ArticleGenetics2019
A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.
Article in Genetics, 2019. 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.
- Emergence Biases in Molecular Evolution.Genome biology and evolution · 2026Review
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- Proteins Rich in Prime Mass Residues and Their Role in Cell Biology.Evolutionary bioinformatics online · 2026Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.bioRxiv : the preprint server for biology · 2024Article
- Article
- The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder.bioRxiv : the preprint server for biology · 2024Article
- Automatic Clustering of Excited-State Trajectories: Application to Photoexcited Dynamics.Journal of chemical theory and computation · 2023Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 2022Article
- Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.Current biology : CB · 2022Article
- Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful.Genome biology and evolution · 2022Article
- Evolution and co-evolution: insights into the divergence of plant heat shock factor genes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution.Genome research · 2021Article
- Article
- Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.Frontiers in molecular biosciences · 2021Article
- Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes.Genetics · 2020Article
- Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions.Journal of molecular biology · 2019Article
- De novo gene birth.PLoS genetics · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
To detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare "more evolved" to "less evolved" entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer. To be retained during evolution, a protein must not only have a function, but must also avoid toxic dysfunction such as protein aggregation. There is conflict between the two requirements: hydrophobic amino acids form the cores of protein folds, but also promote aggregation. Young genes avoid strongly hydrophobic amino acids, which is presumably the simplest solution to the aggregation problem. Here we show that young genes' few hydrophobic residues are clustered near one another along the primary sequence, presumably to assist folding. The higher aggregation risk created by the higher hydrophobicity of older genes is counteracted by more subtle effects in the ordering of the amino acids, including a reduction in the clustering of hydrophobic residues until they eventually become more interspersed than if distributed randomly. This interspersion has previously been reported to be a general property of proteins, but here we find that it is restricted to old genes. Quantitatively, the index of dispersion delineates a gradual trend,
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