The main forces directing long-term molecular evolution remain obscure. A sizable fraction of amino-acid substitutions seem to be fixed by positive selection, but it is unclear to what degree long-term protein evolution is constrained by epistasis, that is, instances when substitutions that are accepted in one genotype are deleterious in another. Here we obtain a quantitative estimate of the prevalence of epistasis in long-term protein evolution by relating data on amino-acid usage in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term evolution. We studied multiple alignments of at least 1,000 orthologues for each of these 16 proteins from species from a diverse phylogenetic background and found that an average site contained approximately eight different amino acids. Thus, without epistasis an average site should accept two-fifths of all possible amino acids, and the average rate of amino-acid substitutions should therefore be about three-fifths lower than the rate of neutral evolution. However, we found that the measured rate of amino-acid substitution in recent evolution is 20 times lower than the rate of neutral evolution and an order of magnitude lower than that expected in the absence of epi...Continue Reading
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
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Evolutionary evidence on suitability of SecD as a target for development of antibacterial agents against Staphylococcus aureus
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A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies
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Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase
Different contribution of conserved amino acids to the global properties of triosephosphate isomerases
Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations
Temperature responses of the Rubisco maximum carboxylase activity across domains of life: phylogenetic signals, trade-offs, and importance for carbon gain
Mutual influence of secondary and key drug-resistance mutations on catalytic properties and thermal stability of TEM-type β-lactamases
Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis
Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases
The evolution of zebrafish RAG2 protein is required for adapting to the elevated body temperature of the higher endothermic vertebrates
Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana
Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance
mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria
Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family
Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference
Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
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