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  1. Article ; Online: Subversion of host stress granules by coronaviruses: Potential roles of π-rich disordered domains of viral nucleocapsids.

    Moosa, Mahdi Muhammad / Banerjee, Priya R

    Journal of medical virology

    2020  Volume 92, Issue 12, Page(s) 2891–2893

    Keywords covid19
    Language English
    Publishing date 2020-07-02
    Publishing country United States
    Document type Letter
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.26195
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  2. Article ; Online: Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex.

    Davis, Richoo B / Supakar, Anushka / Ranganath, Aishwarya Kanchi / Moosa, Mahdi Muhammad / Banerjee, Priya R

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1168

    Abstract: Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian ... ...

    Abstract Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF (mSWI/SNF) complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
    MeSH term(s) Animals ; Prions/metabolism ; Transcription Factors/metabolism ; Chromatin ; Mammals/genetics ; Chromatin Assembly and Disassembly
    Chemical Substances Prions ; Transcription Factors ; Chromatin
    Language English
    Publishing date 2024-02-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-44945-5
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  3. Article ; Online: Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies.

    Davis, Richoo B / Moosa, Mahdi Muhammad / Banerjee, Priya R

    Trends in cell biology

    2022  Volume 32, Issue 8, Page(s) 681–695

    Abstract: Biomolecular condensates are membraneless organelles (MLOs) that are enriched in specific proteins and nucleic acids, compartmentalized to perform biochemical functions. Such condensates are formed by phase separation (PS) enabled by protein domains that ...

    Abstract Biomolecular condensates are membraneless organelles (MLOs) that are enriched in specific proteins and nucleic acids, compartmentalized to perform biochemical functions. Such condensates are formed by phase separation (PS) enabled by protein domains that allow multivalent interactions. Chromosomal translocation-derived in-frame gene fusions often generate proteins with non-native domain combinations that rewire protein-protein interaction networks. Several recent studies have shown that, for a subset of these fusion proteins, pathogenesis can be driven by the ability of the fusion protein to undergo phase transitions at non-physiological cellular locations to form ectopic condensates. We highlight how such ectopic phase transitions can alter biological processes and posit that dysfunction via protein PS at non-physiological locations represents a generic route to oncogenic transformation.
    MeSH term(s) Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Nucleic Acids/metabolism ; Organelles/metabolism ; Phase Transition ; Proteins/metabolism
    Chemical Substances Nucleic Acids ; Proteins
    Language English
    Publishing date 2022-04-25
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2022.03.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Heterotypic interactions in the dilute phase can drive co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex.

    Davis, Richoo B / Supakar, Anushka / Ranganath, Aishwarya Kanchi / Moosa, Mahdi Muhammad / Banerjee, Priya R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian ... ...

    Abstract Prion-like domains (PLDs) are low-complexity protein sequences enriched within nucleic acid-binding proteins including those involved in transcription and RNA processing. PLDs of FUS and EWSR1 play key roles in recruiting chromatin remodeler mammalian SWI/SNF complex to oncogenic FET fusion protein condensates. Here, we show that disordered low-complexity domains of multiple SWI/SNF subunits are prion-like with a strong propensity to undergo intracellular phase separation. These PLDs engage in sequence-specific heterotypic interactions with the PLD of FUS in the dilute phase at sub-saturation conditions, leading to the formation of PLD co-condensates. In the dense phase, homotypic and heterotypic PLD interactions are highly cooperative, resulting in the co-mixing of individual PLD phases and forming spatially homogeneous co-condensates. Heterotypic PLD-mediated positive cooperativity in protein-protein interaction networks is likely to play key roles in the co-phase separation of mSWI/SNF complex with transcription factors containing homologous low-complexity domains.
    Language English
    Publishing date 2023-11-22
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.12.536623
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  5. Article ; Online: FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion-like domains.

    Davis, Richoo B / Kaur, Taranpreet / Moosa, Mahdi Muhammad / Banerjee, Priya R

    Protein science : a publication of the Protein Society

    2021  Volume 30, Issue 7, Page(s) 1454–1466

    Abstract: Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family proteins result from the fusion of the prion-like ... ...

