ArticleScientific reports2015
Extraordinarily adaptive properties of the genetically encoded amino acids.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Emergence of biosignatures on Earth and implications for life detection.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Artificial intelligence aided design of peptides with custom secondary structure motifs and reduced amino acid alphabets.bioRxiv : the preprint server for biology · 2026Article
- Similarity Analysis of Computer-Generated and Commercial Libraries for Targeted Biocompatible Coded Amino Acid Replacement.International journal of molecular sciences · 2024Article
- Alternative Pathways in Astrobiology: Reviewing and Synthesizing Contingency and Non-Biomolecular Origins of Terrestrial and Extraterrestrial Life.Life (Basel, Switzerland) · 2024Review
- Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It.Life (Basel, Switzerland) · 2023Review
- Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability.Journal of the American Chemical Society · 2023Article
- On the Evolutionary History of the Twenty Encoded Amino Acids.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet.Journal of molecular evolution · 2022Article
- Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge.Antioxidants (Basel, Switzerland) · 2022Review
- Differential Oligomerization of Alpha versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions.Life (Basel, Switzerland) · 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
- Exploring and mapping chemical space with molecular assembly trees.Science advances · 2021Article
- Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase.Protein science : a publication of the Protein Society · 2021Article
- Classification of the Biogenicity of Complex Organic Mixtures for the Detection of Extraterrestrial Life.Life (Basel, Switzerland) · 2021Article
- Evolution as a Guide to DesigningInternational journal of molecular sciences · 2021Review
- Universal Codons with Enrichment from GC to AU Nucleotide Composition Reveal a Chronological Assignment from Early to Late Along with LUCA Formation.Life (Basel, Switzerland) · 2020Article
- First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments.Die Naturwissenschaften · 2020Article
- Pentamers with Non-redundant Frames: Bias for Natural Circular Code Codons.Journal of molecular evolution · 2020Article
- Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry.Life (Basel, Switzerland) · 2020Article
- Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.Interface focus · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or "chemistry space." Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set.
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