Intrinsically disordered regions are poised to act as sensors of cellular chemistry

D Moses, GM Ginell, AS Holehouse… - Trends in biochemical …, 2023 - cell.com
Intrinsically disordered proteins and protein regions (IDRs) are abundant in eukaryotic
proteomes and play a wide variety of essential roles. Instead of folding into a stable …

Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins

C Ghosh, S Nagpal, V Muñoz - Current opinion in structural biology, 2024 - Elsevier
Intrinsically disordered proteins (IDPs) exploit their plasticity to deploy a rich panoply of soft
interactions and binding phenomena. Advances in tailoring molecular simulations for IDPs …

Tuning the viscoelastic properties of peptide coacervates by single amino acid mutations and salt kosmotropicity

X Wu, Y Sun, J Yu, A Miserez - Communications Chemistry, 2024 - nature.com
Coacervation, or liquid-liquid phase separation (LLPS) of biomacromolecules, is
increasingly recognized to play an important role both intracellularly and in the extracellular …

A coarse‐grained model for disordered and multi‐domain proteins

F Cao, S von Bülow, G Tesei… - Protein …, 2024 - Wiley Online Library
Many proteins contain more than one folded domain, and such modular multi‐domain
proteins help expand the functional repertoire of proteins. Because of their larger size and …

SOP-MULTI: A Self-Organized Polymer-Based Coarse-Grained Model for Multidomain and Intrinsically Disordered Proteins with Conformation Ensemble Consistent …

K Baratam, A Srivastava - Journal of Chemical Theory and …, 2024 - ACS Publications
Multidomain proteins with long flexible linkers and full-length intrinsically disordered
proteins (IDPs) are best defined as an ensemble of conformations rather than a single …

Complete diagram of conformational regimes for polyampholytic disordered proteins

AM Rumyantsev, AA Gavrilov, A Johner - Macromolecules, 2024 - ACS Publications
Conformations of polyampholytic intrinsically disordered proteins (IDPs) are controlled by
the interplay between Coulomb attractions of the opposite charges and long-range Coulomb …

Ion Mobility mass spectrometry unveils global protein conformations in response to conditions that promote and reverse liquid–liquid phase separation

CG Robb, TP Dao, J Ujma, CA Castañeda… - Journal of the …, 2023 - ACS Publications
Liquid–liquid phase separation (LLPS) is a process by which biomacromolecules,
particularly proteins, condense into a dense phase that resembles liquid droplets …

How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

MC Baxa, X Lin, CD Mukinay, S Chakravarthy… - Protein …, 2024 - Wiley Online Library
Despite the generally accepted role of the hydrophobic effect as the driving force for folding,
many intrinsically disordered proteins (IDPs), including those with hydrophobic content …

Live-cell imaging to resolve salt-induced liquid–liquid phase separation of FUS protein by dye self-labeling

Y Zhang, N Xu, C Yan, X Zhou, Q Qiao… - … & Biomedical Imaging, 2023 - ACS Publications
The aggregation of fusion in sarcoma (FUS) in the cytoplasm and nucleus is a pathological
feature of Amyotrophic lateral sclerosis (ALS) and Frontotemporal Dementia (FTD). Genetic …

A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions

J Prabhu, M Frigerio, E Petretto… - Journal of Chemical …, 2024 - ACS Publications
Aqueous ionic solutions are pivotal in various scientific domains due to their natural
prevalence and vital roles in biological and chemical processes. Molecular dynamics has …