Physical principles underlying the complex biology of intracellular phase transitions

JM Choi, AS Holehouse… - Annual review of …, 2020 - annualreviews.org
Many biomolecular condensates appear to form via spontaneous or driven processes that
have the hallmarks of intracellular phase transitions. This suggests that a common …

A new phase of networking: the molecular composition and regulatory dynamics of mammalian stress granules

SR Millar, JQ Huang, KJ Schreiber, YC Tsai… - Chemical …, 2023 - ACS Publications
Stress granules (SGs) are cytosolic biomolecular condensates that form in response to
cellular stress. Weak, multivalent interactions between their protein and RNA constituents …

Prediction of liquid–liquid phase separating proteins using machine learning

X Chu, T Sun, Q Li, Y Xu, Z Zhang, L Lai, J Pei - BMC bioinformatics, 2022 - Springer
Background The liquid–liquid phase separation (LLPS) of biomolecules in cell underpins
the formation of membraneless organelles, which are the condensates of protein, nucleic …

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro

Q Li, X Peng, Y Li, W Tang, J Zhu, J Huang… - Nucleic acids …, 2020 - academic.oup.com
Liquid-liquid phase separation (LLPS) leads to a conversion of homogeneous solution into a
dense phase that often resembles liquid droplets, and a dilute phase. An increasing number …

Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

AV Fonin, IA Antifeeva, IM Kuznetsova… - Essays in …, 2022 - portlandpress.com
The facts that many proteins with crucial biological functions do not have unique structures
and that many biological processes are compartmentalized into the liquid-like biomolecular …

Aberrant liquid-liquid phase separation and amyloid aggregation of proteins related to neurodegenerative diseases

A Ahmad, VN Uversky, RH Khan - International Journal of Biological …, 2022 - Elsevier
Recent evidence has shown that the processes of liquid-liquid phase separation (LLPS) or
liquid-liquid phase transitions (LLPTs) are a crucial and prevalent phenomenon that …

An interpretable machine-learning algorithm to predict disordered protein phase separation based on biophysical interactions

H Cai, RM Vernon, JD Forman-Kay - Biomolecules, 2022 - mdpi.com
Protein phase separation is increasingly understood to be an important mechanism of
biological organization and biomaterial formation. Intrinsically disordered protein regions …

AlphaFold2-based prediction of the co-condensation propensity of proteins

S Zhang, CM Lim, M Occhetta… - Proceedings of the …, 2024 - pnas.org
The process of protein phase separation into liquid condensates has been implicated in the
formation of membraneless organelles (MLOs), which selectively concentrate biomolecules …

MolPhase, an advanced prediction algorithm for protein phase separation

Q Liang, N Peng, Y Xie, N Kumar, W Gao… - The EMBO …, 2024 - embopress.org
We introduce MolPhase, an advanced algorithm for predicting protein phase separation
(PS) behavior that improves accuracy and reliability by utilizing diverse physicochemical …

Computational resources for identifying and describing proteins driving liquid–liquid phase separation

R Pancsa, W Vranken, B Mészáros - Briefings in Bioinformatics, 2021 - academic.oup.com
One of the most intriguing fields emerging in current molecular biology is the study of
membraneless organelles formed via liquid–liquid phase separation (LLPS). These …