ArticleProtein science : a publication of the Protein Society2016
Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Shining light on the dark proteome with unstructural biology.Current research in structural biology · 2026Article
- I-Shaped Dimers of a Plant Chloroplast FInternational journal of molecular sciences · 2023Article
- Computational Prediction of Protein Intrinsically Disordered Region Related Interactions and Functions.Genes · 2023Review
- Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept.Cellular and molecular life sciences : CMLS · 2022Review
- ATP synthase FCellular and molecular life sciences : CMLS · 2022Review
- Challenges in describing the conformation and dynamics of proteins with ambiguous behavior.Frontiers in molecular biosciences · 2022Article
- Prediction of protein-protein interaction sites in intrinsically disordered proteins.Frontiers in molecular biosciences · 2022Review
- Diffusion of a disordered protein on its folded ligand.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Tuning intrinsic disorder predictors for virus proteins.Virus evolution · 2021Article
- The complexity of protein interactions unravelled from structural disorder.PLoS computational biology · 2021Article
- Short Disordered Epitope of CRTAM Ig-Like V Domain as a Potential Target for Blocking Antibodies.International journal of molecular sciences · 2020Article
- Random Coils of Proteins Situated Between a Beta Strand and an Alpha Helix Demonstrate Decreased Solvent Accessibility.The protein journal · 2020Article
- New technologies to analyse protein function: an intrinsic disorder perspective.F1000Research · 2020Review
- Homology modeling in the time of collective and artificial intelligence.Computational and structural biotechnology journal · 2020Review
- Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions.Biomolecules · 2019Review
- On the Need to Develop Guidelines for Characterizing and Reporting Intrinsic Disorder in Proteins.Proteomics · 2019Article
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- Dissecting physical structure of calreticulin, an intrinsically disordered CaJournal of biomolecular structure & dynamics · 2018Article
- Intrinsic Disorder and Posttranslational Modifications: The Darker Side of the Biological Dark Matter.Frontiers in genetics · 2018Review
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2 authors.
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Abstract
Missing regions in X-ray crystal structures in the Protein Data Bank (PDB) have played a foundational role in the study of intrinsically disordered protein regions (IDPRs), especially in the development of in silico predictors of intrinsic disorder. However, a missing region is only a weak indication of intrinsic disorder, and this uncertainty is compounded by the presence of ambiguous regions, where more than one structure of the same protein sequence "disagrees" in terms of the presence or absence of missing residues. The question is this: are these ambiguous regions intrinsically disordered, or are they the result of static disorder that arises from experimental conditions, ensembles of structures, or domain wobbling? A novel way of looking at ambiguous regions in terms of the pattern between multiple PDB structures has been demonstrated. It was found that the propensity for intrinsic disorder increases as the level of ambiguity decreases. However, it is also shown that ambiguity is more likely to occur as the protein region is placed within different environmental conditions, and even the most ambiguous regions as a set display compositional bias that suggests flexibility. The results suggested that ambiguity is a natural result for many IDPRs crystallized under different conditions and that static disorder and wobbling domains are relatively rare. Instead, it is more likely that ambiguity arises because many of these regions were conditionally or partially disordered.
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