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

Abstract

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.

Ribozyme-phenotype coupling in peptide-based coacervate protocells

“…It should be noted that as a ribozyme developed by in vitro selection, the R3C ligase is already a highly optimized system and offers little potential for further enhancement via selection. Nevertheless, the reciprocal modulation of ribozyme activity and coacervate properties reported here furthers the argument for the early coevolution of RNA and peptides 7–9,18,60 . Whilst the magnitude of behavioural change was greater for active and inactive coacervate populations formed with the longer peptide, clear phenotypic differences were nonetheless also present in the (Lys) 5-24 system.…”

“…Peptide-RNA condensation forms discrete protocellular compartments 5,6 . RNA-peptide interactions are in many cases beneficial for the function of these early catalysts 7,8 , and may promote the folding and oligomerisation of certain peptides 9 . Perhaps surprisingly, the function of ribozymes and other nucleic acid enzymes in coacervate phases has only been recently established, with catalytic rate being enhanced and enzyme function altered in some cases [10][11][12][13][14] .…”

Rheology and Gelation of Hyaluronic Acid/Chitosan Coacervates

“…Complex coacervates are a class of materials formed by liquid–liquid phase separation between oppositely charged macroions. The macroions range from organic macromolecules such as proteins [ 1 , 2 ], surfactant micelles [ 3 , 4 ], polypeptides [ 5 ], synthetic [ 6 ] and biological [ 7 , 8 ] polyelectrolytes to inorganic nanoparticles [ 9 ]. The driving forces for complex coacervation are electrostatic interactions and entropic gain due to the release of counterions [ 5 , 10 ].…”

An evolutionary history of the CoA‐binding protein Nat/Ivy

“…The Tawfik laboratory was a pioneer in early protein evolution, showing the functional potential of simple peptides experimentally 12 , 13 , 60 , 61 , 62 and dissecting their histories through structural bioinformatics and state‐of‐the‐art sequence analysis. 14 , 19 , 32 , 49 Indeed, many of the features discussed within these works are relevant to Nat/Ivy as well, where a nucleotide cofactor is bound at the N‐terminus of an α‐helix, forms bidentate interactions, and interacts with a glycine‐rich motif.…”