Molecular insights into the interaction between a disordered protein and a folded RNA

Rishav Mitra, Emery T. Usher, Selin Dedeoǧlu, Matthew J. Crotteau, Olivia A. Fraser, Neela H. Yennawar, Varun V. Gadkari, Brandon T. Ruotolo, Alex S. Holehouse, Loïc Salmon, Scott A. Showalter, James C.A. Bardwell

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Intrinsically disordered protein regions (IDRs) are well established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, Small ERDK-Rich Factor (SERF). At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein-and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 Trans-Activation Response (TAR) RNA with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.

Original languageEnglish
Article numbere2409139121
JournalProceedings of the National Academy of Sciences of the United States of America
Volume121
Issue number49
DOIs
StatePublished - Dec 3 2024

Keywords

  • disordered proteins
  • molecular condensates
  • RNA binding proteins

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