ArticleGenome biology2015
Domain atrophy creates rare cases of functional partial protein domains.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 26 citations in OpenAlex.
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- Resurrecting Enzymes by Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules.Nature communications · 2021Article
- Evolution, folding, and design of TIM barrels and related proteins.Current opinion in structural biology · 2021Review
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- Improving pairwise comparison of protein sequences with domain co-occurrence.PLoS computational biology · 2018Article
- Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Alternative splicing in tomato pollen in response to heat stress.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.Journal of molecular biology · 2016Article
- Partial protein domains: evolutionary insights and bioinformatics challenges.Genome biology · 2015Article
- Most partial domains in proteins are alignment and annotation artifacts.Genome biology · 2015Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain atrophy, where protein domains lose a significant number of core structural elements.
resultsHere, we implement a new pipeline to systematically identify new cases of domain atrophy across all known protein sequences. The output of this pipeline was carefully checked by hand, which filtered out partial domain instances that were unlikely to represent true domain atrophy due to misannotations or un-annotated sequence fragments. We identify 75 cases of domain atrophy, of which eight cases are found in a three-dimensional protein structure and 67 cases have been inferred based on mapping to a known homologous structure. Domains with structural variations include ancient folds such as the TIM-barrel and Rossmann folds. Most of these domains are observed to show structural loss that does not affect their functional sites.
conclusionOur analysis has significantly increased the known cases of domain atrophy. We discuss specific instances of domain atrophy and see that there has often been a compensatory mechanism that helps to maintain the stability of the partial domain. Our study indicates that although domain atrophy is an extremely rare phenomenon, protein domains under certain circumstances can tolerate extreme mutations giving rise to partial, but functional, domains.
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