ArticleNucleic acids research2014
Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Genomic Landscape of High-Altitude Adaptation in East African Mountain Honey Bees (Ecology and evolution · 2025Article
- Phylogenetic history and temperature adaptation contribute to structural and functional stability of proteins in marine mollusks.Communications biology · 2025Article
- Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation.Current research in structural biology · 2024Article
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
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- Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers.ISME communications · 2022Article
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- The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?Life (Basel, Switzerland) · 2021Article
- Evolution of Protein Structure and Stability in Global Warming.International journal of molecular sciences · 2020Review
- Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness.BMC biology · 2020Article
- Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.Life (Basel, Switzerland) · 2020Article
- Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have.BMC evolutionary biology · 2019Article
- Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.Nature communications · 2018Article
- Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis.Molecular biology and evolution · 2018Article
- Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites.Biophysical journal · 2015Article
- Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns.BioData mining · 2015Article
- The fundamental tradeoff in genomes and proteomes of prokaryotes established by the genetic code, codon entropy, and physics of nucleic acids and proteins.Biology direct · 2014Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.