ArticlePLoS computational biology2020
Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 37 citations in OpenAlex.
- Compositionally Biased Regions Within Structured Protein Domains.Biomolecules · 2026Article
- In-Depth Study of Low-Complexity Domains: From Structural Diversity to Disease Mechanisms.Cells · 2025Review
- A Perspective on the Role of Mitochondrial Biomolecular Condensates (mtBCs) in Neurodegenerative Diseases and Evolutionary Links to Bacterial BCs.International journal of molecular sciences · 2025Review
- Low-complexity regions in fungi display functional groups and are depleted in positively charged amino acids.NAR genomics and bioinformatics · 2025Article
- Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life.PLoS computational biology · 2024Article
- Article
- Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils.Nature communications · 2023Article
- Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia.International journal of molecular sciences · 2023Review
- A brief guideline for studies of phase-separated biomolecular condensates.Nature chemical biology · 2022Review
- Review
- Expansion and functional analysis of the SR-related protein family across the domains of life.RNA (New York, N.Y.) · 2022Article
- Article
- Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.Briefings in bioinformatics · 2022Article
- Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered.Biomolecules · 2022Article
- Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains.Nature chemistry · 2022Article
- Karyopherin abnormalities in neurodegenerative proteinopathies.Brain : a journal of neurology · 2021Review
- Entropy and Fractal Dimension Study of the TDP-43 Protein Low Complexity Domain Sequence in ALS Disease Severity and SARS-CoV-2 Gene Sequences in Virulence Variability.Entropy (Basel, Switzerland) · 2021Article
- The Different Faces of the TDP-43 Low-Complexity Domain: The Formation of Liquid Droplets and Amyloid Fibrils.International journal of molecular sciences · 2021Review
- Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins.Nucleic acids research · 2021Article
- Biological Phase Separation and Biomolecular Condensates in Plants.Annual review of plant biology · 2021Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A variety of studies have suggested that low-complexity domains (LCDs) tend to be intrinsically disordered and are relatively rare within structured proteins in the Protein Data Bank (PDB). Although LCDs are often treated as a single class, we previously found that LCDs enriched in different amino acids can exhibit substantial differences in protein metabolism and function. Therefore, we wondered whether the structural conformations of LCDs are likewise dependent on which specific amino acids are enriched within each LCD. Here, we directly examined relationships between enrichment of individual amino acids and secondary structure tendencies across the entire PDB proteome. Secondary structure tendencies varied as a function of the identity of the amino acid enriched and its degree of enrichment. Furthermore, divergence in secondary structure profiles often occurred for LCDs enriched in physicochemically similar amino acids (e.g. valine vs. leucine), indicating that LCDs composed of related amino acids can have distinct secondary structure tendencies. Comparison of LCD secondary structure tendencies with numerous pre-existing secondary structure propensity scales resulted in relatively poor correlations for certain types of LCDs, indicating that these scales may not capture secondary structure tendencies as sequence complexity decreases. Collectively, these observations provide a highly resolved view of structural tendencies among LCDs parsed by the nature and magnitude of single amino acid enrichment.
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Registered trials
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.