Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

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

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

Structural rearrangements of the histone octamer translocate DNA

(2018) Silvija Bilokapic et al.   Nature Communications

A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA

(2018) Jessica Winger et al.   eLife

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex

(2018) Sebastian Eustermann et al.   NATURE

Structure and regulation of the human INO80–nucleosome complex

(2018) Rafael Ayala et al.   NATURE

The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler

(2017) Jessica Winger et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure

(2017) Xiaoyu Liu et al.   NATURE

Nucleosome–Chd1 structure and implications for chromatin remodelling

(2017) Lucas Farnung et al.   NATURE

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

In silico evidence for sequence-dependent nucleosome sliding

(2017) Joshua Lequieu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distortion of histone octamer core promotes nucleosome mobilization by a chromatin remodeler

(2017) Kalyan K. Sinha et al.   SCIENCE

INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers

(2017) Sandipan Brahma 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

DNA topology in chromatin is defined by nucleosome spacing

(2017) Tatiana Nikitina et al.   Science Advances

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

(2016) Coral Y. Zhou et al.   Annual Review of Biophysics

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

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

Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics

(2016) Cheng Tan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exploring the Free Energy Landscape of Nucleosomes

(2016) Bin Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics of Nucleosome Positioning Maturation following Genomic Replication

(2016) Pauline Vasseur et al.   Cell Reports

Stepwise nucleosome translocation by RSC remodeling complexes

(2016) Bryan T Harada et al.   eLife

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

(2016) Le Chang et al.   Scientific Reports

Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

(2015) Shoji Takada et al.   ACCOUNTS OF CHEMICAL RESEARCH

Molecular mechanisms of ribosomal protein gene coregulation

(2015) Rohit Reja et al.   GENES & DEVELOPMENT

Chromatin-remodeling and the initiation of transcription

(2015) Yahli Lorch et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

(2015) Hiroo Kenzaki et al.   PLoS Computational Biology

Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions

(2014) Yahli Lorch et al.   GENES & DEVELOPMENT

Coarse-grained modeling of DNA curvature

(2014) Gordon S. Freeman et al.   JOURNAL OF CHEMICAL PHYSICS

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

(2014) Tsuyoshi Terakawa et al.   Journal of Chemical Theory and Computation

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

(2014) Gordon S. Freeman et al.   PHYSICAL REVIEW LETTERS

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains

(2014) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome sliding mechanisms: new twists in a looped history

(2013) Felix Mueller-Planitz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler

(2012) Ashok Patel et al.   NUCLEIC ACIDS RESEARCH

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

(2012) T. van der Heijden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Ensemble Modeling of Intrinsically Disordered Proteins: p53 N-Terminal Domain

(2011) Tsuyoshi Terakawa et al.   BIOPHYSICAL JOURNAL

The RSC chromatin remodelling ATPase translocates DNA with high force and small step size

(2011) George Sirinakis et al.   EMBO JOURNAL

The dynamics of the nucleosome: thermal effects, external forces and ATP

(2011) Ralf Blossey et al.   FEBS Journal

Mechanisms for ATP-dependent chromatin remodelling: the means to the end

(2011) Andrew Flaus et al.   FEBS Journal

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

Identification of a Rapidly Formed Nonnucleosomal Histone-DNA Intermediate that Is Converted into Chromatin by ACF

(2011) Sharon E. Torigoe et al.   MOLECULAR CELL

A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization

(2011) T. Gkikopoulos et al.   SCIENCE

A proposal for kinetic proof reading by ISWI family chromatin remodeling motors

(2010) Geeta J Narlikar   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism

(2010) M. Gu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations

(2010) H. Flechsig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug export and allosteric coupling in a multidrug transporter revealed by molecular simulations

(2010) Xin-Qiu Yao et al.   Nature Communications

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

(2009) Alexandre V. Morozov et al.   NUCLEIC ACIDS RESEARCH

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Kinetic proofreading of gene activation by chromatin remodeling

(2008) R. Blossey et al.   HFSP Journal

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

(2008) Sushma Shivaswamy et al.   PLOS BIOLOGY

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology