Rational drug design targeting intrinsically disordered proteins

H Wang, R Xiong, L Lai - Wiley Interdisciplinary Reviews …, 2023 - Wiley Online Library
Intrinsically disordered proteins (IDPs) are proteins that perform important biological
functions without well‐defined structures under physiological conditions. IDPs can form …

Advanced sampling methods for multiscale simulation of disordered proteins and dynamic interactions

X Gong, Y Zhang, J Chen - Biomolecules, 2021 - mdpi.com
Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in
biology and human diseases. It is now also recognized that many IDPs remain dynamic …

Thermodynamic and sequential characteristics of phase separation and droplet formation for an intrinsically disordered region/protein ensemble

WT Chu, J Wang - PLoS computational biology, 2021 - journals.plos.org
Liquid–liquid phase separation (LLPS) of some IDPs/IDRs can lead to the formation of the
membraneless organelles in vitro and in vivo, which are essential for many biological …

Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling

B Sun, PM Kekenes-Huskey - Quarterly reviews of biophysics, 2023 - cambridge.org
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to
contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to …

Binding and folding in transcriptional complexes

NC Smith, M Kuravsky, SL Shammas… - Current Opinion in …, 2021 - Elsevier
Highlights•Many aspects of transcription factor function involve folding upon
binding.•Intrinsic disorder plays a role in both DNA binding and transcriptional activation.• …

Physics of biomolecular recognition and conformational dynamics

WT Chu, Z Yan, X Chu, X Zheng, Z Liu… - Reports on Progress …, 2021 - iopscience.iop.org
Biomolecular recognition usually leads to the formation of binding complexes, often
accompanied by large-scale conformational changes. This process is fundamental to …

[HTML][HTML] Conformational transitions of Streptococcus pyogenes Cas9 induced by salt and single-guide RNA binding

Y He, N Zalenski, AA Stephenson, AT Raper… - Journal of Biological …, 2024 - Elsevier
ABSTRACT Streptococcus pyogenes (Sp) Cas9 has been widely utilized to edit genomes
across diverse species. To achieve high efficiency and specificity as a gene editing enzyme …

Molecular dynamics simulations revealed topological frustration in the binding-wrapping process of eIF4G with eIF4E

M Gao, Y Huang - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
Interaction between the cap-binding protein eIF4E and the scaffolding protein eIF4G is
essential for the cap-dependent translation initiation in eukaryotes. In the Saccharomyces …

Assessing the role of calmodulin's linker flexibility in target binding

B Sun, PM Kekenes-Huskey - International Journal of Molecular Sciences, 2021 - mdpi.com
Calmodulin (CaM) is a highly-expressed Ca 2+ binding protein known to bind hundreds of
protein targets. Its binding selectivity to many of these targets is partially attributed to the …

Regulation of Poly-E Motif Flexibility by pH, Ca2+ and the PPAK Motif

SP Dassanayake Mudiyanselage, MJ Gage - International Journal of …, 2022 - mdpi.com
The disordered PEVK region of titin contains two main structural motifs: PPAK and poly-E.
The distribution of these motifs in the PEVK region contributes to the elastic properties of this …