Conformational Properties of Polymers at Droplet Interfaces as Model Systems for Disordered Proteins

Abstract

Polymer models serve as useful tools for studying the formation and physical properties of biomolecular condensates. In recent years, the interface dividing the dense and dilute phases of condensates has been discovered to be closely related to their functionality, but the conformational preferences of the constituent proteins remain unclear. To elucidate this, we perform molecular simulations of a droplet formed by phase separation of homopolymers as a surrogate model for the prion-like low-complexity domains. By systematically analyzing the polymer conformations at different locations in the droplet, we find that the chains become compact at the droplet interface compared with the droplet interior. Further, segmental analysis revealed that the end sections of the chains are enriched at the interface to maximize conformational entropy and are more expanded than the middle sections of the chains. We find that the majority of chain segments lie tangential to the droplet surface, and only the chain ends tend to align perpendicular to the interface. These trends also hold for the natural proteins FUS LC and LAF-1 RGG, which exhibit more compact chain conformations at the interface compared to the droplet interior. Our findings provide important insights into the interfacial properties of biomolecular condensates and highlight the value of using simple polymer physics models to understand the underlying mechanisms.

Insights into Molecular Diversity within the FUS/EWS/TAF15 Protein Family: Unraveling Phase Separation of the N-Terminal Low-Complexity Domain from RNA-Binding Protein EWS

“…Notably, the R g and scaling of average intramolecular distances ( R ij ) with sequence separation |i–j| show that the chains exhibited expansion in the condensed phase compared to that in the dilute phase (Figure E,F). This is consistent with expectation from homopolymer solution theories as the protein chains inside the condensed phase can form intermolecular contacts that are same as intramolecular contacts . Overall, the atomistic condensed phase simulations strongly suggest that the intramolecular interactions leading to the collapse of the C-terminal and N-terminal regions in the dilute phase also contribute to the phase separation of EWS LCD via intermolecular interactions.…”

“…This expansion occurs because in the dense phase proteins can form intramolecular as well as intermolecular contacts with other proteins. Therefore, the conformation of chains in the dense phase closely resembles the random walk characteristic of an ideal chain upon expansion (Figure F), as discussed in detail elsewhere. ,, Single point mutations changing tyrosines and immediately adjacent residues to serines measurably altered the phase separation propensity of EWS LCD , consistent with the behavior of single point mutations in the FUS LCD . Surprisingly, mutating the residue adjacent Y170, N169, to serine created a more soluble EWS LCD mutant, supporting the hypothesis that in addition to aromatic residues, the immediate chemical environment plays an important role in the molecular grammar governing phase separation. ,, For example, a previous study of the phase separation of SH3 3 -FUS in the presence of PRM 4 emphasized the significance of the quantity of tyrosine rather than its specific placement in FUS .…”

Revealing nanoscale structure and interfaces of protein and polymer condensates via cryo-electron microscopy

“…Recent computational studies aimed at understanding protein conformations at the condensate interface suggest several ways in which proteins might organize themselves at this boundary. 48,49 Measuring the interface of the protein-based condensates revealed the thickness of the surface layer to be ~6 nm (Figure 4ii). Interestingly, this surface layer appears to be longer than the expected RGG domain length of ~3.5 nm inside of condensates based on previous simulation work.…”

Simulations of Thin Polymer Films on Flat and Curved Substrates

“…Films with a thickness H much larger than the radius of gyration of the constituent polymers, R g , are typically characterized by a thin layer of adsorbed polymers near the substrate, followed by a bulk-like region with chain conformations as in the melt. At the liquid–vapor interface, the monomer concentration usually decays exponentially and the chains exhibit collapsed conformations due to the concomitant decrease in the (effective) solvent quality. − …”