Widespread occurrence of the droplet state of proteins in the human proteome

Abstract

A wide range of proteins have been reported to condensate into a dense liquid phase, forming a reversible droplet state. Failure in the control of the droplet state can lead to the formation of the more stable amyloid state, which is often disease-related. These observations prompt the question of how many proteins can undergo liquid–liquid phase separation. Here, in order to address this problem, we discuss the biophysical principles underlying the droplet state of proteins by analyzing current evidence for droplet-driver and droplet-client proteins. Based on the concept that the droplet state is stabilized by the large conformational entropy associated with nonspecific side-chain interactions, we develop the FuzDrop method to predict droplet-promoting regions and proteins, which can spontaneously phase separate. We use this approach to carry out a proteome-level study to rank proteins according to their propensity to form the droplet state, spontaneously or via partner interactions. Our results lead to the conclusion that the droplet state could be, at least transiently, accessible to most proteins under conditions found in the cellular environment.

Interplay between disordered regions in RNAs and proteins modulates interactions within stress granules and processing bodies

“…This result is very well in line with recent reports indicating that unstructured regions modulate the formation of phase separated assemblies [31]. Indeed, phase separation is a widespread phenomenon in the cell [55] and disordered interactions greatly contribute to the assembly formation [56]. By reporting that single-stranded RNAs preferably contact disorder proteins, we extended the concept of "fuzziness" to RNA molecules.…”

Droplet and fibril formation of the functional amyloid Orb2

“…We did not study full-length Orb2A because it does not require its RBD for proper function in vivo [3] and because we were not able to make it in large quantities. Sequence analysis using the database based FuzPred algorithm [21] showed a high propensity for phase separation (pLLPS) for the N-termini of Orb2A and Orb2B until about the beginning of RBD (Figure 1B). Interestingly, the N-terminal residues unique to Orb2A showed a lower pLLPS than the corresponding residues in Orb2B.…”

Solubility Parameters of Amino Acids on Liquid–Liquid Phase Separation and Aggregation of Proteins

“…These differences indicate the importance of the liquid–liquid or liquid–solid phase separations of proteins. In addition, several methods have been developed to predict the PPS of proteins ( Vernon and Forman-Kay, 2019 ; Hardenberg et al, 2021 ; van Mierlo et al, 2021 ). These prediction methods can identify proteins with a high PPS from the proteome, such as the distribution of the amino acid residues and the complexity of the sequence.…”

“…Finally, for future applications, the PSAS at the amino acid level did not fully match that at the protein level. To more clearly illustrate this finding, the PSAS of Trp was relatively large, but is rarely present in the IDR of proteins that are prone to LLPS (Wang et al, 2014;Martin and Mittag, 2018;Martin et al, 2020), while Gly and Ser had PSAS values close to zero, but are known to be abundant in the IDR of proteins that are prone to LLPS (Schuster et al, 2018;Hardenberg et al, 2021). These conflicts are thought to be due to differences in the properties of free amino acids as solutes and amino acids during peptide formation.…”