ArticleProceedings of the National Academy of Sciences of the United States of America2015
tRNA acceptor stem and anticodon bases form independent codes related to protein folding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 82 citations in OpenAlex.
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- Primordial aminoacyl-tRNA synthetases preferred minihelices to full-length tRNA.Nucleic acids research · 2024Article
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- Symmetrical distributions of aminoacyl-tRNA synthetases during the evolution of the genetic code.Theory in biosciences = Theorie in den Biowissenschaften · 2023Article
- Origins of Genetic Coding: Self-Guided Molecular Self-Organisation.Entropy (Basel, Switzerland) · 2023Article
- Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life.Frontiers in microbiology · 2023Review
- The Origin of Translation: Bridging the Nucleotides and Peptides.International journal of molecular sciences · 2022Review
- A Leucyl-tRNA Synthetase Urzyme: Authenticity of tRNA Synthetase Catalytic Activities and Promiscuous Phosphorylation of Leucyl-5'AMP.International journal of molecular sciences · 2022Article
- Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.Biomolecules · 2021Review
- Driving forces in the origins of life.Open biology · 2021Article
- The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases.Scientific reports · 2020Article
- The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies.Journal of molecular evolution · 2020Article
- Experimental solutions to problems defining the origin of codon-directed protein synthesis.Bio Systems · 2019Review
- tRNA Metabolism and Neurodevelopmental Disorders.Annual review of genomics and human genetics · 2019Review
- Review
- Ribosome Evolution and Structural Capacitance.Frontiers in molecular biosciences · 2019Article
- Hierarchical groove discrimination by Class I and II aminoacyl-tRNA synthetases reveals a palimpsest of the operational RNA code in the tRNA acceptor-stem bases.Nucleic acids research · 2018Article
- In the Beginning was a Mutualism - On the Origin of Translation.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Aminoacyl-tRNA synthetases recognize tRNA anticodon and 3' acceptor stem bases. Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition. Representing tRNA identity elements with two bits per base, we show that the anticodon encodes the hydrophobicity of each amino acid side-chain as represented by its water-to-cyclohexane distribution coefficient, and this relationship holds true over the entire temperature range of liquid water. The acceptor stem codes preferentially for the surface area or size of each side-chain, as represented by its vapor-to-cyclohexane distribution coefficient. These orthogonal experimental properties are both necessary to account satisfactorily for the exposed surface area of amino acids in folded proteins. Moreover, the acceptor stem codes correctly for β-branched and carboxylic acid side-chains, whereas the anticodon codes for a wider range of such properties, but not for size or β-branching. These and other results suggest that genetic coding of 3D protein structures evolved in distinct stages, based initially on the size of the amino acid and later on its compatibility with globular folding in water.
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