Expanding the paradigm: intrinsically disordered proteins and allosteric regulation

RB Berlow, HJ Dyson, PE Wright - Journal of molecular biology, 2018 - Elsevier
Allosteric regulatory processes are implicated at all levels of biological function. Recent
advances in our understanding of the diverse and functionally significant class of intrinsically …

[HTML][HTML] Bacterial replisomes

ZQ Xu, NE Dixon - Current opinion in structural biology, 2018 - Elsevier
Highlights•Cryo-EM structures of Escherichia coli DNA polymerase III complexes.•Bacterial
polymerases quickly exchange at replication forks.•Bacterial replisomes can work in a …

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 …

Facilitated dissociation of transcription factors from single DNA binding sites

RI Kamar, EJ Banigan, A Erbas… - Proceedings of the …, 2017 - National Acad Sciences
The binding of transcription factors (TFs) to DNA controls most aspects of cellular function,
making the understanding of their binding kinetics imperative. The standard description of …

Recycling of single-stranded DNA-binding protein by the bacterial replisome

LM Spenkelink, JS Lewis, S Jergic, ZQ Xu… - Nucleic acids …, 2019 - academic.oup.com
Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-
stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing …

[HTML][HTML] Role of Shape Deformation of DNA-Binding Sites in Regulating the Efficiency and Specificity in Their Recognition by DNA-Binding Proteins

SK Mishra, A Bhattacherjee - JACS Au, 2024 - ncbi.nlm.nih.gov
Accurate transcription of genetic information is crucial, involving precise recognition of the
binding motifs by DNA-binding proteins. While some proteins rely on short-range …

The role of charge density coupled DNA bending in transcription factor sequence binding specificity: a generic mechanism for indirect readout

X Chen, MY Tsai, PG Wolynes - Journal of the American Chemical …, 2022 - ACS Publications
The accurate reading of genetic information during transcription is essential for the
expression of genes. Sequence binding specificity very often is attributed to short-range …

Facilitated unbinding via multivalency-enabled ternary complexes: New paradigm for protein–DNA interactions

TY Chen, YS Cheng, PS Huang… - Accounts of Chemical …, 2018 - ACS Publications
Conspectus Dynamic protein–DNA interactions constitute highly robust cellular machineries
to fulfill cellular functions. A vast number of studies have focused on how DNA-binding …

Improving coarse-grained protein force fields with small-angle X-ray scattering data

AP Latham, B Zhang - The Journal of Physical Chemistry B, 2019 - ACS Publications
Small-angle X-ray scattering (SAXS) experiments provide valuable structural data for
biomolecules in solution. We develop a highly efficient maximum entropy approach to fit …

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 …