Liquid–Liquid Phase Separation of an Intrinsically Disordered Region of a Germ Cell-Specific Protein Modulates the Stability and Conformational Exchange Rate of SH3 Domain

Luo, Liang; Wu, Qiong; Ji, Shixia; Liu, Yixiang; Cheng, Kai; Liu, Maili; Jiang, Ling; Li, Conggang

doi:10.1021/acs.jpclett.2c01920

Cited by 6 publications

(1 citation statement)

References 41 publications

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“…However, insights into the conformational changes of proteins inside condensed phases have thus far been inferred based on enhancements of enzymatic activities that are not fully accounted for by mass action (6, 24, 25). In some cases they have been directly observed, albeit at low resolution (26), precluding meaningful insights into structure-function relationships inside condensates.…”

Section: Introductionmentioning

confidence: 99%

Atomic resolution map of the solvent interactions driving SOD1 unfolding in CAPRIN1 condensates

Ahmed,

Liang,

Hudson

et al. 2024

Preprint

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Biomolecules can be sequestered into membrane-less compartments, referred to as biomolecular condensates. Experimental and computational methods have helped define the physical-chemical properties of condensates. Less is known about how the high macromolecule concentrations in condensed phases contribute solvent interactions that can remodel the free-energy landscape of other condensate-resident proteins, altering thermally accessible conformations and, in turn, modulating function. Here, we use solution Nuclear Magnetic Resonance (NMR) spectroscopy to obtain atomic resolution insights into the interactions between the immature form of superoxide dismutase 1 (SOD1), which can mislocalize and aggregate in stress granules, and the RNA-binding protein CAPRIN1, a component of stress granules. NMR studies of CAPRIN1:SOD1, focused on both unfolded and folded SOD1 states in mixed phase and de-mixed CAPRIN1-based condensates, establish that CAPRIN1 shifts the folding equilibrium of SOD1 towards the unfolded state through preferential interactions with the unfolded ensemble, with little change to the structure of the folded conformation. Key contacts between CAPRIN1 and the H80-H120 region of unfolded SOD1 are identified, as well as SOD1 interaction sites near both the arginine-rich and aromatic-rich regions of CAPRIN1. Unfolding of immature SOD1 in the CAPRIN1 condensed phase is shown to be coupled to aggregation, while a more stable zinc-bound, dimeric form of SOD1 is less susceptible to unfolding when solvated by CAPRIN1. Our work underscores the impact of the condensate solvent environment on the conformational states of resident proteins and supports the hypothesis that ALS mutations that decrease metal binding or dimerization function as drivers of aggregation in condensates.

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Section: Introductionmentioning

confidence: 99%

Atomic resolution map of the solvent interactions driving SOD1 unfolding in CAPRIN1 condensates

Ahmed,

Liang,

Hudson

et al. 2024

Preprint

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Protein Condensates Unfold G‐Quadruplex Resembling a Helicase Activity

Luo,

Ji,

et al. 2024

ChemBioChem

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Membrane‐less organelles, formed by liquid‐liquid phase separation, participate in many vital cellular processes and have received extensive attention recently. A notable form of noncanonical nucleic acid secondary structure, G‐quadruplex (G4), interacts with the scaffolding proteins in these membrane‐less organelles and becomes an integral part of this condensed phase. However, the structure and stability features of the integrated G4 remain poorly characterized. Herein, we employed NMR along with other biophysical methods to investigate the conformation of a G4 within condensates formed by a disordered protein known as DDX4N1. We discovered that the human telomeric sequence MHT24, which forms a G4 structure in a non‐condensed phase solution of protein DDX4N1, unfolds when it is within DDX4N1 condensates due to phase separation. Our findings provide an instance of a protein acquiring new functionality through phase separation process, which deepen our understanding of how protein condensates regulate G4 structure and their functions.

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Studying protein stability in crowded environments by NMR

Xu,

Cheng,

Liu

et al. 2024

Progress in Nuclear Magnetic Resonance Spectroscopy

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Liquid–Liquid Phase Separation of an Intrinsically Disordered Region of a Germ Cell-Specific Protein Modulates the Stability and Conformational Exchange Rate of SH3 Domain

Abstract: Experimental methods, HSQC spectra, 19F spectra, microscope images of DDX4N1, exchange rate, and thermodynamics parameters for SH3 (PDF)■ AUTHOR INFORMATION

Cited by 6 publications

References 41 publications

Atomic resolution map of the solvent interactions driving SOD1 unfolding in CAPRIN1 condensates

Atomic resolution map of the solvent interactions driving SOD1 unfolding in CAPRIN1 condensates

Protein Condensates Unfold G‐Quadruplex Resembling a Helicase Activity

Studying protein stability in crowded environments by NMR

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