ArticlePLoS computational biology2013
Evolutionary optimization of protein folding.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 59 citations in OpenAlex.
- Beyond Algorithmic Phase Transitions: Integrating Evolutionary Contingency, Biophysical Constraints, and System-Level Organization in Eukaryogenesis.FASEB bioAdvances · 2026Article
- Phylogeny and Molecular Characterisation ofBrain sciences · 2025Article
- Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes.Scientific reports · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- Evolution of Intrinsic Disorder in Protein Loops.Life (Basel, Switzerland) · 2023Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Protein length distribution is remarkably uniform across the tree of life.Genome biology · 2023Article
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Menzerath-Altmann's Law of Syntax in RNA Accretion History.Life (Basel, Switzerland) · 2021Article
- Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7.Chemical science · 2020Article
- Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures.International journal of molecular sciences · 2019Article
- Nature and Regulation of Protein Folding on the Ribosome.Trends in biochemical sciences · 2019Review
- Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis.Evolutionary bioinformatics online · 2019Review
- Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification.Science progress · 2018Review
- Selective pressure for rapid membrane integration constrains the sequence of bacterial outer membrane proteins.Molecular microbiology · 2017Article
- Family-specific scaling laws in bacterial genomes.Nucleic acids research · 2017Article
- Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks.Life (Basel, Switzerland) · 2016Article
- Evolutionary trend toward kinetic stability in the folding trajectory of RNases H.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- The early history and emergence of molecular functions and modular scale-free network behavior.Scientific reports · 2016Article
- Two independently folding units of Plasmodium profilin suggest evolution via gene fusion.Cellular and molecular life sciences : CMLS · 2015Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nature has shaped the make up of proteins since their appearance, [Formula: see text]3.8 billion years ago. However, the fundamental drivers of structural change responsible for the extraordinary diversity of proteins have yet to be elucidated. Here we explore if protein evolution affects folding speed. We estimated folding times for the present-day catalog of protein domains directly from their size-modified contact order. These values were mapped onto an evolutionary timeline of domain appearance derived from a phylogenomic analysis of protein domains in 989 fully-sequenced genomes. Our results show a clear overall increase of folding speed during evolution, with known ultra-fast downhill folders appearing rather late in the timeline. Remarkably, folding optimization depends on secondary structure. While alpha-folds showed a tendency to fold faster throughout evolution, beta-folds exhibited a trend of folding time increase during the last [Formula: see text]1.5 billion years that began during the "big bang" of domain combinations. As a consequence, these domain structures are on average slow folders today. Our results suggest that fast and efficient folding of domains shaped the universe of protein structure. This finding supports the hypothesis that optimization of the kinetic and thermodynamic accessibility of the native fold reduces protein aggregation propensities that hamper cellular functions.
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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.