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A short peptide synthon for liquid–liquid phase separation

Abstract

Liquid–liquid phase separation of disordered proteins has emerged as a ubiquitous route to membraneless compartments in living cells, and similar coacervates may have played a role when the first cells formed. However, existing coacervates are typically made of multiple macromolecular components, and designing short peptide analogues capable of self-coacervation has proven difficult. Here we present a short peptide synthon for phase separation, made of only two dipeptide stickers linked via a flexible, hydrophilic spacer. These small-molecule compounds self-coacervate into micrometre-sized liquid droplets at sub-millimolar concentrations, which retain up to 75 wt% water. The design is general and we derive guidelines for the required sticker hydrophobicity and spacer polarity. To illustrate their potential as protocells, we create a disulfide-linked derivative that undergoes reversible compartmentalization controlled by redox chemistry. The resulting coacervates sequester and melt nucleic acids, and act as microreactors that catalyse two different anabolic reactions yielding molecules of increasing complexity. This provides a stepping stone for new coacervate-based protocells made of single peptide species.

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Fig. 1: Liquid–liquid phase separation of cystamine-linked phenylalanine dipeptides.
Fig. 2: Reversible reduction and oxidation of FFssFF.
Fig. 3: Partitioning of guest molecules in FFssFF coacervates.
Fig. 4: Enhanced rates of addition reactions in FFssFF coacervates.

Data availability

All data supporting the findings of this study are available within the article and in the Supplementary Information and Data files. Source data are provided with this paper.

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Acknowledgements

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement number 851963, and from the Netherlands Organization for Scientific Research (NWO-Startup to E.S.). M.A. gratefully acknowledges a Marie Skłodowska Curie Individual Fellowship (project number 839177).

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Contributions

M.A. and E.S. conceived the idea and designed the experiments. M.A. and W.P.L. synthesized the peptide derivatives and performed their analysis. M.A. performed redox, microscopy and microreactor experiments. K.K.N. performed microscopy experiments with FFssFF. All authors discussed the results and interpreted data. M.A., E.S. and W.T.S.H. wrote the manuscript.

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Correspondence to Evan Spruijt.

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The authors declare no competing interests.

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Peer review information Nature Chemistry thanks Samrat Mukhopadhyay and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary Information

Supplementary materials and methods 1 and 2, Figs. 1–28, discussion and Table 1.

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Abbas, M., Lipiński, W.P., Nakashima, K.K. et al. A short peptide synthon for liquid–liquid phase separation. Nat. Chem. 13, 1046–1054 (2021). https://doi.org/10.1038/s41557-021-00788-x

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