Pragmatic coarse-graining of proteins: models and applications

L Borges-Araújo, I Patmanidis, AP Singh… - Journal of Chemical …, 2023 - ACS Publications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

IHF and Fis as Escherichia coli Cell Cycle Regulators: Activation of the Replication Origin oriC and the Regulatory Cycle of the DnaA Initiator

K Kasho, S Ozaki, T Katayama - International journal of molecular …, 2023 - mdpi.com
This review summarizes current knowledge about the mechanisms of timely binding and
dissociation of two nucleoid proteins, IHF and Fis, which play fundamental roles in the …

The marionette mechanism of domain–domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor

X Chen, S Jin, M Chen, C Bueno… - Proceedings of the …, 2023 - National Acad Sciences
The human estrogen receptor α (hER α) is involved in the regulation of growth,
development, and tissue homeostasis. Agonists that bind to the receptor's ligand-binding …

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 …

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 …

Mechanism of dynamic binding of replication protein A to ssDNA

A Mondal, A Bhattacherjee - Journal of Chemical Information and …, 2020 - ACS Publications
Replication protein A (RPA) serves as a hub protein inside eukaryotic cells, where it
coordinates crucial DNA metabolic processes and activates the DNA-damage response …

Fibril surface-dependent amyloid precursors revealed by coarse-grained molecular dynamics simulation

YW Ma, TY Lin, MY Tsai - Frontiers in Molecular Biosciences, 2021 - frontiersin.org
Amyloid peptides are known to self-assemble into larger aggregates that are linked to the
pathogenesis of many neurodegenerative disorders. In contrast to primary nucleation, recent …

Genomic inversions in Escherichia coli alter gene expression and are associated with nucleoid protein binding sites

DF Lato, Q Zeng, GB Golding - Genome, 2022 - cdnsciencepub.com
Genomic reorganization, such as rearrangements and inversions, influences how genetic
information is organized within the bacterial genomes. Inversions, in particular, facilitate …

[HTML][HTML] How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations

F Kozak, D Kurzbach - Computational and Structural Biotechnology Journal, 2021 - Elsevier
We review recent advances in modeling structural ensembles of transcription factors from
nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) …

Exploring Abeta42 Monomer Diffusion Dynamics on Fibril Surfaces through Molecular Simulations

YW Ma, GF Wang, HY Chen, MY Tsai - bioRxiv, 2024 - biorxiv.org
This study provides critical insights into the role of surface-mediated secondary processes in
Alzheimer's disease, particularly regarding the aggregation of Abeta42 peptides. Employing …