Phase separation in amino acid mixtures is governed by composition

Abstract

Liquid-liquid phase separation (LLPS) has recently come to immense prominence as it is central to the formation of membraneless organelles, leading to a new paradigm of cellular organization. This type of phase transition is mediated by molecular interactions between biomolecules, including nucleic acids and both ordered and disordered proteins. In the latter case, the separation between protein-dense and dilute phases is often interpreted using models adapted from polymer theory. Specifically, the "stickers and spacers" model proposes that LLPS originates from the interplay between two classes of residues and that the main determinants for phase separation are multivalency and sequence patterning. The duality of roles of stickers (aromatics like Phe and Tyr) and spacers (Gly and polar residues) may apply more broadly in protein-like mixtures, and the presence of these two types of components alone may suffice for LLPS to take place. In order to explore this hypothesis, we use atomistic molecular dynamics simulations of capped amino-acid residues as a minimal model system. We study the behaviour of pure amino acids in water for three types of residues that are thought to play critical roles in LLPS, corresponding to the spacer and sticker categories, and their multicomponent mixtures. In agreement with previous observations, we find that the spacer type amino acids fail to phase-separate on their own, while the sticker is prone to aggregation. However, ternary amino acid mixtures involving both types of amino acids phase-separate into two phases that retain intermediate degrees of compaction and considerable fluidity. Our results suggest that LLPS is an emergent property of amino acid mixtures determined by composition.

Mass photometric detection and quantification of nanoscale α-synuclein phase separation

“…Protein LLPS is largely driven by transient, multivalent, intermolecular interactions which are defined by the interplay of amino acid sequence and solution conditions 40 . Intrinsically disordered regions (IDRs) and low complexity domains (LCDs) comprising of 'sticker' and 'spacer' motifs 41,42 not only play a significant role in droplet formation but can also be used to tune the material properties of LLPS [43][44][45][46][47][48][49][50] . Intrinsically disordered proteins/peptides (IDPs) are also generally more susceptible towards LLPS compared to folded proteins.…”

Structural and Dynamical Properties of Elastin-Like Peptides near their Lower Critical Solution Temperature

“…To probe the utility and generality of our findings, we generate six new peptide sequences where we modify Val at the position of the guest residue at positions 7, 12, and 17 with more hydrophilic amino acid alanine (Ala) and Gly which is a residue that suppresses aggregation in IDPs. 69 Experimentally, it was also shown that using both sequence modifications results in the shift of the LCST temperature to values above 60 ◦ C. 70 We investigate new sequences at two temperatures T =288 K, and 350 K, i. e. below and above LCST for the original sequence, and for three concentrations investigate single-chain ( c pept = 11.5 mg/ml), two-chain ( c pept = 23 mg/ml), and ten-chain systems ( c pept = 115 mg/ml). At a single-chain level, the modification of the sequence shows only a minor influence on the chain dimensions (shown in Fig.…”