ArticleBiology letters2012
Fitness conferred by replaced amino acids declines with time.
Article in Biology letters, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins.The journal of physical chemistry. B · 2022Article
- Phylogenetic inference of changes in amino acid propensities with single-position resolution.PLoS computational biology · 2022Article
- Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.Protein science : a publication of the Protein Society · 2021Review
- Senescence and entrenchment in evolution of amino acid sites.Nature communications · 2020Article
- Allele-specific nonstationarity in evolution of influenza A virus surface proteins.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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- Compensatory mutations and epistasis for protein function.Current opinion in structural biology · 2018Review
- Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution.Molecular biology and evolution · 2017Article
- Parallel Evolution of Metazoan Mitochondrial Proteins.Genome biology and evolution · 2017Article
- Article
- Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data.Genome biology and evolution · 2016Article
- Article
- Epistasis in protein evolution.Protein science : a publication of the Protein Society · 2016Review
- Causes of molecular convergence and parallelism in protein evolution.Nature reviews. Genetics · 2016Review
- Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.Biology letters · 2015Review
- Contingency and entrenchment in protein evolution under purifying selection.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- A model of substitution trajectories in sequence space and long-term protein evolution.Molecular biology and evolution · 2015Article
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3 authors.
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Abstract
The fitness landscape of a locus, the array of fitnesses conferred by its alleles, can be affected by allele replacements at other loci, in the presence of epistatic interactions between loci. In a pair of diverging homologous proteins, the initially high probability that an amino acid replacement in one of them will make it more similar to the other declines with time, implying that the fitness landscapes of homologous sites diverge. Here, we use data on within-population non-synonymous polymorphisms and on amino acid replacements between species to study the dynamics, after an amino acid replacement, of the fitness of the ancestral amino acid, and show that selection against its restoration increases with time. This effect can be owing to increase of fitness conferred by the new amino acid occupying the site, and/or to decline of fitness conferred by the replaced amino acid. We show that the fitness conferred by the replaced amino acid rapidly declines, reaching a new lower steady-state level after approximately 20 per cent of amino acids in the protein get replaced. Therefore, amino acid replacements in evolving proteins are routinely involved in negative epistatic interactions with currently absent amino acids, and chisel off the unused parts of the fitness landscape.
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