ArticleComputational and structural biotechnology journal2022
Regions with two amino acids in protein sequences: A step forward from homorepeats into the low complexity landscape.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life.PLoS computational biology · 2024Article
- Article
- Phase separating Rho: a widespread regulatory function of disordered regions in proteins revealed in bacteria.Signal transduction and targeted therapy · 2023Article
- The nucleotide landscape of polyXY regions.Computational and structural biotechnology journal · 2023Article
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2 authors.
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Abstract
Low complexity regions (LCRs) differ in amino acid composition from the background provided by the corresponding proteomes. The simplest LCRs are homorepeats (or polyX), regions composed of mostly-one amino acid type. Extensive research has been done to characterize homorepeats, and their taxonomic, functional and structural features depend on the amino acid type and sequence context. From them, the next step towards the study of LCRs are the regions composed of two types of amino acids, which we call polyXY. We classify polyXY in three categories based on the arrangement of the two amino acid types 'X' and 'Y': direpeats (e.g. 'XYXYXY'), joined (e.g. 'XXXYYY') and shuffled (e.g. 'XYYXXY'). We developed a script to search for polyXY, and located them in a comprehensive set of 20,340 reference proteomes. These results are available in a dedicated web server called XYs, in which the user can also submit their own protein datasets to detect polyXY. We studied the distribution of polyXY types by amino acid pair XY and category, and show that polyXY in Eukaryota are mainly located within intrinsically disordered regions. Our study provides a first step towards the characterization of polyXY as protein motifs.
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