The force is strong with this epigenome: chromatin structure and mechanobiology

CR Hsia, DP Melters, Y Dalal - Journal of Molecular Biology, 2023 - Elsevier
All life forms sense and respond to mechanical stimuli. Throughout evolution, organisms
develop diverse mechanosensing and mechanotransduction pathways, leading to fast and …

Chiral systems made from DNA

D Winogradoff, PY Li, H Joshi, L Quednau… - Advanced …, 2021 - Wiley Online Library
The very chemical structure of DNA that enables biological heredity and evolution has non‐
trivial implications for the self‐organization of DNA molecules into larger assemblies and …

AWSEM-IDP: a coarse-grained force field for intrinsically disordered proteins

H Wu, PG Wolynes, GA Papoian - The Journal of Physical …, 2018 - ACS Publications
The associative memory, water-mediated, structure and energy model (AWSEM) has been
successfully used to study protein folding, binding, and aggregation problems. In this work …

Exploring the free energy landscape of nucleosomes

B Zhang, W Zheng, GA Papoian… - Journal of the American …, 2016 - ACS Publications
The nucleosome is the fundamental unit for packaging the genome. A detailed molecular
picture for its conformational dynamics is crucial for understanding transcription and gene …

Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly

D Winogradoff, S John, A Aksimentiev - Nanoscale, 2020 - pubs.rsc.org
The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are
fundamental to the most common laboratory technique used to separate proteins and …

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

DP Melters, M Pitman, T Rakshit… - Proceedings of the …, 2019 - National Acad Sciences
Histone variants fine-tune transcription, replication, DNA damage repair, and faithful
chromosome segregation. Whether and how nucleosome variants encode unique …

Explicit ion modeling predicts physicochemical interactions for chromatin organization

X Lin, B Zhang - Elife, 2024 - elifesciences.org
Molecular mechanisms that dictate chromatin organization in vivo are under active
investigation, and the extent to which intrinsic interactions contribute to this process remains …

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 …

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

T Niina, GB Brandani, C Tan… - PLoS computational …, 2017 - journals.plos.org
While nucleosome positioning on eukaryotic genome play important roles for genetic
regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not …

[HTML][HTML] Breaths, twists, and turns of atomistic nucleosomes

J Huertas, V Cojocaru - Journal of molecular biology, 2021 - Elsevier
Gene regulation programs establish cellular identity and rely on dynamic changes in the
structural packaging of genomic DNA. The DNA is packaged in chromatin, which is formed …