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  1. Article ; Online: Recent advances in proximity-based labeling methods for interactome mapping.

    Trinkle-Mulcahy, Laura

    F1000Research

    2019  Volume 8

    Abstract: Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein-protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved ... ...

    Abstract Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein-protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved both temporal and spatial resolution, and the technique has been successfully employed in numerous small-scale (single complex mapping) and large-scale (network mapping) initiatives. When paired with quantitative proteomic approaches, the ability of these assays to provide snapshots of stable and transient interactions over time greatly facilitates the mapping of dynamic interactomes. Furthermore, recent innovations have extended biotin-based proximity labeling techniques such as BioID and APEX beyond classic protein-centric assays (tag a protein to label neighboring proteins) to include RNA-centric (tag an RNA species to label RNA-binding proteins) and DNA-centric (tag a gene locus to label associated protein complexes) assays.
    MeSH term(s) Multiprotein Complexes/chemistry ; Protein Interaction Mapping ; Proteomics
    Chemical Substances Multiprotein Complexes
    Language English
    Publishing date 2019-01-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.16903.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: BioID organelle mapping: you are the company you keep.

    Gaudreau-Lapierre, Antoine / Trinkle-Mulcahy, Laura

    Trends in biochemical sciences

    2021  Volume 46, Issue 12, Page(s) 950–952

    Abstract: In a recent study, Go, Knight et al. combined a panel of protein markers with BioID proximity-dependent labeling to profile the composition of 20 distinct subcellular compartments. Comparison with similar global datasets acquired using imaging or ... ...

    Abstract In a recent study, Go, Knight et al. combined a panel of protein markers with BioID proximity-dependent labeling to profile the composition of 20 distinct subcellular compartments. Comparison with similar global datasets acquired using imaging or fractionation-based approaches confirmed the consistency of the results while highlighting unique advantages.
    MeSH term(s) Biotinylation ; Organelles/metabolism ; Protein Interaction Mapping/methods ; Proteins/metabolism
    Chemical Substances Proteins
    Language English
    Publishing date 2021-09-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2021.09.003
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1207: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Mapping New Residents of the Mitochondrial Nucleoid.

    Trinkle-Mulcahy, Laura

    Cell chemical biology

    2017  Volume 24, Issue 3, Page(s) 250–251

    Abstract: In this issue of Cell Chemical Biology, Han et al. (2017) used a powerful combination of quantitative ratiometric mass spectrometry with APEX peroxidase-catalyzed proximity biotinylation to selectively highlight proteins associated with mitochondrial DNA ...

    Abstract In this issue of Cell Chemical Biology, Han et al. (2017) used a powerful combination of quantitative ratiometric mass spectrometry with APEX peroxidase-catalyzed proximity biotinylation to selectively highlight proteins associated with mitochondrial DNA above the background of contaminants and matrix proteins. In addition to identifying novel nucleoid factors, this study extends the APEX strategy to the proteomic mapping of non-membrane-bound multiprotein complexes.
    MeSH term(s) Biotinylation ; DNA, Mitochondrial ; Mitochondria/genetics ; Proteins ; Proteomics
    Chemical Substances DNA, Mitochondrial ; Proteins
    Language English
    Publishing date 2017-03-15
    Publishing country United States
    Document type Journal Article ; Comment
    ISSN 2451-9448
    ISSN (online) 2451-9448
    DOI 10.1016/j.chembiol.2017.03.006
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  4. Article ; Online: Cooperative assembly of filopodia by the formin FMNL2 and I-BAR domain protein IRTKS.

    Fox, Sarah / Tran, Amanda / Trinkle-Mulcahy, Laura / Copeland, John W

    The Journal of biological chemistry

    2022  Volume 298, Issue 11, Page(s) 102512

    Abstract: Filopodia are long finger-like actin-based structures that project out from the plasma membrane as cells navigate and explore their extracellular environment. The initiation of filopodia formation requires release of tension at the plasma membrane ... ...

