Analysis of Evolutionarily Independent Protein-RNA Complexes Yields a Criterion to Evaluate the Relevance of Prebiotic Scenarios
Celia Blanco
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Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA,
Marco Bayas
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Departamento de Fisica, Escuela Politécnica Nacional, Quito, Ladron de Guevara E11-253, Ecuador,
Fu Yan
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Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA,
Irene A. Chen
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Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
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Correspondence information about the author Irene A. ChenSearch for articles by this author
Affiliations
Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
Program in Biomolecular Sciences and Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-9510, USA
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Published: February 1, 2018
Publication stage: In Press Corrected Proof
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DOI: https://doi.org/10.1016/j.cub.2018.01.014
Article Info
Publication History
Published: February 1, 2018
Accepted: January 3, 2018; Received in revised form: December 4, 2017; Received: October 23, 2017
Highlights
• Protein-aptamer interactions are a useful model for the prebiotic RNA World
• Cationic amino acids (mainly arginine) are critical in protein-aptamer interactions
• The path to the genetic code may have depended on cationic amino acids
Summary
A central difficulty facing study of the origin of life on Earth is evaluating the relevance of different proposed prebiotic scenarios. Perhaps the most established feature of the origin of life was the progression through an RNA World, a prebiotic stage dominated by functional RNA. We use the appearance of proteins in the RNA World to understand the prebiotic milieu and develop a criterion to evaluate proposed synthetic scenarios. Current consensus suggests that the earliest amino acids of the genetic code were anionic or small hydrophobic or polar amino acids. However, the ability to interact with the RNA World would have been a crucial feature of early proteins. To determine which amino acids would be important for the RNA World, we analyze non-biological protein-aptamer complexes in which the RNA or DNA is the result of in vitro evolution. This approach avoids confounding effects of biological context and evolutionary history. We use bioinformatic analysis and molecular dynamics simulations to characterize these complexes. We find that positively charged and aromatic amino acids are over-represented whereas small hydrophobic amino acids are under-represented. Binding enthalpy is found to be primarily electrostatic, with positively charged amino acids contributing cooperatively to binding enthalpy. Arginine dominates all modes of interaction at the interface. These results suggest that proposed prebiotic syntheses must be compatible with cationic amino acids, particularly arginine or a biophysically similar amino acid, in order to be relevant to the invention of protein by the RNA World.
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