ArticleMolecular biology and evolution2022
In Vitro Evolution Reveals Noncationic Protein-RNA Interaction Mediated by Metal Ions.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Artificial intelligence aided design of peptides with custom secondary structure motifs and reduced amino acid alphabets.bioRxiv : the preprint server for biology · 2026Article
- The Borderlands of Foldability: Lessons from Simplified Proteins.Trends in chemistry · 2026Article
- Complex and Messy Prebiotic Chemistry: Obstacles and Opportunities for an RNA World.Life (Basel, Switzerland) · 2026Review
- Coenzyme-protein interactions since early life.eLife · 2025Article
- Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures.bioRxiv : the preprint server for biology · 2025Article
- Discovery of Macrocyclic Peptide Binders, Covalent Modifiers, and Degraders of a Structured RNA by mRNA Display.Journal of the American Chemical Society · 2025Article
- RNA binding and coacervation promote preservation of peptide form and function across the heterochiral-homochiral divide.Protein science : a publication of the Protein Society · 2025Article
- Meeting Proceedings from 4th Minimal Cell Workshop: Exploring JCVI Minimal Cell Fundamental Insights and Integrative Applications.ACS synthetic biology · 2025Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- Peptides En Route from Prebiotic to Biotic Catalysis.Accounts of chemical research · 2024Article
- The prebiotic emergence of biological evolution.Royal Society open science · 2024Article
- Article
- Origin of ribonucleotide recognition motifs through ligand mimicry at early earth.RNA biology · 2024Review
- Experimental characterization of de novo proteins and their unevolved random-sequence counterparts.Nature ecology & evolution · 2023Article
- Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability.Journal of the American Chemical Society · 2023Article
- Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains.Journal of the American Chemical Society · 2022Article
- Modern and prebiotic amino acids support distinct structural profiles in proteins.Open biology · 2022Article
- Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids.Journal of the Royal Society, Interface · 2022Review
- Sequencing the origins of life.BBA advances · 2022Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 1010 library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.
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