Breaths, Twists, and Turns of Atomistic Nucleosomes

Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding

(2020) Jan Huertas et al.   BIOPHYSICAL JOURNAL

Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes

(2020) Mary Pitman et al.   BIOPHYSICAL JOURNAL

Beads on a string—nucleosome array arrangements and folding of the chromatin fiber

(2020) Sandro Baldi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Elucidating the influence of linker histone variants on chromatosome dynamics and energetics

(2020) Dustin C Woods et al.   NUCLEIC ACIDS RESEARCH

Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling

(2020) Joshua Moller et al.   BIOPHYSICAL JOURNAL

Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends

(2020) Ramachandran Boopathi et al.   NUCLEIC ACIDS RESEARCH

Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1

(2020) Akshay Sridhar et al.   NUCLEIC ACIDS RESEARCH

Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

(2020) Akshay Sridhar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of OCT4-SOX2 motif readout on nucleosomes

(2020) Alicia K. Michael et al.   SCIENCE

Nucleosome allostery in pioneer transcription factor binding

(2020) Cheng Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures

(2020) Junhui Peng et al.   Epigenetics & Chromatin

Nucleosome unwrapping and unstacking

(2020) Hidetoshi Kono et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Impact of the Nucleosome Histone Core on the Structure and Dynamics of DNA-Containing Pyrimidine–Pyrimidone (6–4) Photoproduct

(2020) Eva Matoušková et al.   Journal of Chemical Theory and Computation

Near-atomic resolution structures of interdigitated nucleosome fibres

(2020) Zenita Adhireksan et al.   Nature Communications

Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs

(2019) Masae Ohno et al.   CELL

Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR

(2019) Clara van Emmerik et al.   PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

DNA Crookedness Regulates DNA Mechanical Properties at Short Length Scales

(2019) Alberto Marin-Gonzalez et al.   PHYSICAL REVIEW LETTERS

Post-translational modifications and chromatin dynamics

(2019) Thomas O. Tolsma et al.   Essays in Biochemistry

Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

(2019) Jaewoon Jung et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The base pair-scale diffusion of nucleosomes modulates binding of transcription factors

(2019) Sergei Rudnizky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling

(2019) Arjan Hada et al.   Cell Reports

CENP ‐C unwraps the human CENP ‐A nucleosome through the H2A C‐terminal tail

(2019) Ahmad Ali‐Ahmad et al.   EMBO REPORTS

TMB Library of Nucleosome Simulations

(2019) Ran Sun et al.   Journal of Chemical Information and Modeling

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

(2019) Daniël P. Melters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Studies of Overlapping Dinucleosomes in Solution

(2019) Atsushi Matsumoto et al.   BIOPHYSICAL JOURNAL

Variable impact of conformationally distinct DNA lesions on nucleosome structure and dynamics: Implications for nucleotide excision repair

(2019) Yuqin Cai et al.   DNA REPAIR

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

Orientation Dependence of Inter-NCP Interaction: Insights into the Behavior of Liquid Crystal Phase and Chromatin Fiber Organization

(2019) Suman Saurabh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET

(2019) Kathrin Lehmann et al.   NUCLEIC ACIDS RESEARCH

Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding

(2018) Gavin D. Bascom et al.   BIOPHYSICAL JOURNAL

Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition

(2018) Yuqin Cai et al.   DNA REPAIR

DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

(2018) Giovanni B Brandani et al.   NUCLEIC ACIDS RESEARCH

Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many

(2018) Mehmet Ali Öztürk et al.   STRUCTURE

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

(2018) Hidetoshi Kono et al.   PLoS Computational Biology

Mechanical evolution of DNA double-strand breaks in the nucleosome

(2018) Fabrizio Cleri et al.   PLoS Computational Biology

Investigating the Influence of Arginine Dimethylation on Nucleosome Dynamics Using All-Atom Simulations and Kinetic Analysis

(2018) Zhenhai Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome

(2018) Iwen Fu et al.   DNA REPAIR

Molecular Mechanism of Spontaneous Nucleosome Unraveling

(2018) David Winogradoff et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Studies of Intrinsically Disordered Proteins

(2018) Vy T. Duong et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unique Dynamics in Asymmetric macroH2A–H2A Hybrid Nucleosomes Result in Increased Complex Stability

(2018) Samuel Bowerman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning

(2018) Kaushik Chakraborty et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nucleosome structure and dynamics are coming of age

(2018) Keda Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The role of DNA sequence in nucleosome breathing