    Abstract Filopodia are long finger-like actin-based structures that project out from the plasma membrane as cells navigate and explore their extracellular environment. The initiation of filopodia formation requires release of tension at the plasma membrane followed by the coordinated assembly of long unbranched actin filaments. Filopodia growth is maintained by a tip complex that promotes actin polymerization and protects the growing barbed ends of the actin fibers from capping proteins. Filopodia growth also depends on additional F-actin bundling proteins to stiffen the actin filaments as well as extension of the membrane sheath projecting from the cell periphery. These activities can be provided by a number of actin-binding and membrane-binding proteins including formins such as formin-like 2 (FMNL2) and FMNL3, and Inverse-Bin-Amphiphysin-Rvs (I-BAR) proteins such as IRTKS and IRSp53, but the specific requirement for these proteins in filopodia assembly is not clear. We report here that IRTKS and IRSp53 are FMNL2-binding proteins. Coexpression of FMNL2 with either I-BAR protein promotes cooperative filopodia assembly. We find IRTKS, but not IRSp53, is required for FMNL2-induced filopodia assembly, and FMNL2 and IRTKS are mutually dependent cofactors in this process. Our results suggest that the primary function for FMNL2 during filopodia assembly is binding to the plasma membrane and that regulation of actin dynamics by its formin homology 2 domain is secondary. From these results, we conclude that FMNL2 initiates filopodia assembly via an unexpected novel mechanism, by bending the plasma membrane to recruit IRTKS and thereby nucleate filopodia assembly.
    MeSH term(s) Pseudopodia/metabolism ; Formins ; Actins/metabolism ; Actin Cytoskeleton/metabolism ; Carrier Proteins/metabolism
    Chemical Substances Formins ; amphiphysin (147954-52-7) ; Actins ; Carrier Proteins
    Language English
    Publishing date 2022-09-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2022.102512
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.108: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  5. Article ; Online: Recent advances in proximity-based labeling methods for interactome mapping [version 1; referees

    Laura Trinkle-Mulcahy

    F1000Research, Vol

    2 approved]

    2019  Volume 8

    Abstract: Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein–protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved ... ...

    Abstract Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein–protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved both temporal and spatial resolution, and the technique has been successfully employed in numerous small-scale (single complex mapping) and large-scale (network mapping) initiatives. When paired with quantitative proteomic approaches, the ability of these assays to provide snapshots of stable and transient interactions over time greatly facilitates the mapping of dynamic interactomes. Furthermore, recent innovations have extended biotin-based proximity labeling techniques such as BioID and APEX beyond classic protein-centric assays (tag a protein to label neighboring proteins) to include RNA-centric (tag an RNA species to label RNA-binding proteins) and DNA-centric (tag a gene locus to label associated protein complexes) assays.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: SPECC1L binds the myosin phosphatase complex MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin.

    Mehta, Virja / Decan, Nathalie / Ooi, Sarah / Gaudreau-Lapierre, Antoine / Copeland, John W / Trinkle-Mulcahy, Laura

    The Journal of biological chemistry

    2023  Volume 299, Issue 2, Page(s) 102893

    Abstract: The subcellular localization, activity , and substrate specificity of the serine/threonine protein phosphatase 1 catalytic subunit ( ... ...

    Abstract The subcellular localization, activity , and substrate specificity of the serine/threonine protein phosphatase 1 catalytic subunit (PP1
    MeSH term(s) Humans ; Actins/metabolism ; Microtubules/metabolism ; Myosin-Light-Chain Phosphatase/metabolism ; Phosphorylation ; Protein Phosphatase 1/metabolism ; Protein Binding
    Chemical Substances Actins ; Myosin-Light-Chain Phosphatase (EC 3.1.3.53) ; Protein Phosphatase 1 (EC 3.1.3.16) ; SPECC1 protein, human ; PPP1R12A protein, human (EC 3.1.3.53) ; PPP1CB protein, human (EC 3.1.3.16)
    Language English
    Publishing date 2023-01-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.102893
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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.108: Show issues Location:
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  7. Article ; Online: Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling.

    Gaudreau-Lapierre, Antoine / Klonisch, Thomas / Nicolas, Hannah / Thanasupawat, Thatchawan / Trinkle-Mulcahy, Laura / Hombach-Klonisch, Sabine

    International journal of molecular sciences

    2023  Volume 24, Issue 4

    Abstract: The non-histone chromatin binding protein High Mobility Group AT-hook protein 2 (HMGA2) has important functions in chromatin remodeling, and genome maintenance and protection. Expression of HMGA2 is highest in embryonic stem cells, declines during cell ... ...

