR AND CELLULAR BIOLOGY (2011)
Accounting for electronic polarization in non-polarizable force fields
Igor Leontyev et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
Nucleosome accessibility governed by the dimer/tetramer interface
Vera Boehm et al.
NUCLEIC ACIDS RESEARCH (2011)
Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome
Ed Luk et al.
CELL (2010)
Mechanisms of ATP-dependent nucleosome sliding
Gregory D. Bowman
CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)
SWI/SNF Has Intrinsic Nucleosome Disassembly Activity that Is Dependent on Adjacent Nucleosomes
Mekonnen Lemma Dechassa et al.
MOLECULAR CELL (2010)
Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T
Hiroaki Tachiwana et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
Christine Vogler et al.
PLOS GENETICS (2010)
A Method for Genetically Installing Site-Specific Acetylation in Recombinant Histories Defines the Effects of H3 K56 Acetylation
Heinz Neumann et al.
MOLECULAR CELL (2009)
Path of Nascent Polypeptide in Exit Tunnel Revealed by Molecular Dynamics Simulation of Ribosome
Hisashi Ishida et al.
BIOPHYSICAL JOURNAL (2008)
Quickly evolving histones, nucleosome stability and chromatin folding:: All about histone H2A.Bbd
Rodrigo Gonzalez-Romero et al.
GENE (2008)
Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method
Ilja V. Khavrutskii et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
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)
Nap1 links transcription elongation, chromatin assembly, and messenger RNP complex biogenesis
Brian C. Del Rosario et al.
MOLECULAR AND CELLULAR BIOLOGY (2008)
Protein-protein forster resonance energy transfer analysis of nucleosome core particles containing H2A and H2A.Z
Duane A. Hoch et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Histone tails and the H3 αN helix regulate nucleosome mobility and stability
Helder Ferreira et al.
MOLECULAR AND CELLULAR BIOLOGY (2007)
A comparison of methods to compute the potential of mean force
Daniel Trzesniak et al.
CHEMPHYSCHEM (2007)
On the mechanism of nucleosome assembly by histone chaperone NAP1
Jacek Mazurkiewicz et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2006)
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
P Raiteri et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Chromatin remodeling by nucleosome disassembly in vitro
Y Lorch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae
EA Hyland et al.
MOLECULAR AND CELLULAR BIOLOGY (2005)
Histone H4 lysine 91 acetylation: A core domain modification associated with chromatin assembly
JX Ye et al.
MOLECULAR CELL (2005)
Rapid spontaneous accessibility of nucleosomal DNA
G Li et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2005)
Sin mutations alter inherent nucleosome mobility
A Flaus et al.
EMBO JOURNAL (2004)
ATP-Driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex
G Mizuguchi et al.
SCIENCE (2004)
Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities
M Bruno et al.
MOLECULAR CELL (2003)
FACT facilitates transcription-dependent nucleosome alteration
R Belotserkovskaya et al.
SCIENCE (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)
Nucleosome remodeling induced by RNA polymerase II: Loss of the H2A/H2B dimer during transcription
ML Kireeva et al.
MOLECULAR CELL (2002)
A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage
TT Paull et al.
CURRENT BIOLOGY (2000)