Genome modeling: from chromatin fibers to genes
The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …
many creative modeling studies. The specific model/simulation technique combination …
[HTML][HTML] Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
GA Armeev, AS Kniazeva, GA Komarova… - Nature …, 2021 - nature.com
Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly
wrap∼ 147 DNA base pairs around an octamer of histone proteins. How nucleosome …
wrap∼ 147 DNA base pairs around an octamer of histone proteins. How nucleosome …
Linking chromatin composition and structural dynamics at the nucleosome level
Nucleosomes are fundamental units of chromatin compaction, which organize∼ 200 DNA
base pairs using an octamer of histone proteins. Their ubiquitous presence in the cell …
base pairs using an octamer of histone proteins. Their ubiquitous presence in the cell …
[HTML][HTML] Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations
Residue-level coarse-grained (CG) models have become one of the most popular tools in
biomolecular simulations in the trade-off between modeling accuracy and computational …
biomolecular simulations in the trade-off between modeling accuracy and computational …
[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
Three-dimensional (3D) organization of the human genome plays an essential role in all
DNA-templated processes, including gene transcription, gene regulation, and DNA …
DNA-templated processes, including gene transcription, gene regulation, and DNA …
Determining sequence-dependent DNA oligonucleotide hybridization and dehybridization mechanisms using coarse-grained molecular simulation, markov state …
A robust understanding of the sequence-dependent thermodynamics of DNA hybridization
has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the …
has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the …
A bottom-up coarse-grained model for nucleosome–nucleosome interactions with explicit ions
The nucleosome core particle (NCP) is a large complex of 145–147 base pairs of DNA and
eight histone proteins and is the basic building block of chromatin that forms the …
eight histone proteins and is the basic building block of chromatin that forms the …
DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
While nucleosomes are highly stable structures as fundamental units of chromatin, they also
slide along the DNA, either spontaneously or by active remodelers. Here, we investigate the …
slide along the DNA, either spontaneously or by active remodelers. Here, we investigate the …
[PDF][PDF] Nucleosomal DNA dynamics mediate Oct4 pioneer factor binding
Transcription factor (TF) proteins bind to DNA to regulate gene expression. Normally,
accessibility to DNA is required for their function. However, in the nucleus, the DNA is often …
accessibility to DNA is required for their function. However, in the nucleus, the DNA is often …
Molecular mechanism of spontaneous nucleosome unraveling
D Winogradoff, A Aksimentiev - Journal of molecular biology, 2019 - Elsevier
Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-
diameter nucleus. For the genetic information encoded in the DNA to become available for …
diameter nucleus. For the genetic information encoded in the DNA to become available for …