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  1. Article ; Online: The return of the rings: Evolutionary convergence of aromatic residues in the intrinsically disordered regions of RNA-binding proteins for liquid-liquid phase separation.

    Ho, Wen-Lin / Huang, Jie-Rong

    Protein science : a publication of the Protein Society

    2022  Volume 31, Issue 5, Page(s) e4317

    Abstract: Aromatic residues appeared relatively late in the evolution of protein sequences to stabilize the globular proteins' folding core and are less in the intrinsically disordered regions (IDRs). Recent advances in protein liquid-liquid phase separation (LLPS) ...

    Abstract Aromatic residues appeared relatively late in the evolution of protein sequences to stabilize the globular proteins' folding core and are less in the intrinsically disordered regions (IDRs). Recent advances in protein liquid-liquid phase separation (LLPS) studies have also shown that aromatic residues in IDRs often act as "stickers" to promote multivalent interactions in forming higher-order oligomers. To study how general these structure-promoting residues are in IDRs, we compared levels of sequence disorder in RNA binding proteins (RBPs), which are often found to undergo LLPS, and the human proteome. We found that aromatic residues appear more frequently than expected in the IDRs of RBPs and, through multiple sequence alignment analysis, those aromatic residues are often conserved among chordates. Using TDP-43, FUS, and some other well-studied LLPS proteins as examples, the conserved aromatic residues are important to their LLPS-related functions. These analyses suggest that aromatic residues may have contributed twice to evolution: stabilizing structured proteins and assembling biomolecular condensates.
    MeSH term(s) Amino Acid Sequence ; Humans ; Intrinsically Disordered Proteins/chemistry ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Sequence Alignment
    Chemical Substances Intrinsically Disordered Proteins ; RNA-Binding Proteins
    Language English
    Publishing date 2022-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4317
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: IFF: Identifying key residues in intrinsically disordered regions of proteins using machine learning.

    Ho, Wen-Lin / Huang, Hsuan-Cheng / Huang, Jie-Rong

    Protein science : a publication of the Protein Society

    2023  Volume 32, Issue 9, Page(s) e4739

    Abstract: Conserved residues in protein homolog sequence alignments are structurally or functionally important. For intrinsically disordered proteins or proteins with intrinsically disordered regions (IDRs), however, alignment often fails because they lack a ... ...

    Abstract Conserved residues in protein homolog sequence alignments are structurally or functionally important. For intrinsically disordered proteins or proteins with intrinsically disordered regions (IDRs), however, alignment often fails because they lack a steric structure to constrain evolution. Although sequences vary, the physicochemical features of IDRs may be preserved in maintaining function. Therefore, a method to retrieve common IDR features may help identify functionally important residues. We applied unsupervised contrastive learning to train a model with self-attention neuronal networks on human IDR orthologs. Parameters in the model were trained to match sequences in ortholog pairs but not in other IDRs. The trained model successfully identifies previously reported critical residues from experimental studies, especially those with an overall pattern (e.g., multiple aromatic residues or charged blocks) rather than short motifs. This predictive model can be used to identify potentially important residues in other proteins, improving our understanding of their functions. The trained model can be run directly from the Jupyter Notebook in the GitHub repository using Binder (mybinder.org). The only required input is the primary sequence. The training scripts are available on GitHub (https://github.com/allmwh/IFF). The training datasets have been deposited in an Open Science Framework repository (https://osf.io/jk29b).
    MeSH term(s) Humans ; Intrinsically Disordered Proteins/chemistry ; Sequence Alignment ; Machine Learning ; Models, Molecular ; Protein Conformation
    Chemical Substances Intrinsically Disordered Proteins
    Language English
    Publishing date 2023-07-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4739
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3407: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 1: Show issues

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

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

    Communications biology

    2022  Volume 5, Issue 1, Page(s) 400

    Abstract: Paralogs, arising from gene duplications, increase the functional diversity of proteins. Protein functions in paralog families have been extensively studied, but little is known about the roles that intrinsically disordered regions (IDRs) play in their ... ...

    Abstract Paralogs, arising from gene duplications, increase the functional diversity of proteins. Protein functions in paralog families have been extensively studied, but little is known about the roles that intrinsically disordered regions (IDRs) play in their paralogs. Without a folded structure to restrain them, IDRs mutate more diversely along with evolution. However, how the diversity of IDRs in a paralog family affects their functions is unexplored. Using the RNA-binding protein Musashi family as an example, we applied multiple structural techniques and phylogenetic analysis to show how members in a paralog family have evolved their IDRs to different physicochemical properties but converge to the same function. In this example, the lower prion-like tendency of Musashi-1's IDRs, rather than Musashi-2's, is compensated by its higher α-helical propensity to assist their assembly. Our work suggests that, no matter how diverse they become, IDRs could evolve different traits to a converged function, such as liquid-liquid phase separation.
    MeSH term(s) Humans ; Phylogeny ; Proteins/metabolism
    Chemical Substances Proteins
    Language English
    Publishing date 2022-04-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-022-03354-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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