ArticlePLoS computational biology2018
Proteome-scale relationships between local amino acid composition and protein fates and functions.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- A composition-matching algorithm, MatchIDR, identifies prion-like domains that localize to stress granules.Protein science : a publication of the Protein Society · 2026Article
- Tracking Down the Evolution of Microorganisms by Exhaustive Bottom-Up Analysis of Proteomes.International journal of molecular sciences · 2025Article
- Proline-, Glutamic Acid-, Leucine-Rich Protein 1 (PELP1): Diversity, Structural Conservation, and Evolutionary Origins Across the Species.International journal of molecular sciences · 2025Article
- Depletion of tryptophanyl-tRNA synthetase and tryptophan accumulation triggers p53-dependent apoptosis.Cell death discovery · 2025Article
- In-Depth Study of Low-Complexity Domains: From Structural Diversity to Disease Mechanisms.Cells · 2025Review
- Sliding Window Interaction Grammar (SWING): a generalized interaction language model for peptide and protein interactions.Nature methods · 2025Article
- Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost.Protein science : a publication of the Protein Society · 2025Article
- Preserving condensate structure and composition by lowering sequence complexity.Biophysical journal · 2024Article
- Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life.PLoS computational biology · 2024Article
- Tryptophanyl-tRNA synthetase-1 (WARS-1) depletion and high tryptophan concentration lead to genomic instability in Caenorhabditis elegans.Cell death discovery · 2024Article
- Preserving condensate structure and composition by lowering sequence complexity.bioRxiv : the preprint server for biology · 2023Article
- The GGDEF protein Dgc2 suppresses both motility and biofilm formation in the filamentous cyanobacteriumMicrobiology spectrum · 2023Article
- The LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins.Bioinformatics (Oxford, England) · 2022Article
- A brief guideline for studies of phase-separated biomolecular condensates.Nature chemical biology · 2022Review
- Expansion and functional analysis of the SR-related protein family across the domains of life.RNA (New York, N.Y.) · 2022Article
- Article
- Low Complexity Regions in Mammalian Proteins are Associated with Low Protein Abundance and High Transcript Abundance.Molecular biology and evolution · 2022Article
- Determinants of the temperature adaptation of mRNA degradation.Nucleic acids research · 2022Article
- Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains.International journal of molecular sciences · 2021Article
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Proteins with low-complexity domains continue to emerge as key players in both normal and pathological cellular processes. Although low-complexity domains are often grouped into a single class, individual low-complexity domains can differ substantially with respect to amino acid composition. These differences may strongly influence the physical properties, cellular regulation, and molecular functions of low-complexity domains. Therefore, we developed a bioinformatic approach to explore relationships between amino acid composition, protein metabolism, and protein function. We find that local compositional enrichment within protein sequences is associated with differences in translation efficiency, abundance, half-life, protein-protein interaction promiscuity, subcellular localization, and molecular functions of proteins on a proteome-wide scale. However, local enrichment of related amino acids is sometimes associated with opposite effects on protein regulation and function, highlighting the importance of distinguishing between different types of low-complexity domains. Furthermore, many of these effects are discernible at amino acid compositions below those required for classification as low-complexity or statistically-biased by traditional methods and in the absence of homopolymeric amino acid repeats, indicating that thresholds employed by classical methods may not reflect biologically relevant criteria. Application of our analyses to composition-driven processes, such as the formation of membraneless organelles, reveals distinct composition profiles even for closely related organelles. Collectively, these results provide a unique perspective and detailed insights into relationships between amino acid composition, protein metabolism, and protein functions.
Indexed as
Identifiers
What OpenQuestion holds
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.