[HTML][HTML] Structural dynamics in chromatin unraveling by pioneer transcription factors

A Orsetti, D van Oosten, RG Vasarhelyi… - Biophysical …, 2024 - Springer
Pioneer transcription factors are proteins with a dual function. First, they regulate
transcription by binding to nucleosome-free DNA regulatory elements. Second, they bind to …

Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations

R Patel, A Onyema, PK Tang… - Journal of Chemical …, 2024 - ACS Publications
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the
chromatin structure and biological processes such as transcription and DNA repair. One of …

Sequence dependence in nucleosome dynamics

P Khatua, P Tang, AG Moulick, R Patel, A Manandhar… - Biophysical …, 2024 - cell.com
The basic packaging unit of chromatin is the nucleosome, which consists of a 145-147 base
pair DNA wrapped around the histone. The interplay between DNA sequence and …

Monitoring Anthracycline Cancer Drug‐Nucleosome Interaction by NMR Using a Specific Isotope Labeling Approach for Nucleosomal DNA

CL van Emmerik, V Lobbia, J Neefjes… - …, 2024 - Wiley Online Library
Chromatinized DNA is targeted by proteins and small molecules to regulate chromatin
function. For example, anthracycline cancer drugs evict nucleosomes in a mechanism that is …

What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.

M Kermarrec, E Dumont, N Gillet - Biophysical Journal, 2024 - cell.com
Guanine radical cations are precursors to oxidatively-induced DNA lesions and the
determination of oxidative DNA hot spots beyond oligonucleotides remains a current …

Histone Tetrasome Dynamics Affects Chromatin Transcription

X Shi, A Fedulova, E Kotova, N Maluchenko, G Armeev… - bioRxiv, 2024 - biorxiv.org
During various DNA-centered processes in the cell nucleus, the minimal structural units of
chromatin organization, nucleosomes, are often transiently converted to hexasomes and …

Development of an Integrated Workflow for Nucleosome Modeling and Simulations

R Sun - 2024 - digitalcommons.latech.edu
Nucleosomes are the building blocks of eukaryotic genomes and thus fundamental to to all
genetic processes. Any protein or drug that binds DNA must either cooperate or compete …

INVESTIGATING THE DOWNSTREAM REACTIONS AND EFFECTS OF DNA METHYLATION AND ONE ELECTRON OXIDATION IN NUCLEOSOME CORE …

T Wen - 2024 - jscholarship.library.jhu.edu
DNA damage caused by alkylation and oxidation is harmful to cells, potentially leading to
cell death or cancer. Alkylating drugs and radiotherapy exploit this cytotoxicity to kill tumor …