Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity

Abstract

The formation of droplets of bio-molecular condensates through liquid-liquid phase separation (LLPS) of their component proteins is a key factor in the maintenance of cellular homeostasis. Different protein properties were shown to be important in LLPS onset, making it possible to develop predictors, which try to discriminate a positive set of proteins involved in LLPS against a negative set of proteins not involved in LLPS. On the other hand, the redundancy and multivalency of the interactions driving LLPS led to the suggestion that the large conformational entropy associated with non specific side-chain interactions is also a key factor in LLPS. In this work we build a LLPS predictor which combines the ability to form pi-pi interactions, with an unrelated feature, the propensity to stabilize the β-pairing interaction mode. The cross-β structure is formed in the amyloid aggregates, which are involved in degenerative diseases and may be the final thermodynamically stable state of protein condensates. Our results show that the combination of pi-pi and β-pairing propensity yields an improved performance. They also suggest that protein sequences are more likely to be involved in phase separation if the main chain conformational entropy of the β-pairing maintained droplet state is increased. This would stabilize the droplet state against the more ordered amyloid state. Interestingly, the entropic stabilization of the droplet state appears to proceed according to different mechanisms, depending on the fraction of “droplet-driving“ proteins present in the positive set.

Location and concentration of aromatic-rich segments dictates the percolating inter-molecular network and viscoelastic properties of ageing condensates

“…According to our results shown in Figs.2(b) and 2(c), this approach should decrease the probability of the LARKS to form part of a high-density protein cluster, hence, decelerating the β-sheet transition rate within condensates and its associated increase of viscosity over time. Moreover, the entropy of the condensed phase should be lower when long-lived β-sheet pairings are closer to the center of the chain than to its tails95 . We reasoned that in case that FUS phase-separation would occur in presence of RNA18,96,97 , such reordering could also potentially frustrate LARKS high-density fluctuations by virtue of the FUS arginine-glycine rich-regions (RGGs) and RNArecognition motifs (RRMs) flanking the low-complexity domain (Fig.3(a)) and recruiting high concentrations of RNA60,83 .…”

Location and Concentration of Aromatic‐Rich Segments Dictates the Percolating Inter‐Molecular Network and Viscoelastic Properties of Ageing Condensates

“…Moreover, the entropy of the condensed phase should be lower when long‐lived β‐sheet pairings are closer to the center of the chain than to its tails. [ 97 ] We reasoned that in case that FUS phase‐separation would occur in presence of RNA, [ 18 , 98 , 99 ] such reordering could also potentially frustrate LARKS high‐density fluctuations by virtue of the FUS arginine‐glycine rich‐regions (RGGs) and RNA‐recognition motifs (RRMs) flanking the low‐complexity domain (Figure 3a ) and recruiting high concentrations of RNA. [ 62 , 85 ] In addition to the reordering of domains, we also test the impact of mutating adjacent glycines (G) and serines (S) to the three FUS LARKS by arginines (R) across the original FUS sequence (Figure 3a Middle).…”