Abstract
Many RNA-binding proteins (RBPs) that assemble into membraneless organelles, have a common architecture including disordered prion-like domain (PLD) and folded RNA-binding domain (RBD). An enrichment of PLD within the condensed phase gives rise to formation, on longer time scales, amyloid-like fibrils (aging). In this study, we employ coarse-grained Langevin dynamics simulations to explore the physical basis for the structural diversity in condensed phases of multi-domain RBPs. We discovered a highly cooperative first order transition between disordered structures and an ordered phase whereby chains of PLD organize in fibrils with high nematic orientational order. An interplay between homo-domain (PLD-PLD) and hetero-domain (PLD-RBD) interactions results in variety of structures with distinct spatial architectures. Interestingly, the different structural phases also exhibit vastly different intra-cluster dynamics of proteins, with diffusion coefficients 5 (disordered structures) to 50 times (ordered structures) lower than that of the dilute phase. Cooperativity of this liquid-solid transition makes fibril formation highly malleable to mutations or post-translational modifications. Our results provide a mechanistic understanding of how multi-domain RBPs could form assemblies with distinct structural and material properties.
Significance Statement Assembly of proteins and nucleic acids into dense, liquid-like pockets is associated with several key functions including stress response, gene-regulation, DNA-repair and RNA processing. Several RNA binding proteins such as FUS are known to form liquid-like condensates that progressively harden into more dynamically, solid-like structures, a phenomenon that gets accelerated by disease mutations. In this study, we discover the mechanistic origins of this transition and show that small mutational or posttranslational modifications could result in sharp disorder-order transitions that could characterize accelerated liquid-solid transition in disease mutants.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Email: shakhnovich{at}chemistry.harvard.edu
The introduction of the paper has been reworded to make it more concise and improve overall readability The Model and Methods sections have now been expanded to elaborate on the choice of model parameters (coarse-graining resolution, key simulation variables) We add a new subsection in results titled 'Slowdown in intra-cluster polymer dynamics results in altered inter-cluster coalescence behavior' and a new Figure.8 where we highlight the differences in coalescence behaviour in different interaction regimes. Under Discussion, we add a new subsection 'The origins of structural order in the semi-flexible polymer model' where we provide a detailed physical interpretation of the origins of structural order in semi-flexible polymer assemblies Figure 2 has now been modified, with the emphasis on switching in interaction networks and the effect on structural order. Note that the free energy profiles from metadynamics have now been moved to Supplementary Information. In Supplementary Table S1 and S2, we provide the human FUS sequence and the phosphorylation site locations. In Table S3, we provide a detailed list of all pairwise interaction parameters used in the paper