    Abstract Fusion transcription factors generated by genomic translocations are common drivers of several types of cancers including sarcomas and leukemias. Oncofusions of the FET (FUS, EWSR1, and TAF15) family proteins result from the fusion of the prion-like domain (PLD) of FET proteins to the DNA-binding domain (DBD) of certain transcription regulators and are implicated in aberrant transcriptional programs through interactions with chromatin remodelers. Here, we show that FUS-DDIT3, a FET oncofusion protein, undergoes PLD-mediated phase separation into liquid-like condensates. Nuclear FUS-DDIT3 condensates can recruit essential components of the global transcriptional machinery such as the chromatin remodeler SWI/SNF. The recruitment of mammalian SWI/SNF (mSWI/SNF) is driven by heterotypic PLD-PLD interactions between FUS-DDIT3 and core subunits of SWI/SNF, such as the catalytic component BRG1. Further experiments with single-molecule correlative force-fluorescence microscopy support a model wherein the fusion protein forms condensates on DNA surface and enrich BRG1 to activate transcription by ectopic chromatin remodeling. Similar PLD-driven co-condensation of mSWI/SNF with transcription factors can be employed by other oncogenic fusion proteins with a generic PLD-DBD domain architecture for global transcriptional reprogramming.
    MeSH term(s) Cell Line ; Chromosomal Proteins, Non-Histone/chemistry ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Humans ; Microscopy, Fluorescence ; Oncogene Proteins, Fusion/chemistry ; Oncogene Proteins, Fusion/genetics ; Oncogene Proteins, Fusion/metabolism ; Prions/chemistry ; Prions/genetics ; Prions/metabolism ; Protein Domains ; RNA-Binding Protein FUS/chemistry ; RNA-Binding Protein FUS/genetics ; RNA-Binding Protein FUS/metabolism ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Chromosomal Proteins, Non-Histone ; FUS protein, human ; Oncogene Proteins, Fusion ; Prions ; RNA-Binding Protein FUS ; SWI-SNF-B chromatin-remodeling complex ; Transcription Factors
    Language English
    Publishing date 2021-06-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4127
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  6. Article ; Online: Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides

    Ibraheem Alshareedah / Mahdi Muhammad Moosa / Matthew Pham / Davit A. Potoyan / Priya R. Banerjee

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Volume 14

    Abstract: Here the authors show that disordered polypeptide-RNA condensates exhibit rheological properties similar to that of a viscoelastic Maxwell fluid, and use simple polypeptide design rules to create microcondensates with tunable viscoelasticity. ...

    Abstract Here the authors show that disordered polypeptide-RNA condensates exhibit rheological properties similar to that of a viscoelastic Maxwell fluid, and use simple polypeptide design rules to create microcondensates with tunable viscoelasticity.
    Keywords Science ; Q
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Single-Molecule FRET Detection of Early-Stage Conformations in α-Synuclein Aggregation.

    Moosa, Mahdi Muhammad / Ferreon, Josephine C / Ferreon, Allan Chris M

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 1948, Page(s) 221–233

    Abstract: Misfolding and aggregation of α-synuclein are linked to many neurodegenerative disorders, including Parkinson's and Alzheimer's disease. Despite intense research efforts, detailed structural characterization of early conformational transitions that ... ...

    Abstract Misfolding and aggregation of α-synuclein are linked to many neurodegenerative disorders, including Parkinson's and Alzheimer's disease. Despite intense research efforts, detailed structural characterization of early conformational transitions that initiate and drive α-synuclein aggregation remains elusive often due to the low sensitivity and ensemble averaging of commonly used techniques. Single-molecule Förster resonance energy transfer (smFRET) provides unique advantages in detecting minor conformations that initiate protein pathologic aggregation. In this chapter, we describe an smFRET-based method for characterizing early conformational conversions that are responsible for α-synuclein self-assembly and aggregation.
    MeSH term(s) Fluorescence Resonance Energy Transfer ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Neurodegenerative Diseases/metabolism ; Protein Aggregation, Pathological/metabolism ; Protein Conformation ; Protein Folding ; Spectrum Analysis ; alpha-Synuclein/chemistry ; alpha-Synuclein/metabolism
    Chemical Substances Intrinsically Disordered Proteins ; alpha-Synuclein
    Language English
    Publishing date 2019-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9124-2_17
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  8. Article: Subversion of host stress granules by coronaviruses: Potential roles of π-rich disordered domains of viral nucleocapsids

    Muhammad Moosa, Mahdi / Banerjee, Priya R

    J. med. virol

    Abstract: Coronavirus nucleocapsids (CoV N's) play both structural and non-structural roles in viral life-cycle. Here, we propose a mechanism for host stress granule (SG) subversion by CoV N proteins. We posit that disordered domains of CoV N's can engage in π-π ... ...

