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  1. Article ; Online: Protocol to prepare doubly labeled fluorescent nucleosomes for single-molecule fluorescence microscopy.

    Ghoneim, Mohamed / Musselman, Catherine A

    STAR protocols

    2023  Volume 4, Issue 2, Page(s) 102229

    Abstract: Single-molecule fluorescence microscopy (SMFM) has been shown to be informative in understanding the interaction of chromatin-associated factors with nucleosomes, the basic building unit of chromatin. Here, we present a protocol for preparing doubly ... ...

    Abstract Single-molecule fluorescence microscopy (SMFM) has been shown to be informative in understanding the interaction of chromatin-associated factors with nucleosomes, the basic building unit of chromatin. Here, we present a protocol for preparing doubly labeled fluorescent nucleosomes for SMFM. We describe steps for over-expression in E. coli and purification of recombinant human core histones. We then detail fluorescent labeling of histones and nucleosomal double-stranded DNA followed by octamer refolding and nucleosome reconstitution.
    Language English
    Publishing date 2023-04-19
    Publishing country United States
    Document type Journal Article
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2023.102229
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  2. Article ; Online: Dynamic views of molecular recognition in protein-nucleic acid complexes.

    Musselman, Catherine A / Valkov, Eugene

    Current opinion in structural biology

    2022  Volume 77, Page(s) 102500

    Language English
    Publishing date 2022-11-16
    Publishing country England
    Document type Editorial
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2022.102500
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3206: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  3. Article ; Online: Protocol to prepare doubly labeled fluorescent nucleosomes for single-molecule fluorescence microscopy

    Mohamed Ghoneim / Catherine A. Musselman

    STAR Protocols, Vol 4, Iss 2, Pp 102229- (2023)

    2023  

    Abstract: Summary: Single-molecule fluorescence microscopy (SMFM) has been shown to be informative in understanding the interaction of chromatin-associated factors with nucleosomes, the basic building unit of chromatin. Here, we present a protocol for preparing ... ...

    Abstract Summary: Single-molecule fluorescence microscopy (SMFM) has been shown to be informative in understanding the interaction of chromatin-associated factors with nucleosomes, the basic building unit of chromatin. Here, we present a protocol for preparing doubly labeled fluorescent nucleosomes for SMFM. We describe steps for over-expression in E. coli and purification of recombinant human core histones. We then detail fluorescent labeling of histones and nucleosomal double-stranded DNA followed by octamer refolding and nucleosome reconstitution. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
    Keywords Biophysics ; Single-molecule Assays ; Microscopy ; Molecular Biology ; Molecular/Chemical Probes ; Protein Biochemistry ; Science (General) ; Q1-390
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Visualizing Conformational Ensembles of the Nucleosome by NMR.

    Musselman, Catherine A / Kutateladze, Tatiana G

    ACS chemical biology

    2022  Volume 17, Issue 3, Page(s) 495–502

    Abstract: The formation of chromatin not only compacts the eukaryotic genome into the nucleus but also provides a mechanism for the regulation of all DNA templated processes. Spatial and temporal modulation of the chromatin structure is critical in such regulation ...

    Abstract The formation of chromatin not only compacts the eukaryotic genome into the nucleus but also provides a mechanism for the regulation of all DNA templated processes. Spatial and temporal modulation of the chromatin structure is critical in such regulation and involves fine-tuned functioning of the basic subunit of chromatin, the nucleosome. It has become apparent that the nucleosome is an inherently dynamic system, but characterization of these dynamics at the atomic level has remained challenging. NMR spectroscopy is a powerful tool for investigating the conformational ensemble and dynamics of proteins and protein complexes, and recent advances have made the study of large systems possible. Here, we review recent studies which utilize NMR spectroscopy to uncover the atomic level conformation and dynamics of the nucleosome and provide a better understanding of the importance of these dynamics in key regulatory events.
    MeSH term(s) Chromatin ; Chromatin Assembly and Disassembly ; Magnetic Resonance Spectroscopy ; Molecular Conformation ; Nucleosomes
    Chemical Substances Chromatin ; Nucleosomes
    Language English
    Publishing date 2022-02-23
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.1c00954
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  5. Article ; Online: Single-Molecule Characterization of Cy3.5 -Cy5.5 Dye Pair for FRET Studies of Nucleic Acids and Nucleosomes.

