Protein allostery and conformational dynamics

J Guo, HX Zhou - Chemical reviews, 2016 - ACS Publications
The functions of many proteins are regulated through allostery, whereby effector binding at a
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …

CHARMM at 45: Enhancements in accessibility, functionality, and speed

W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Role of molecular dynamics and related methods in drug discovery

M De Vivo, M Masetti, G Bottegoni… - Journal of medicinal …, 2016 - ACS Publications
Molecular dynamics (MD) and related methods are close to becoming routine computational
tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and …

Allosteric activation of vinculin by talin

F Franz, R Tapia-Rojo, S Winograd-Katz… - Nature …, 2023 - nature.com
The talin-vinculin axis is a key mechanosensing component of cellular focal adhesions. How
talin and vinculin respond to forces and regulate one another remains unclear. By …

Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain–domain coupling

N Soya, H Xu, A Roldan, Z Yang, H Ye, F Jiang… - Nature …, 2023 - nature.com
The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette
(ABC) C-subfamily transporters, essential for organismal health, remain incompletely …

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …

Delineating the stepwise millisecond allosteric activation mechanism of the class C GPCR dimer mGlu5

M Li, X Lan, X Shi, C Zhu, X Lu, J Pu, S Lu… - Nature …, 2024 - nature.com
Two-thirds of signaling hormones and one-third of approved drugs exert their effects by
binding and modulating the G protein-coupled receptors (GPCRs) activation. While the …

Distant residues modulate conformational opening in SARS-CoV-2 spike protein

D Ray, L Le, I Andricioaei - Proceedings of the National …, 2021 - National Acad Sciences
Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the
attachment of the receptor-binding domain (RBD) of its spike proteins to the ACE2 receptors …

Eigenvector centrality for characterization of protein allosteric pathways

CFA Negre, UN Morzan… - Proceedings of the …, 2018 - National Acad Sciences
Determining the principal energy-transfer pathways responsible for allosteric communication
in biomolecules remains challenging, partially due to the intrinsic complexity of the systems …

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics …

MCR Melo, RC Bernardi… - The Journal of …, 2020 - pubs.aip.org
Molecular interactions are essential for regulation of cellular processes from the formation of
multi-protein complexes to the allosteric activation of enzymes. Identifying the essential …