    Abstract Coronavirus nucleocapsids (CoV N's) play both structural and non-structural roles in viral life-cycle. Here, we propose a mechanism for host stress granule (SG) subversion by CoV N proteins. We posit that disordered domains of CoV N's can engage in π-π intermolecular fuzzy interactions with host SG proteins and are crucial to the viral hijacking of host machineries. This article is protected by copyright. All rights reserved.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #32558957
    Database COVID19

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  9. Article ; Online: Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides.

    Alshareedah, Ibraheem / Moosa, Mahdi Muhammad / Pham, Matthew / Potoyan, Davit A / Banerjee, Priya R

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 6620

    Abstract: Liquid-liquid phase separation of multivalent proteins and RNAs drives the formation of biomolecular condensates that facilitate membrane-free compartmentalization of subcellular processes. With recent advances, it is becoming increasingly clear that ... ...

    Abstract Liquid-liquid phase separation of multivalent proteins and RNAs drives the formation of biomolecular condensates that facilitate membrane-free compartmentalization of subcellular processes. With recent advances, it is becoming increasingly clear that biomolecular condensates are network fluids with time-dependent material properties. Here, employing microrheology with optical tweezers, we reveal molecular determinants that govern the viscoelastic behavior of condensates formed by multivalent Arg/Gly-rich sticker-spacer polypeptides and RNA. These condensates behave as Maxwell fluids with an elastically-dominant rheological response at shorter timescales and a liquid-like behavior at longer timescales. The viscous and elastic regimes of these condensates can be tuned by the polypeptide and RNA sequences as well as their mixture compositions. Our results establish a quantitative link between the sequence- and structure-encoded biomolecular interactions at the microscopic scale and the rheological properties of the resulting condensates at the mesoscale, enabling a route to systematically probe and rationally engineer biomolecular condensates with programmable mechanics.
    MeSH term(s) Base Sequence ; Biomolecular Condensates ; Biophysics ; Genetic Techniques ; Intrinsically Disordered Proteins ; Microscopy/methods ; Optical Tweezers ; Peptides/chemistry ; Peptides/genetics ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism ; RNA/chemistry ; RNA/metabolism ; Software ; Viscosity
    Chemical Substances Intrinsically Disordered Proteins ; Peptides ; Proteins ; RNA (63231-63-0)
    Language English
    Publishing date 2021-11-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-26733-7
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  10. Article ; Online: Ligand interactions and the protein order-disorder energetic continuum.

    Moosa, Mahdi Muhammad / Ferreon, Josephine C / Ferreon, Allan Chris M

    Seminars in cell & developmental biology

    2018  Volume 99, Page(s) 78–85

    Abstract: Intrinsically disordered proteins as computationally predicted account for ∼1/3 of eukaryotic proteomes, are involved in a plethora of biological functions, and have been linked to several human diseases as a result of their dysfunctions. Here, we ... ...

    Abstract Intrinsically disordered proteins as computationally predicted account for ∼1/3 of eukaryotic proteomes, are involved in a plethora of biological functions, and have been linked to several human diseases as a result of their dysfunctions. Here, we present a picture wherein an energetic continuum describes protein structural and conformational propensities, ranging from the hyperstable folded proteins on one end to the hyperdestabilized and sometimes functionally disordered proteins on the other. We distinguish between proteins that are folding-competent but disordered because of marginal stability and those that are disordered due mainly to the absence of folding code-completing structure-determining interactions, and postulate that disordered proteins that are unstructured by way of partial population of protein denatured states represent a sizable proportion of the proteome.
    MeSH term(s) Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Ligands ; Protein Conformation ; Protein Folding ; Proteome/chemistry ; Proteome/metabolism
    Chemical Substances Intrinsically Disordered Proteins ; Ligands ; Proteome
    Language English
    Publishing date 2018-06-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2018.05.007
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