ArticleBioinformatics (Oxford, England)2010
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 64 citations in OpenAlex.
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Computational drug repurposing effort for identifying novel hits for the treatment of diseases such as endometriosis, uterine fibroids, and prostate cancer.Turkish journal of chemistry · 2024Article
- Evolution of Intrinsic Disorder in Protein Loops.Life (Basel, Switzerland) · 2023Article
- Review
- Exploring the Peptide Potential of Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Implications of divergence of methionine adenosyltransferase in archaea.FEBS open bio · 2022Article
- Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin.Developmental biology · 2020Article
- Robustness by intrinsically disordered C-termini and translational readthrough.Nucleic acids research · 2018Article
- The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions.The Journal of biological chemistry · 2018Article
- Evolution of intrinsic disorder in eukaryotic proteins.Cellular and molecular life sciences : CMLS · 2017Review
- An Evolution-Based Approach to De Novo Protein Design.Methods in molecular biology (Clifton, N.J.) · 2017Article
- A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication.Scientific reports · 2016Article
- A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence.Frontiers in plant science · 2016Article
- Article
- Intrinsically disordered regions of p53 family are highly diversified in evolution.Biochimica et biophysica acta · 2013Article
- Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.Protein science : a publication of the Protein Society · 2013Article
- Large extent of disorder in Adenomatous Polyposis Coli offers a strategy to guard Wnt signalling against point mutations.PloS one · 2013Article
- Marked variability in the extent of protein disorder within and between viral families.PloS one · 2013Article
- The dynamics and evolutionary potential of domain loss and emergence.Molecular biology and evolution · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationThe mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured (intrinsically disordered) regions. Is the formation of regular secondary structure an intrinsic feature of amino acid sequences, or is it a feature that is lost upon mutation and is maintained by evolution against the odds? Similarly, is disorder an intrinsic sequence feature or is it difficult to maintain? To tackle these questions, we in silico mutated native protein sequences into random sequence-like ensembles and monitored the change in predicted secondary structure and disorder.
resultsWe established that by our coarse-grained measures for change, predictions and observations were similar, suggesting that our results were not biased by prediction mistakes. Changes in secondary structure and disorder predictions were linearly proportional to the change in sequence. Surprisingly, neither the content nor the length distribution for the predicted secondary structure changed substantially. Regions with long disorder behaved differently in that significantly fewer such regions were predicted after a few mutation steps. Our findings suggest that the formation of regular secondary structure is an intrinsic feature of random amino acid sequences, while the formation of long-disordered regions is not an intrinsic feature of proteins with disordered regions. Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely.
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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.