Condensates of disordered proteins have small-world network structures and interfaces defined by expanded conformations

Abstract

The formation of membraneless biomolecular condensates is driven by macromolecules with sticker- and-spacer architectures that undergo phase separation coupled to percolation (PSCP). Driving forces for PSCP are governed by the interplay between reversible inter-sticker crosslinks and solvation preferences of spacers. Here, we introduce molecular and mesoscale descriptions of structures within, outside, and at the interfaces of condensates that are formed by prion-like low complexity domains (PLCDs). These systems are exemplars of intrinsically disordered multivalent proteins that drive PSCP. Our studies are based on computations that accurately describe sequence-specific phase behaviors of PLCDs. We find that networks of reversible, intermolecular, inter-sticker crosslinks organize PLCDs into small-world topologies within condensates. These topologies result from distinct conformational preferences within dense, dilute, and interfacial regions. Specifically, the degree of conformational expansion varies non-monotonically, being most expanded at the interface and most compact in the dilute phase with molecules preferring to be oriented perpendicular to condensate interfaces. This contrasts with dense and dilute phases where molecules are randomly oriented relative to one another. Our results demonstrate that even simple condensates, with only one type of macromolecule, feature inhomogeneous spatial organizations of molecules and interfacial features that likely prime them for being locations of biochemical activity.

The interface of condensates of the hnRNPA1 low complexity domain promotes formation of amyloid fibrils

“…have recently shown that LCD molecules of hnRNPA1 are organized in different topologies inside the condensates 59 . Specifically, proteins are more expanded at the interface compared to both the interior of the condensate and the dilute phase 59 . Moreover, molecules prefer to be oriented perpendicularly to the condensate interface 59 .…”

“…In addition to conformational changes inside and outside the condensate, Farag et al have recently shown that LCD molecules of hnRNPA1 are organized in different topologies inside the condensates 59 . Specifically, proteins are more expanded at the interface compared to both the interior of the condensate and the dilute phase 59 . Moreover, molecules prefer to be oriented perpendicularly to the condensate interface 59 .…”

“…Specifically, proteins are more expanded at the interface compared to both the interior of the condensate and the dilute phase 59 . Moreover, molecules prefer to be oriented perpendicularly to the condensate interface 59 .…”

“…In addition to promoting conformational changes and orientation 59 , interfaces of condensates can preferentially partition components 66 and accelerate or inhibit fibrillation of client molecules 67 . Overall, interfaces can therefore represent a special location for biochemical activity within condensates and contribute to the complex interplay between condensation and fibrillation.…”

Improved Predictions of Phase Behaviour of Intrinsically Disordered Proteins by Tuning the Interaction Range

“…This has been achieved by leveraging (i) experimental data on single-chain properties, (ii) statistical analyses of protein structures, and (iii) residue-residue free energy profiles calculated from all-atom simulations [26][27][28][29][30][31]. In particular, we and others have proposed an automated procedure to optimize the "stickiness" parameters so as to maximize the agreement with experimental data small-angle X-ray scattering (SAXS) and paramagnetic relaxation enhancement (PRE) NMR data for a large set of IDPs [26,28,29,32]. To ensure the transferability of the model across sequence space, we employed a Bayesian regularization approach [32,33].…”