(2017) Jamie Culkin et al.   EUROPEAN PHYSICAL JOURNAL E

Asymmetric breathing motions of nucleosomal DNA and the role of histone tails

(2017) Kaushik Chakraborty et al.   JOURNAL OF CHEMICAL PHYSICS

Biophysical studies of cholesterol effects on chromatin

(2017) Isabel T. G. Silva et al.   JOURNAL OF LIPID RESEARCH

The effect of epigenetic modifications on the secondary structures and possible binding positions of the N-terminal tail of histone H3 in the nucleosome: a computational study

(2017) Louis L. du Preez et al.   JOURNAL OF MOLECULAR MODELING

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1

(2017) Jan Bednar et al.   MOLECULAR CELL

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Internal modifications in the CENP-A nucleosome modulate centromeric dynamics

(2017) Minh Bui et al.   Epigenetics & Chromatin

Histone isoform H2A1H promotes attainment of distinct physiological states by altering chromatin dynamics

(2017) Saikat Bhattacharya et al.   Epigenetics & Chromatin

Accessibility of the histone H3 tail in the nucleosome for binding of paired readers

(2017) Jovylyn Gatchalian et al.   Nature Communications

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

(2017) Toru Niina et al.   PLoS Computational Biology

Effects of charge-modifying mutations in histone H2A α3-domain on nucleosome stability assessed by single-pair FRET and MD simulations

(2017) Kathrin Lehmann et al.   Scientific Reports

Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study

(2016) Iwen Fu et al.   BIOCHEMISTRY

Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations

(2016) Samuel Bowerman et al.   BIOPHYSICAL JOURNAL

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122

(2016) Muthukumaran Rajagopalan et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber

(2016) Saeed Izadi et al.   Journal of Chemical Theory and Computation

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

(2016) Alexey K. Shaytan et al.   JOURNAL OF MOLECULAR BIOLOGY

Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces

(2016) Suman Saurabh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones

(2016) Haiqing Zhao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails

(2016) Alexandra Stützer et al.   MOLECULAR CELL

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

(2016) Marco Pasi et al.   NUCLEIC ACIDS RESEARCH

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

(2016) Mehmet Ali Öztürk et al.   NUCLEIC ACIDS RESEARCH

Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability

(2016) Zhenhai Li et al.   Scientific Reports

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

(2016) Jinzen Ikebe et al.   PLoS Computational Biology

Differences in the Access of Lesions to the Nucleotide Excision Repair Machinery in Nucleosomes

(2015) Yuqin Cai et al.   BIOCHEMISTRY

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

(2015) Ramu Anandakrishnan et al.   BIOPHYSICAL JOURNAL

The chromatin fiber: multiscale problems and approaches

(2015) Gungor Ozer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

(2015) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

(2015) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Elasticity from Short DNA to Nucleosomal DNA

(2015) Ashok Garai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study

(2015) Rosana Collepardo-Guevara et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects

(2015) David Winogradoff et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics

(2015) Yuqing Zheng et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Two Arginine Residues Suppress the Flexibility of Nucleosomal DNA in the Canonical Nucleosome Core

(2015) Hidetoshi Kono et al.   PLoS One

The Role of Histone Tails in the Nucleosome: A Computational Study

(2014) Jochen Erler et al.   BIOPHYSICAL JOURNAL

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

Chromatin fiber polymorphism triggered by variations of DNA linker lengths

(2014) R. Collepardo-Guevara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Gas-Phase Structure of the Histone Multimers Characterized by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

(2013) Kazumi Saikusa et al.   ANALYTICAL CHEMISTRY

Histone- and DNA sequence-dependent stability of nucleosomes studied by single-pair FRET

(2013) Katalin Tóth et al.   CYTOMETRY PART A

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

(2013) Guillem Portella et al.   PLoS Computational Biology

Short nucleosome repeats impose rotational modulations on chromatin fibre folding

(2012) Sarah J Correll et al.   EMBO JOURNAL

The mechanics behind DNA sequence-dependent properties of the nucleosome

(2012) Eugene Y. D. Chua et al.   NUCLEIC ACIDS RESEARCH

Dissecting DNA-Histone Interactions in the Nucleosome by Molecular Dynamics Simulations of DNA Unwrapping

(2011) Ramona Ettig et al.   BIOPHYSICAL JOURNAL

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence

(2010) Dileep Vasudevan et al.   JOURNAL OF MOLECULAR BIOLOGY

The histone variant CENP-A and centromere specification

(2008) Ben E Black et al.   CURRENT OPINION IN CELL BIOLOGY