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  1. Article ; Online: Musashi-1

    Tsai-Chen Chen / Jie-rong Huang

    International Journal of Molecular Sciences, Vol 21, Iss 7, p

    An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

    2020  Volume 2289

    Abstract: RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular ... ...

    Abstract RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208−218 and ~270−284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer’s disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly.
    Keywords rna-binding proteins ; intrinsically disordered proteins ; polyalanine ; liquid–liquid phase separation ; self-association ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Phase separation driven by interchangeable properties in the intrinsically disordered regions of protein paralogs

    Shih-Hui Chiu / Wen-Lin Ho / Yung-Chen Sun / Jean-Cheng Kuo / Jie-rong Huang

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 12

    Abstract: A comparison of structure-function relationship for intrinsically disordered regions (IDRs) among paralogs shows that differences in physicochemical properties of the IDR between paralogs are compensated for to converge on the same biophysical function. ...

    Abstract A comparison of structure-function relationship for intrinsically disordered regions (IDRs) among paralogs shows that differences in physicochemical properties of the IDR between paralogs are compensated for to converge on the same biophysical function.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Interactions between the Intrinsically Disordered Regions of hnRNP-A2 and TDP-43 Accelerate TDP-43′s Conformational Transition

    Wan-Chin Chiang / Ming-Hsuan Lee / Tsai-Chen Chen / Jie-rong Huang

    International Journal of Molecular Sciences, Vol 21, Iss 5930, p

    2020  Volume 5930

    Abstract: Most biological functions involve protein–protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically ... ...

    Abstract Most biological functions involve protein–protein interactions. Our understanding of these interactions is based mainly on those of structured proteins, because encounters between intrinsically disordered proteins (IDPs) or proteins with intrinsically disordered regions (IDRs) are much less studied, regardless of the fact that more than half eukaryotic proteins contain IDRs. RNA-binding proteins (RBPs) are a large family whose members almost all have IDRs in addition to RNA binding domains. These IDRs, having low sequence similarity, interact, but structural details on these interactions are still lacking. Here, using the IDRs of two RBPs (hnRNA-A2 and TDP-43) as a model, we demonstrate that the rate at which TDP-43′s IDR undergoes the neurodegenerative disease related α-helix-to-β-sheet transition increases in relation to the amount of hnRNP-A2′s IDR that is present. There are more than 1500 RBPs in human cells and most of them have IDRs. RBPs often join the same complexes to regulate genes. In addition to the structured RNA-recognition motifs, our study demonstrates a general mechanism through which RBPs may regulate each other’s functions through their IDRs.
    Keywords intrinsically disordered protein ; liquid–liquid phase separation ; membraneless organelle ; NMR spectroscopy ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 612
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Liquid-liquid phase separation and extracellular multivalent interactions in the tale of galectin-3

    Yi-Ping Chiu / Yung-Chen Sun / De-Chen Qiu / Yu-Hao Lin / Yin-Quan Chen / Jean-Cheng Kuo / Jie-rong Huang

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: Galectin-3 consists of an unstructured N-terminal domain (NTD) and a structured carbohydrate-recognition domain and agglutinates neutrophils and glycosylated molecules in the extracellular milieu. Here the authors combine biophysical and biochemical ... ...

    Abstract Galectin-3 consists of an unstructured N-terminal domain (NTD) and a structured carbohydrate-recognition domain and agglutinates neutrophils and glycosylated molecules in the extracellular milieu. Here the authors combine biophysical and biochemical experiments with NMR measurements and show that the galectin-3 NTD undergoes liquid-liquid phase separation (LLPS) and agglutinates other molecules through this process.
    Keywords Science ; Q
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43

    Li, Hao-Ru / Chih-Lun Hsiao / Chi-Yuan Chou / Jie-rong Huang / Lin Shi / Tsai-Chen Chen

    BBA - Proteins and Proteomics. 2017,

    2017  

    Abstract: The TAR DNA-binding protein of 43kDa (TDP-43) has been identified as the main component of amyotrophic lateral sclerosis (ALS) cytoplasmic inclusions. The link between this proteinopathy and TDP-43′s intrinsically disordered C-terminal domain is well ... ...

    Abstract The TAR DNA-binding protein of 43kDa (TDP-43) has been identified as the main component of amyotrophic lateral sclerosis (ALS) cytoplasmic inclusions. The link between this proteinopathy and TDP-43′s intrinsically disordered C-terminal domain is well known, but recently also, this domain has been shown to be involved in the formation of the membraneless organelles that mediate TDP-43′s functions. The mechanisms that underpin the liquid-liquid phase separation (LLPS) of these membraneless organelles undergo remain elusive. Crucially though, these factors may be the key to understanding the delicate balance between TDP-43′s physiological and pathological functions. In this study, we used nuclear magnetic resonance spectroscopy and optical methods to demonstrate that an α-helical component in the centre (residues 320–340) of the C-terminal domain is related to the protein's self-association and LLPS. Systematically analysing ALS-related TDP-43 mutants (G298S, M337V, and Q331K) in different buffer conditions at different temperatures, we prove that this phase separation is driven by hydrophobic interactions but is inhibited by electrostatic repulsion. Based on these findings, we rationally introduced a mutant, W334G, and demonstrate that this mutant disrupts LLPS without disturbing this α-helical propensity. This tryptophan may serve as a key residue in this protein's LLPS.
    Keywords amino acid sequences ; amyotrophic lateral sclerosis ; cytoplasmic inclusions ; DNA-binding proteins ; electrostatic interactions ; hydrophobic bonding ; mutants ; nuclear magnetic resonance spectroscopy ; organelles ; separation ; temperature ; tryptophan
    Language English
    Size p. .
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 2918798-9
    ISSN 1878-1454 ; 1570-9639
    ISSN (online) 1878-1454
    ISSN 1570-9639
    DOI 10.1016/j.bbapap.2017.10.001
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions

    Elise Delaforge / Sigrid Milles / Jie-rong Huang / Denis Bouvier / Malene Ringkjøbing Jensen / Darren Hart / Michael Sattler / Martin Blackledge

    Frontiers in Molecular Biosciences, Vol

    2016  Volume 3

    Abstract: Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical ... ...

    Abstract Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.
    Keywords Nuclear Magnetic Resonance ; protein ; Conformational selection ; Small-angle scattering ; Chemical exchange saturation transfer (CEST) ; conformational dynamics ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2016-09-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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