Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains

Manas Seal, Orit Weil-Ktorza, Dragana Despotović, Dan S. Tawfik, Yaakov Levy, Norman Metanis, Liam M. Longo*, Daniella Goldfarb*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance spectroscopy (EPR) to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif revealed the presence of dimers, even in the absence of RNA. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. DEER measurements of spin-diluted, doubly labeled peptides in solution indicated transient α-helical character. The distance distributions between spin labels in the dimer and the signatures of α-helical folding are consistent with the symmetric (HhH)2-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.

Original languageAmerican English
Pages (from-to)14150-14160
Number of pages11
JournalJournal of the American Chemical Society
Issue number31
StatePublished - 10 Aug 2022

Bibliographical note

Funding Information:
Our dear friend and mentor Prof. Dan S. Tawfik died during the course of this study. His contributions to our understanding of protein evolution were immeasurable, and his insights suffuse the present work. This work was funded by the Israeli Science Foundation (grant numbers 2253/18 and 783/18 to D.G. and N.M., respectively). M.S. acknowledges the Weizmann Institute of Science and the PBC Postdoctoral Fellowship Program for financial support. O.W.K. acknowledges the Kaete Klausner Fellowship for financial support. We thank Dr. Akiva Feintuch for his help with the W-band measurements. This research was made possible in part by the historic generosity of the Harold Perlman Family (D. G.). D. G. holds the Erich Klieger Professorial Chair in Chemical Physics.

Publisher Copyright:
© 2022 American Chemical Society.


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