    Ghoneim, Mohamed / Musselman, Catherine A

    Journal of fluorescence

    2022  Volume 33, Issue 2, Page(s) 413–421

    Abstract: Single molecule FRET (Forster resonance energy transfer) is very powerful method for studying biomolecular binding dynamics and conformational transitions. Only a few donor - acceptor dye pairs have been characterized for use in single-molecule FRET ( ... ...

    Abstract Single molecule FRET (Forster resonance energy transfer) is very powerful method for studying biomolecular binding dynamics and conformational transitions. Only a few donor - acceptor dye pairs have been characterized for use in single-molecule FRET (smFRET) studies. Hence, introducing and characterizing additional FRET dye pairs is important in order to widen the scope of applications of single-molecule FRET in biomolecular studies. Here we characterize the properties of the Cy3.5 and Cy5.5 dye pair under FRET at the single-molecule level using naked double-stranded DNA (dsDNA) and the nucleosome. We show that this pair of dyes is photostable for ~ 5 min under continuous illumination. We also report Cy3.5-Cy5.5 FRET proximity dependence and stability in the presence of several biochemical buffers and photoprotective reagents in the context of double-stranded DNA. Finally, we demonstrate compatibility of the Cy3.5-Cy5.5 pair for smFRET in vitro studies of nucleosomes.
    MeSH term(s) Fluorescence Resonance Energy Transfer/methods ; Nucleic Acids ; Nucleosomes ; Carbocyanines/chemistry ; DNA/chemistry ; Coloring Agents ; Fluorescent Dyes/chemistry
    Chemical Substances Nucleic Acids ; Nucleosomes ; cyanine dye 3 ; Carbocyanines ; DNA (9007-49-2) ; Coloring Agents ; Fluorescent Dyes
    Language English
    Publishing date 2022-11-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2016892-5
    ISSN 1573-4994 ; 1053-0509
    ISSN (online) 1573-4994
    ISSN 1053-0509
    DOI 10.1007/s10895-022-03093-z
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  6. Article ; Online: Characterization of functional disordered regions within chromatin-associated proteins.

    Musselman, Catherine A / Kutateladze, Tatiana G

    iScience

    2021  Volume 24, Issue 2, Page(s) 102070

    Abstract: Intrinsically disordered regions (IDRs) are abundant and play important roles in the function of chromatin-associated proteins (CAPs). These regions are often found at the N- and C-termini of CAPs and between structured domains, where they can act as ... ...

    Abstract Intrinsically disordered regions (IDRs) are abundant and play important roles in the function of chromatin-associated proteins (CAPs). These regions are often found at the N- and C-termini of CAPs and between structured domains, where they can act as more than just linkers, directly contributing to function. IDRs have been shown to contribute to substrate binding, act as auto-regulatory regions, and drive liquid-liquid droplet formation. Their disordered nature provides increased functional diversity and allows them to be easily regulated through post-translational modification. However, these regions can be especially challenging to characterize on a structural level. Here, we review the prevalence of IDRs in CAPs, highlighting several studies that address their importance in CAP function and show progress in structural characterization of these regions. A focus is placed on the unique opportunity to apply nuclear magnetic resonance (NMR) spectroscopy alongside cryo-electron microscopy to characterize IDRs in CAPs.
    Language English
    Publishing date 2021-01-20
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2021.102070
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  7. Article: Histone Tail Conformations: A Fuzzy Affair with DNA.

    Ghoneim, Mohamed / Fuchs, Harrison A / Musselman, Catherine A

    Trends in biochemical sciences

    2021  Volume 46, Issue 7, Page(s) 564–578

    Abstract: The core histone tails are critical in chromatin structure and signaling. Studies over the past several decades have provided a wealth of information on the histone tails and their interaction with chromatin factors. However, the conformation of the ... ...

