相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Breaths, Twists, and Turns of Atomistic Nucleosomes
Jan Huertas et al.
JOURNAL OF MOLECULAR BIOLOGY (2021)
Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET
Kathrin Lehmann et al.
NUCLEIC ACIDS RESEARCH (2020)
Post-translational modifications and chromatin dynamics
Thomas O. Tolsma et al.
DNA PACKAGING: NUCLEOSOME AND CHROMATIN (2019)
Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners
Daniel P. Melters et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Molecular Mechanism of Spontaneous Nucleosome Unraveling
David Winogradofft et al.
JOURNAL OF MOLECULAR BIOLOGY (2019)
Nucleosome structure and dynamics are coming of age
Keda Zhou et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)
Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency
Kenjiro Adachi et al.
CELL STEM CELL (2018)
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
Hidetoshi Kono et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning
Kaushik Chakraborty et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA
Giovanni B. Brandani et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Changing POU dimerization preferences converts Oct6 into a pluripotency inducer
Stepan Jerabek et al.
EMBO REPORTS (2017)
Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core
Yujie Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
The role of DNA sequence in nucleosome breathing
Jamie Culkin et al.
EUROPEAN PHYSICAL JOURNAL E (2017)
Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail-H2A Acidic Patch Interaction
Qinming Chen et al.
JOURNAL OF MOLECULAR BIOLOGY (2017)
In silico evidence for sequence-dependent nudeosome sliding
Joshua Lequieu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
Toru Niina et al.
PLOS COMPUTATIONAL BIOLOGY (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)
Parmbsc1: a refined force field for DNA simulations
Ivan Ivani et al.
NATURE METHODS (2016)
Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations
Samuel Bowerman et al.
BIOPHYSICAL JOURNAL (2016)
LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency
Jin Zhang et al.
CELL STEM CELL (2016)
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)
Exploring the Free Energy Landscape of Nucleosomes
Bin Zhang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome
Mehmet Ali Oeztuerk et al.
NUCLEIC ACIDS RESEARCH (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)
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
Abdenour Soufi et al.
CELL (2015)
Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model
Pengfei Li 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)
DNA Elasticity from Short DNA to Nucleosomal DNA
Ashok Garai et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2015)
Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study
Rosana Collepardo-Guevara et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (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)
Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations
Hiroo Kenzaki et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Post-Translational Modifications of Histones That Influence Nucleosome Dynamics
Gregory D. Bowman et al.
CHEMICAL REVIEWS (2015)
The Role of Histone Tails in the Nucleosome: A Computational Study
Jochen Erler et al.
BIOPHYSICAL JOURNAL (2014)
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S. P. Rao et al.
CELL (2014)
DNA Shape Dominates Sequence Affinity in Nucleosome Formation
Gordon S. Freeman et al.
PHYSICAL REVIEW LETTERS (2014)
Clipping of Flexible Tails of Histones H3 and H4 Affects the Structure and Dynamics of the Nucleosome
Nathan P. Nurse et al.
BIOPHYSICAL JOURNAL (2013)
Histone- and DNA sequence-dependent stability of nucleosomes studied by single-pair FRET
Katalin Toth et al.
CYTOMETRY PART A (2013)
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Using collective variables to drive molecular dynamics simulations
Giacomo Fiorin et al.
MOLECULAR PHYSICS (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)
Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome
Abdenour Soufi et al.
CELL (2012)
The mechanics behind DNA sequence-dependent properties of the nucleosome
Eugene Y. D. Chua et al.
NUCLEIC ACIDS RESEARCH (2012)
Dissecting DNA-Histone Interactions in the Nucleosome by Molecular Dynamics Simulations of DNA Unwrapping
Ramona Ettig et al.
BIOPHYSICAL JOURNAL (2011)
Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics
Davit A. Potoyan et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Role of Histone Tails in Structural Stability of the Nucleosome
Mithun Biswas et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
Crystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence
Dileep Vasudevan et al.
JOURNAL OF MOLECULAR BIOLOGY (2010)
Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
Christine Vogler et al.
PLOS GENETICS (2010)
Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle
Christopher K. Materese et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Mesoscale simulations of two nucleosome-repeat length oligonucleosomes
Tamar Schlick et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2009)
High-resolution profiling of histone methylations in the human genome
Artern Barski et al.
CELL (2007)
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
Danilo Roccatano et al.
BIOPOLYMERS (2007)
A computational study of nucleosomal DNA flexibility
Jory Z. Ruscio et al.
BIOPHYSICAL JOURNAL (2006)
Histone H4-K16 acetylation controls chromatin structure and protein interactions
M Shogren-Knaak et al.
SCIENCE (2006)
Scalable molecular dynamics with NAMD
JC Phillips et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Salt-dependent intra- and internucleosomal interactions of the H3 tail domain in a model oligonucleosomal array
CY Zheng et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2005)
Molecular dynamics simulations of a nucleosome and free DNA
TC Bishop
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2005)
Rapid spontaneous accessibility of nucleosomal DNA
G Li et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2005)
The structure of DNA in the nucleosome core
TJ Richmond et al.
NATURE (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)
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins
M Lachner et al.
NATURE (2001)
分享论文
