Physics-based computational and theoretical approaches to intrinsically disordered proteins

JE Shea, RB Best, J Mittal - Current opinion in structural biology, 2021 - Elsevier
Highlights•Liquid-liquid phase separation underlies the formation of membraneless
organelles within cells.•Theory and molecular simulations help to relate interactions at the …

Interaction dynamics of intrinsically disordered proteins from single-molecule spectroscopy

A Chowdhury, D Nettels… - Annual review of …, 2023 - annualreviews.org
Many proteins contain large structurally disordered regions or are entirely disordered under
physiological conditions. The functions of these intrinsically disordered proteins (IDPs) often …

Extreme dynamics in a biomolecular condensate

N Galvanetto, MT Ivanović, A Chowdhury, A Sottini… - Nature, 2023 - nature.com
Proteins and nucleic acids can phase-separate in the cell to form concentrated biomolecular
condensates,,–. The functions of condensates span many length scales: they modulate …

Competing protein-RNA interaction networks control multiphase intracellular organization

DW Sanders, N Kedersha, DSW Lee, AR Strom… - Cell, 2020 - cell.com
Liquid-liquid phase separation (LLPS) mediates formation of membraneless condensates
such as those associated with RNA processing, but the rules that dictate their assembly …

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

EW Martin, AS Holehouse, I Peran, M Farag, JJ Incicco… - Science, 2020 - science.org
Prion-like domains (PLDs) can drive liquid-liquid phase separation (LLPS) in cells. Using an
integrative biophysical approach that includes nuclear magnetic resonance spectroscopy …

Liquid–liquid phase separation modifies the dynamic properties of intrinsically disordered proteins

S Guseva, V Schnapka, W Adamski… - Journal of the …, 2023 - ACS Publications
Liquid–liquid phase separation of flexible biomolecules has been identified as a ubiquitous
phenomenon underlying the formation of membraneless organelles that harbor a multitude …

Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins

S Das, YH Lin, RM Vernon… - Proceedings of the …, 2020 - National Acad Sciences
Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for
biomolecular condensates underlain by liquid–liquid phase separation (LLPS) of proteins …

Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction

JM Eeftens, M Kapoor, D Michieletto… - Nature …, 2021 - nature.com
Organization of the genome into transcriptionally active euchromatin and silenced
heterochromatin is essential for eukaryotic cell function. Phase-separation has been …

The protein folding problem: the role of theory

R Nassar, GL Dignon, RM Razban, KA Dill - Journal of molecular biology, 2021 - Elsevier
The protein folding problem was first articulated as question of how order arose from
disorder in proteins: How did the various native structures of proteins arise from interatomic …

Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase

TH Kim, BJ Payliss, ML Nosella… - Proceedings of the …, 2021 - National Acad Sciences
The role of biomolecular condensates in regulating biological function and the importance of
dynamic interactions involving intrinsically disordered protein regions (IDRs) in their …