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

• 成果类型: Article
• 署名作者: Mitra, Rishav; Usher, Emery T.; Dedeoglu, Selin; Crotteau, Matthew J.; Fraser, Olivia A.; Yennawar, Neela H.; Gadkari, Varun V.; Ruotolo, Brandon T.; Holehouse, Alex S.; Salmon, Loic; Showalter, Scott A.; Bardwell, James C. A.
• 署名单位: University of Michigan System; University of Michigan; Howard Hughes Medical Institute; University of Michigan System; University of Michigan; Washington University (WUSTL); Washington University (WUSTL); Centre National de la Recherche Scientifique (CNRS); Ecole Normale Superieure de Lyon (ENS de LYON); Universite Claude Bernard Lyon 1; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; University of Michigan System; University of Michigan; Pennsylvania Commonwealth System of Higher Education (PCSHE); Pennsylvania State University; Pennsylvania State University - University Park; University of California System; University of California San Francisco; University of Minnesota System; University of Minnesota Twin Cities; University of California System; University of California San Francisco
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-15328
• DOI: 10.1073/pnas.2409139121
• 发表日期: 2024-12-03
• 关键词: hiv-1 tar rna; mobility-mass spectrometry; phase-separation; alpha-synuclein; nmr; binding; complex; sequence; DYNAMICS; MODEL

摘要

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.