Disordered regions tune order in chromatin organization and function

S Shukla, P Agarwal, A Kumar - Biophysical Chemistry, 2022‏ - Elsevier
Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered
regions (both collectively designated as IDP (R) s) defy the well-established structure …

Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins

JC Sanders, ED Holmstrom - Essays in biochemistry, 2021‏ - portlandpress.com
The conformations of biological macromolecules are intimately related to their cellular
functions. Conveniently, the well-characterized dipole–dipole distance-dependence of …

Tuning formation of protein–DNA coacervates by sequence and environment

KM Lebold, RB Best - The Journal of Physical Chemistry B, 2022‏ - ACS Publications
The high concentration of nucleic acids and positively charged proteins in the cell nucleus
provides many possibilities for complex coacervation. We consider a prototypical mixture of …

Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins

JJ Alston, A Soranno, AS Holehouse - Methods, 2021‏ - Elsevier
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have
emerged from a niche corner of biophysics to be recognized as essential drivers of cellular …

Binding dynamics of disordered linker histone H1 with a nucleosomal particle

H Wu, Y Dalal, GA Papoian - Journal of molecular biology, 2021‏ - Elsevier
Linker histone H1 is an essential regulatory protein for many critical biological processes,
such as eukaryotic chromatin packaging and gene expression. Mis-regulation of H1s is …

Single-molecule conformational dynamics of a transcription factor reveals a continuum of binding modes controlling association and dissociation

W Chen, W Lu, PG Wolynes… - Nucleic Acids …, 2021‏ - academic.oup.com
Binding and unbinding of transcription factors to DNA are kinetically controlled to regulate
the transcriptional outcome. Control of the release of the transcription factor NF-κB from DNA …

Extended and dynamic linker histone-DNA Interactions control chromatosome compaction

S Rudnizky, H Khamis, Y Ginosar, E Goren, P Melamed… - Molecular Cell, 2021‏ - cell.com
Chromatosomes play a fundamental role in chromatin regulation, but a detailed
understanding of their structure is lacking, partially due to their complex dynamics. Using …

DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study

M De, MA Öztürk, S Isbaner, K Tóth, RC Wade - Biophysical journal, 2021‏ - cell.com
Linker histones (LHs) bind to nucleosomes with their globular domain (gH) positioned in
either an on-or an off-dyad binding mode. Here, we study the effect of the linker DNA (L …

In vitro characterization of histone chaperones using analytical, pull-down and chaperoning assays

RC Bobde, K Saharan, S Baral, S Gandhi… - Journal of Visualized …, 2021‏ - app.jove.com
Histone proteins associate with DNA to form the eukaryotic chromatin. The basic unit of
chromatin is a nucleosome, made up of a histone octamer consisting of two copies of the …

Protein intrinsic disorder on a dynamic nucleosomal landscape

S Bjarnason, SF Ruidiaz, J McIvor… - Progress in Molecular …, 2021‏ - Elsevier
The complex nucleoprotein landscape of the eukaryotic cell nucleus is rich in dynamic
proteins that lack a stable three-dimensional structure. Many of these intrinsically disordered …