IMR Press / FBL / Volume 28 / Issue 8 / DOI: 10.31083/j.fbl2808183
Open Access Review
Protein Condensates and Protein Aggregates: In Vitro, in the Cell, and In Silico
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1 Theory Department, National Institute of Chemistry, 1000 Ljubljana, Slovenia
2 Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
3 Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
*Correspondence: katja.venko@ki.si (Katja Venko); eva.zerovnik@ijs.si (Eva Žerovnik)
Front. Biosci. (Landmark Ed) 2023, 28(8), 183; https://doi.org/10.31083/j.fbl2808183
Submitted: 23 May 2023 | Revised: 25 July 2023 | Accepted: 3 August 2023 | Published: 28 August 2023
Copyright: © 2023 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.
Abstract

Similar to other polypeptides and electrolytes, proteins undergo phase transitions, obeying physicochemical laws. They can undergo liquid-to-gel and liquid-to-liquid phase transitions. Intrinsically disordered proteins are particularly susceptible to phase separation. After a general introduction, the principles of in vitro studies of protein folding, aggregation, and condensation are described. Numerous recent and older studies have confirmed that the process of liquid-liquid phase separation (LLPS) leads to various condensed bodies in cells, which is one way cells manage stress. We review what is known about protein aggregation and condensation in the cell, notwithstanding the protective and pathological roles of protein aggregates. This includes membrane-less organelles and cytotoxicity of the prefibrillar oligomers of amyloid-forming proteins. We then describe and evaluate bioinformatic (in silico) methods for predicting protein aggregation-prone regions of proteins that form amyloids, prions, and condensates.

Keywords
neurodegeneration
protein aggregation
protein condensation
LLPS
membrane-less organelles
amyloid
intrinsically disordered proteins (IDPs)
prion
prediction by in silico methods
Figures
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