Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures

Abstract

Liquid-liquid phase separation (LLPS) of hetero-geneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid-liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.

Published in

Journal of the American Chemical Society
2023, volume: 145, number: 19, pages: 10659-10668
Publisher: AMER CHEMICAL SOC

SLU Authors

• Rising, Anna

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    
  • Karolinska Institute

Global goals (SDG)

SDG3 Good health and well-being

UKÄ Subject classification

Physical Chemistry
Biochemistry and Molecular Biology

Publication identifier

• DOI: https://doi.org/10.1021/jacs.3c00932

Permanent link to this page (URI)

https://res.slu.se/id/publ/122371