    Abstract The core histone tails are critical in chromatin structure and signaling. Studies over the past several decades have provided a wealth of information on the histone tails and their interaction with chromatin factors. However, the conformation of the histone tails in a chromatin relevant context has remained elusive. Only recently has enough evidence emerged to start to build a structural model of the tails in the context of nucleosomes and nucleosome arrays. Here, we review these studies and propose that the histone tails adopt a high-affinity fuzzy complex with DNA, characterized by robust but dynamic association. Furthermore, we discuss how these DNA-bound conformational ensembles promote distinct chromatin structure and signaling, and that their fuzzy nature is important in transitioning between functional states.
    MeSH term(s) Chromatin ; DNA ; Histones/metabolism ; Nucleic Acid Conformation ; Nucleosomes
    Chemical Substances Chromatin ; Histones ; Nucleosomes ; DNA (9007-49-2)
    Language English
    Publishing date 2021-02-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    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.2020.12.012
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1207: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  8. Article ; Online: The PHD finger of Spp1 mediates histone modification cross-talk.

    Musselman, Catherine A / Kutateladze, Tatiana G

    The Biochemical journal

    2019  Volume 476, Issue 16, Page(s) 2351–2354

    Abstract: Binding of the Spp1 PHD finger to histone H3K4me3 is sensitive to adjacent post-translational modifications in the histone tail. This commentary discusses the findings of He and colleagues [ ...

    Abstract Binding of the Spp1 PHD finger to histone H3K4me3 is sensitive to adjacent post-translational modifications in the histone tail. This commentary discusses the findings of He and colleagues [
    MeSH term(s) Animals ; Histone Code ; Histones ; Models, Molecular ; PHD Zinc Fingers ; Protein Binding ; Protein Processing, Post-Translational
    Chemical Substances Histones ; histone H3 trimethyl Lys4
    Language English
    Publishing date 2019-08-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 2969-5
    ISSN 1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
    ISSN (online) 1470-8728
    ISSN 0006-2936 ; 0306-3275 ; 0264-6021
    DOI 10.1042/BCJ20190492
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    Uc I Zs.110: Show issues Location:
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  9. Article ; Online: Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies.

    Musselman, Catherine A / Kutateladze, Tatiana G

    ACS chemical biology

    2019  Volume 14, Issue 4, Page(s) 579–586

    Abstract: Post-translational modifications on histone proteins play critical roles in the regulation of chromatin structure and all DNA-templated processes. Accumulating evidence suggests that these covalent modifications can directly alter chromatin structure, or ...

    Abstract Post-translational modifications on histone proteins play critical roles in the regulation of chromatin structure and all DNA-templated processes. Accumulating evidence suggests that these covalent modifications can directly alter chromatin structure, or they can modulate activities of chromatin-modifying and -remodeling factors. Studying these modifications in the context of the nucleosome, the basic subunit of chromatin, is thus of great interest; however, the generation of specifically modified nucleosomes remains challenging. This is especially problematic for most structural biology approaches in which a large amount of material is often needed. Here we discuss the strategies currently available for generation of these substrates. We in particular focus on novel ideas and discuss challenges in the application to structural biology studies.
    MeSH term(s) Chromatin Assembly and Disassembly ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Protein Conformation ; Protein Processing, Post-Translational ; Proteins/chemistry
    Chemical Substances Nucleosomes ; Proteins
    Language English
    Publishing date 2019-03-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.8b01049
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  10. Article: Multiscale genome organization symposium - annual biophysical society meeting 2023.

    Akbari, Ehsan / Park, Eui-Jin / Singh, Ajit K / Vinayak, Vinayak / Virk, Ranya K A / Wereszczynksi, Jeff / Musselman, Catherine A

    Biophysical reviews

    2023  Volume 15, Issue 3, Page(s) 313–315

    Language English
    Publishing date 2023-05-31
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-023-01063-8
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