Amyloid formation as a protein phase transition

TCT Michaels, D Qian, A Šarić, M Vendruscolo… - Nature Reviews …, 2023 - nature.com
The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which
is associated with both functional biology and the development of a number of disorders …

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 …

RNAs undergo phase transitions with lower critical solution temperatures

GM Wadsworth, WJ Zahurancik, X Zeng, P Pullara… - Nature Chemistry, 2023 - nature.com
Co-phase separation of RNAs and RNA-binding proteins drives the biogenesis of
ribonucleoprotein granules. RNAs can also undergo phase transitions in the absence of …

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 …

Determinants that enable disordered protein assembly into discrete condensed phases

RM Welles, KA Sojitra, MV Garabedian, B Xia… - Nature Chemistry, 2024 - nature.com
Cells harbour numerous mesoscale membraneless compartments that house specific
biochemical processes and perform distinct cellular functions. These protein-and RNA-rich …

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 …

Tie-line analysis reveals interactions driving heteromolecular condensate formation

D Qian, TJ Welsh, NA Erkamp, S Qamar, J Nixon-Abell… - Physical Review X, 2022 - APS
Phase separation of biomolecules gives rise to membraneless organelles that contribute to
the spatiotemporal organization of the cell. In most cases, such biomolecular condensates …

[HTML][HTML] On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins

K Lindorff-Larsen, BB Kragelund - Journal of Molecular Biology, 2021 - Elsevier
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and
many diverging properties. IDPs—and intrinsically disordered regions (IDRs) interspersed …

Rules of physical mathematics govern intrinsically disordered proteins

K Ghosh, J Huihui, M Phillips… - Annual Review of …, 2022 - annualreviews.org
In stark contrast to foldable proteins with a unique folded state, intrinsically disordered
proteins and regions (IDPs) persist in perpetually disordered ensembles. Yet an IDP …

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model …

T Pal, J Wessén, S Das, HS Chan - The Journal of Physical …, 2024 - ACS Publications
Conformational properties of intrinsically disordered proteins (IDPs) are governed by a
sequence-ensemble relationship. To differentiate the impact of sequence-local versus …