☆ 3.9 Review

Enrichment patterns of intrinsic disorder in proteins

BIOPHYSICAL REVIEWS (2022)

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Intrinsically disordered proteins play diverse roles in cell signaling

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Summary: Signaling pathways allow cells to detect and respond to various chemical and physical stimuli, forming a communication network that regulates cell activities and coordinates cell function. Successful signaling requires proteins that can form active and inactive states and engage in multiple interactions. Intrinsically disordered proteins play a critical role in cell signaling, present in diverse organisms and stages of signaling pathways.

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Intrinsically disordered signaling proteins: Essential hub players in the control of stress responses in Saccharomyces cerevisiae

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Summary: Cells have developed mechanisms to monitor changes in their environment and respond effectively. In the yeast Saccharomyces cerevisiae, structural disorder plays a key role in adjusting growth and development under stressful conditions. Analysis of 170 transcription factors in yeast reveals that most of them contain intrinsically disordered regions (IDRs) and have a higher number of protein-protein interactions. The presence of structural disorder is not limited to transcription factors but is also found in other signaling proteins, indicating their importance in stress responses. Furthermore, a significant proportion of intrinsically disordered transcription factors may undergo liquid-liquid phase separation.

PLOS ONE (2022)

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Article Biochemical Research Methods

Characterization of intrinsically disordered regions in proteins informed by human genetic diversity

Shehab S. Ahmed et al.

Summary: This study investigates the functional importance of intrinsically disordered proteins and regions (IDPs and IDRs) using protein sequence annotations and genetic variant data. The study identifies functional features commonly located in IDRs and observes that some IDRs tolerate more mutations in the general population. However, it also finds that a proportion of pathogenic mutations are located in IDRs. Based on statistical analysis and machine learning, the study shows that mutation-intolerant IDRs have distinct functional signatures.

PLOS COMPUTATIONAL BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell

Bi Zhao et al.

Summary: The study found that human proteins are significantly enriched in intrinsic disorder, with proteins localized in the nucleus and cytoskeleton having higher levels of disorder. On average, human proteins are assigned to 2.3 subcellular compartments, with proteins localized to fewer compartments being more disordered. Disordered proteins in the most disorder-enriched subcellular compartments primarily interact with nucleic acids and protein partners, adding a missing piece to the puzzle of functional disorder within the cell.

CELLULAR AND MOLECULAR LIFE SCIENCES (2021)

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αα-Hub domains and intrinsically disordered proteins: A decisive combo

Katrine Bugge et al.

Summary: Hub proteins are essential in protein-protein interaction networks, with alpha alpha-hubs being a newly defined group of folded hub domains. They play a crucial role in organizing disordered transcriptional regulators and membrane scaffolds, showcasing multifaceted protein-protein interaction properties facilitated by the alpha alpha-hub fold.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity

Sagie Brodsky et al.

Summary: Transcription factors (TFs) recognize specific DNA sequences through DNA-binding domains (DBDs), but the presence of intrinsically disordered regions (IDRs) also play a crucial role in DNA binding specificity.

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Characterization of functional disordered regions within chromatin-associated proteins

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Summary: Intrinsically disordered regions (IDRs) are abundant and important in the function of chromatin-associated proteins (CAPs), where they contribute to substrate binding, auto-regulation, and liquid-liquid droplet formation. Their disordered nature allows for increased functional diversity but presents challenges in structural characterization. Nuclear magnetic resonance (NMR) spectroscopy alongside cryo-electron microscopy offers a unique opportunity to study IDRs in CAPs.

ISCIENCE (2021)

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Intrinsic Disorder in Human RNA-Binding Proteins

Bi Zhao et al.

Summary: This study focused on the interaction between RNA-binding proteins (RBPs) and specific RNA types, revealing varying levels of intrinsic disorder in different RNA types. The results showed that disorder is relatively rarely utilized in RNA-binding regions, while disorder in non-RNA-binding regions may be involved in posttranslational modifications and interactions with DNA.

JOURNAL OF MOLECULAR BIOLOGY (2021)

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Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions

Chao Gao et al.

Summary: The study reveals that intrinsic domain disorder is associated with both organism complexity and clade-specific functions. Additionally, the disorder degree of protein domains may differ in different clades, with some domains being highly disordered in specific clades.

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Seeing Keratinocyte Proteins through the Looking Glass of Intrinsic Disorder

Rambon Shamilov et al.

Summary: Epidermal keratinocyte proteins exhibit unique characteristics in amino acid content, ultrastructural fate, and assembly visible at the light microscope level. Through the lens of intrinsic disorder, these oddities become expected, with highly repetitive motif proteins providing low-complexity, high adaptation polymers. Liquid-liquid phase separation in keratohyalin granules demonstrates the occurrence of unique biomolecular condensates in these specialized cells. Further examination of keratinocyte-specific proteins may lead to new discoveries in understanding intrinsically disordered proteins as reflected by keratinocyte biology.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications

Niccolo Candelise et al.

Summary: Intrinsic disorder in polypeptide chains leads to a lack of defined structure, with conformational changes potentially resulting in stable proteinaceous aggregates. Evidence suggests protein conformation may initiate signaling pathways. Understanding the structural heterogeneity of protein aggregates may aid in comprehending the phenotypic diversity in neurodegenerative disorders.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

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Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs

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Modulation of Intrinsically Disordered Protein Function by Post-translational Modifications

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