The Role of Histone Tails in the Nucleosome: A Computational Study
Reads0
Chats0
TLDR
Results from both implicit and explicit solvent models show that large portions of the histone tails are not bound to DNA, supporting the complex role of these tails in gene transcription and expression and making them possible candidates for binding sites of transcription factors, enzymes, and other proteins.About:
This article is published in Biophysical Journal.The article was published on 2014-12-16 and is currently open access. It has received 66 citations till now. The article focuses on the topics: Histone octamer & Linker DNA.read more
Citations
More filters
Journal ArticleDOI
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions
Alexey K. Shaytan,G. A. Armeev,Alexander Goncearenco,Victor B. Zhurkin,David Landsman,Anna R. Panchenko +5 more
TL;DR: An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin, suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of hist one tail modifications and binding of the effector proteins.
Journal ArticleDOI
Multiscale simulation of DNA.
TL;DR: The most recent theoretical methods that have been considered to study DNA, from the electron to the chromosome, are described, enriching knowledge on this fascinating molecule.
Journal ArticleDOI
A Current Overview of the Biological and Cellular Effects of Nanosilver.
TL;DR: The interactions and effects of nanosilver on cellular uptake, oxidative stress (reactive oxygen species), inflammation, hypoxic response, mitochondrial function, endoplasmic reticulum (ER) function and the unfolded protein response, autophagy and apoptosis, angiogenesis, epigenetics, genotoxicity, and cancer development and tumorigenesis—as well as other pathway alterations—are examined in this review.
Journal ArticleDOI
Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter-nucleosome Interaction
TL;DR: This study suggests that H4K16Ac directly reduces the inter-nucleosome interaction mediated by the H4 tail, which might further encourage the binding of nonhistone proteins on the acidic patch.
Journal ArticleDOI
The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome
TL;DR: This work finds that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding, and alters the electrostatics of the H3 tail via modification or mutation, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation.
References
More filters
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Journal ArticleDOI
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
TL;DR: A new implementation of the molecular simulation toolkit GROMACS is presented which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines.
Journal ArticleDOI
GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI
LINCS : A linear constraint solver for molecular simulations
TL;DR: Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules.