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  1. Article ; Online: Excluded Volume and Weak Interactions in Crowded Solutions Modulate Conformations and RNA Binding of an Intrinsically Disordered Tail.

    Stringer, Madison A / Cubuk, Jasmine / Incicco, J Jeremías / Roy, Debjit / Hall, Kathleen B / Stuchell-Brereton, Melissa D / Soranno, Andrea

    The journal of physical chemistry. B

    2023  Volume 127, Issue 26, Page(s) 5837–5849

    Abstract: The cellular milieu is a solution crowded with a significant concentration of different components (proteins, nucleic acids, metabolites, ...

    Abstract The cellular milieu is a solution crowded with a significant concentration of different components (proteins, nucleic acids, metabolites,
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2 ; Protein Conformation ; Polyethylene Glycols/chemistry ; RNA ; Nucleocapsid Proteins
    Chemical Substances Polyethylene Glycols (3WJQ0SDW1A) ; RNA (63231-63-0) ; Nucleocapsid Proteins
    Language English
    Publishing date 2023-06-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c02356
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Detecting protein–protein interactions by Xe-129 NMR

    Zhao, Zhuangyu / Roose, Benjamin W. / Zemerov, Serge D. / Stringer, Madison A. / Dmochowski, Ivan J.

    Chemical communications. 2020 Sept. 22, v. 56, no. 75

    2020  

    Abstract: Detection of protein–protein interactions (PPIs) is limited by current bioanalytical methods. A protein complementation assay (PCA), split TEM-1 β-lactamase, interacts with xenon at the interface of the TEM-1 fragments. Reconstitution of TEM-1—promoted ... ...

    Abstract Detection of protein–protein interactions (PPIs) is limited by current bioanalytical methods. A protein complementation assay (PCA), split TEM-1 β-lactamase, interacts with xenon at the interface of the TEM-1 fragments. Reconstitution of TEM-1—promoted here by cFos/cJun leucine zipper interaction—gives rise to sensitive ¹²⁹Xe NMR signal in bacterial cells.
    Keywords analytical methods ; bacteria ; chemical communication ; leucine zipper ; protein-protein interactions ; proteins ; xenon
    Language English
    Dates of publication 2020-0922
    Size p. 11122-11125.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d0cc02988b
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Detecting protein-protein interactions by Xe-129 NMR.

    Zhao, Zhuangyu / Roose, Benjamin W / Zemerov, Serge D / Stringer, Madison A / Dmochowski, Ivan J

    Chemical communications (Cambridge, England)

    2020  Volume 56, Issue 75, Page(s) 11122–11125

    Abstract: Detection of protein-protein interactions (PPIs) is limited by current bioanalytical methods. A protein complementation assay (PCA), split TEM-1 β-lactamase, interacts with xenon at the interface of the TEM-1 fragments. Reconstitution of TEM-1-promoted ... ...

    Abstract Detection of protein-protein interactions (PPIs) is limited by current bioanalytical methods. A protein complementation assay (PCA), split TEM-1 β-lactamase, interacts with xenon at the interface of the TEM-1 fragments. Reconstitution of TEM-1-promoted here by cFos/cJun leucine zipper interaction-gives rise to sensitive 129Xe NMR signal in bacterial cells.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Escherichia coli/cytology ; Escherichia coli/enzymology ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Xenon Isotopes ; beta-Lactamases/chemistry ; beta-Lactamases/genetics ; beta-Lactamases/metabolism
    Chemical Substances Bacterial Proteins ; Xenon Isotopes ; Xenon-129 ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase TEM-1 (EC 3.5.2.6)
    Language English
    Publishing date 2020-08-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d0cc02988b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: 129

    Zemerov, Serge D / Roose, Benjamin W / Farenhem, Kelsey L / Zhao, Zhuangyu / Stringer, Madison A / Goldman, Aaron R / Speicher, David W / Dmochowski, Ivan J

    Analytical chemistry

    2020  Volume 92, Issue 19, Page(s) 12817–12824

    Abstract: Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly ... ...

    Abstract Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable
    MeSH term(s) Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/isolation & purification ; Escherichia coli Proteins/metabolism ; Humans ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Periplasmic Binding Proteins/chemistry ; Periplasmic Binding Proteins/isolation & purification ; Periplasmic Binding Proteins/metabolism ; Ribose/analysis ; Ribose/metabolism ; Xenon Isotopes
    Chemical Substances Escherichia coli Proteins ; Periplasmic Binding Proteins ; RbsB protein, E coli ; Xenon Isotopes ; Ribose (681HV46001)
    Language English
    Publishing date 2020-09-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c00967
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
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  5. Article: ¹²⁹Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration

    Zemerov, Serge D / Roose, Benjamin W / Farenhem, Kelsey L / Zhao, Zhuangyu / Stringer, Madison A / Goldman, Aaron R / Speicher, David W / Dmochowski, Ivan J

    Analytical chemistry. 2020 Sept. 08, v. 92, no. 19

    2020  

    Abstract: Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly ... ...

    Abstract Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable via a sensitive NMR technique known as hyperpolarized ¹²⁹Xe chemical exchange saturation transfer (hyper-CEST). We demonstrate that RBP, with a tunable ribose-binding site and further engineered to bind xenon, enables the quantitation of ribose over a wide concentration range (nM to mM). Ribose binding induces the RBP “closed” conformation, which slows Xe exchange to a rate detectable by hyper-CEST. Such detection is remarkably specific for ribose, with the minimal background signal from endogenous sugars of similar size and structure, for example, glucose or ribose-6-phosphate. Ribose concentration was measured for mammalian cell lysate and serum, which led to estimates of low-mM ribose in a HeLa cell line. This highlights the potential for using genetically encoded periplasmic binding proteins such as RBP to measure metabolites in different biological fluids, tissues, and physiologic states.
    Keywords analytical chemistry ; blood serum ; carcinogenesis ; glucose ; human cell lines ; mammals ; metabolites ; ribose ; xenon
    Language English
    Dates of publication 2020-0908
    Size p. 12817-12824.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c00967
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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