ArticleMolecular biology and evolution2014
Amino Acid metabolism conflicts with protein diversity.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 59 citations in OpenAlex.
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- Sequence to structure insights into Lassa virus population-level biophysical properties and glycoprotein structure catalogue.Npj viruses · 2026Article
- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
- In-Context Learning can distort the relationship between sequence likelihoods and biological fitness.ArXiv · 2025Article
- Does metabolic rate influence genome-wide amino acid composition in the course of animal evolution?Evolution letters · 2025Article
- Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities.Scientific reports · 2024Article
- Predictive Models and Impact of Interfacial Contacts and Amino Acids on Protein-Protein Binding Affinity.ACS omega · 2024Article
- The Effects of Mesenchymal Stem Cells-Derived Exosomes on Metabolic Reprogramming in Scar Formation and Wound Healing.International journal of nanomedicine · 2024Review
- Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes.Biomedicines · 2023Article
- Biosynthetic constraints on amino acid synthesis at the base of the food chain may determine their use in higher-order consumer genomes.PLoS genetics · 2023Article
- Evolutionary analysis of KED-rich proteins in plants.PloS one · 2023Article
- Method for Accurate Detection of Amino Acids and Mycotoxins in Planetary Atmospheres.Life (Basel, Switzerland) · 2022Article
- Amino acid variability, tradeoffs and optimality in human diet.Nature communications · 2022Article
- Convergent Usage of Amino Acids in Human Cancers as A Reversed Process of Tissue Development.Genomics, proteomics & bioinformatics · 2022Article
- Yeast has evolved to minimize protein resource cost for synthesizing amino acids.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Sample-to-analysis platform for rapid intracellular mass spectrometry from small numbers of cells.Lab on a chip · 2021Article
- Thermodynamic Formalism in Neuronal Dynamics and Spike Train Statistics.Entropy (Basel, Switzerland) · 2020Review
- Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes.NPJ systems biology and applications · 2020Article
- On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences.The journal of physical chemistry. B · 2018Article
- Biosynthetic energy cost for amino acids decreases in cancer evolution.Nature communications · 2018Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data are remarkably well explained when the cost function accounts for amino acid chemical decay. More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse.
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