    Abstract The non-histone chromatin binding protein High Mobility Group AT-hook protein 2 (HMGA2) has important functions in chromatin remodeling, and genome maintenance and protection. Expression of HMGA2 is highest in embryonic stem cells, declines during cell differentiation and cell aging, but it is re-expressed in some cancers, where high HMGA2 expression frequently coincides with a poor prognosis. The nuclear functions of HMGA2 cannot be explained by binding to chromatin alone but involve complex interactions with other proteins that are incompletely understood. The present study used biotin proximity labeling, followed by proteomic analysis, to identify the nuclear interaction partners of HMGA2. We tested two different biotin ligase HMGA2 constructs (BioID2 and miniTurbo) with similar results, and identified known and new HMGA2 interaction partners, with functionalities mainly in chromatin biology. These HMGA2 biotin ligase fusion constructs offer exciting new possibilities for interactome discovery research, enabling the monitoring of nuclear HMGA2 interactomes during drug treatments.
    MeSH term(s) Biotin ; Cell Differentiation ; Chromatin ; Ligases ; Proteomics ; HMGA2 Protein
    Chemical Substances Biotin (6SO6U10H04) ; Chromatin ; Ligases (EC 6.-) ; HMGA2 Protein
    Language English
    Publishing date 2023-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24044246
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  8. Article: Recent advances in large-scale protein interactome mapping.

    Mehta, Virja / Trinkle-Mulcahy, Laura

    F1000Research

    2016  Volume 5

    Abstract: Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can ... ...

    Abstract Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other 'omics' data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases.
    Language English
    Publishing date 2016
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2699932-8
    ISSN 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.7629.1
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  9. Article ; Online: Expansion microscopy-based imaging of nuclear structures in cultured cells.

    Gaudreau-Lapierre, Antoine / Mulatz, Kirk / Béïque, Jean-Claude / Trinkle-Mulcahy, Laura

    STAR protocols

    2021  Volume 2, Issue 3, Page(s) 100630

    Abstract: Expansion microscopy is a sample preparation technique in which fixed and immunostained cells or tissues are embedded in a cross-linked network of swellable polyelectrolyte hydrogel that expands isotropically upon addition of deionized water. We utilize ... ...

    Abstract Expansion microscopy is a sample preparation technique in which fixed and immunostained cells or tissues are embedded in a cross-linked network of swellable polyelectrolyte hydrogel that expands isotropically upon addition of deionized water. We utilize the X10 method for tenfold expansion of U2OS cells with concurrent DNA staining. A custom 3D-printed gel cutter and chambered slides minimize gel drift, facilitating analysis of the components of nuclear structures at nanoscale resolution by conventional microscopy or Airyscan confocal imaging. For complete information on the generation and use of this protocol, please refer to Do et al. (2020).
    MeSH term(s) Cell Line ; Cell Nucleus/ultrastructure ; Microscopy/methods ; Reproducibility of Results ; Software
    Language English
    Publishing date 2021-06-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2021.100630
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  10. Article: BioID organelle mapping: you are the company you keep

    Gaudreau-Lapierre, Antoine / Trinkle-Mulcahy, Laura

    Trends in biochemical sciences. 2021 Dec., v. 46, no. 12

    2021  

    Abstract: In a recent study, Go, Knight et al. combined a panel of protein markers with BioID proximity-dependent labeling to profile the composition of 20 distinct subcellular compartments. Comparison with similar global datasets acquired using imaging or ... ...

    Abstract In a recent study, Go, Knight et al. combined a panel of protein markers with BioID proximity-dependent labeling to profile the composition of 20 distinct subcellular compartments. Comparison with similar global datasets acquired using imaging or fractionation-based approaches confirmed the consistency of the results while highlighting unique advantages.
    Keywords business enterprises ; data collection ; image analysis ; proteins
    Language English
    Dates of publication 2021-12
    Size p. 950-952.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2021.09.003
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 78/716: Show issues

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