Cited by 4Protein Structure and DynamicsGenomics and Chromatin DynamicsBioinformatics and Genomic Networks

High‐throughput Discovery of Functional Disordered Regions

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Ali, Muhammad, Ivarsson, Ylva·2018·Molecular Systems Biology

Abstract

Partially or fully intrinsically disordered proteins are widespread in eukaryotic proteomes and play important biological functions. With the recognition that well defined protein structure is not a fundamental requirement for function come novel challenges, such as assigning function to disordered regions. In their recent work, Babu and colleagues (Ravarani et al , 2018) took on this challenge by developing IDR‐Screen, a robust high‐throughput approach for identifying functions of disordered regions.

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Crossref · 10.15252/msb.20188377

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  • The lack of readily druggable pockets for most transcription factors is a challenge for targeting them therapeutically.

    “These include the inherent complexity of their protein‒protein interactions [15] and the lack of readily druggable pockets for most transcription factors [16].”

    From Targeting Microglial Transcriptional Reprogramming as a Therapy Strategy for Alzheimer's Disease (2026) · cites this paper as [16]

    The discussion of transactivation domains in the paper’s Abstract describes disordered regions and their binding to coactivators, but does not address whether most transcription factors lack druggable pockets or whether that limits therapeutic targeting. Searches for druggable pockets and therapeutic targeting found no passage addressing that claim (page not available in our copy). (LLM, conf=0.72)

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Research works printed but not linked: 9

  1. Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y (2017) Discovery of short linear motif‐mediated interactions through phage display of intrinsically disordered regions of the human proteome. FEBS J 284: 485– 498 28002650
  2. Erkine AM, Gross DS (2003) Dynamic chromatin alterations triggered by natural and synthetic activation domains. J Biol Chem 278: 7755– 7764 12499367
  3. Luck K, Travé G (2011) Phage display can select over‐hydrophobic sequences that may impair prediction of natural domain–peptide interactions. Bioinformatics 27: 899– 902 21300698
  4. Ma J, Ptashne M (1987) A new class of yeast transcriptional activators. Cell 51: 113– 119 3115591
  5. Ravarani CNJ, Erkina TY, De Baets G, Dudman DC, Erikine AM, Babu MM (2018) High‐throughput discovery of functional disordered regions: investigation of transactivation domains. Mol Syst Biol 14: e8190 29759983 PMC5949888
  6. Sigler PB (1988) Transcriptional activation. Acid blobs and negative noodles. Nature 333: 210– 212 3367995
  7. Staller MV, Holehouse AS, Swain‐Lenz D, Das RK, Pappu RV, Cohen BA (2018) A high‐throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain. Cell Syst 6: 444– 455 29525204 PMC5920710
  8. Tompa P, Davey NE, Gibson TJ, Babu MM (2014) A million peptide motifs for the molecular biologist. Mol Cell 55: 161– 169 25038412
  9. Uesugi M, Nyanguile O, Lu H, Levine AJ, Verdine GL (1997) Induced α helix in the VP16 activation domain upon binding to a human TAF. Science 277: 1310– 1313 9271577

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Authors
Ali, M., & Ivarsson, Y.
Affiliations
Uppsala University (SE)
Venue
Molecular Systems Biology
Published
2018-05-01
Volume
14
Issue
5
Pages
e8377-e8377
ISSN
1744-4292 (ISSN-L)
OpenAlex
W2803402887
Cited by
4
References
1
Citations by year
2026: 1 · 2024: 2 · 2022: 1
FWCI
0.00
Type
journal article
Language
en
Open access
Locations
  • Molecular Systems Biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
intrinsically disordered regions, disordered proteins, high-throughput functional screening, eukaryotic proteomes
MeSH terms
Amino Acid Sequence, Protein Conformation, Proteins, Databases, Protein

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