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  1. Article ; Online: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.

    Nordeen, Sarah A / Turman, Daniel L / Schwartz, Thomas U

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 6060

    Abstract: The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential ... ...

    Abstract The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133
    MeSH term(s) Amino Acid Motifs ; Cell Membrane/metabolism ; Conserved Sequence ; Humans ; Models, Molecular ; Nuclear Pore Complex Proteins/chemistry ; Nuclear Pore Complex Proteins/metabolism ; Protein Domains ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Homology, Amino Acid
    Chemical Substances NUP133 protein, S cerevisiae ; NUP84 protein, S cerevisiae ; Nuclear Pore Complex Proteins ; Saccharomyces cerevisiae Proteins
    Language English
    Publishing date 2020-11-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-19885-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Structure and specificity of an anti-chloramphenicol single domain antibody for detection of amphenicol residues.

    Swofford, Charles A / Nordeen, Sarah A / Chen, Lu / Desai, Mahaam M / Chen, Joanna / Springs, Stacy L / Schwartz, Thomas U / Sinskey, Anthony J

    Protein science : a publication of the Protein Society

    2022  Volume 31, Issue 11, Page(s) e4457

    Abstract: Antibiotics in aquaculture prevent bacterial infection of fish, but their misuse is a public health risk and contributes to the unintentional creation of multiresistant pathogens. Regulatory agencies cannot do the rigorous, expensive testing required to ... ...

    Abstract Antibiotics in aquaculture prevent bacterial infection of fish, but their misuse is a public health risk and contributes to the unintentional creation of multiresistant pathogens. Regulatory agencies cannot do the rigorous, expensive testing required to keep up with the volume of seafood shipments. Current rapid test kits for these drugs enable the increase in testing needed for adequate monitoring of food supply chains, but they lack a high degree of accuracy. To combat this, we set out to discover and engineer single-domain antibodies (VHHs) that bind to small molecule antibiotics, and that can be used in rapid test kits. The small size, solubility, and stability of VHHs are useful properties that can improve the reliability and shelf-life of test kits for these adulterants. Here, we report a novel anti-chloramphenicol VHH (Chl-VHH) with a disassociation constant of 57 nM. This was achieved by immunizing a llama against a chloramphenicol-keyhole limpet hemocyanin (KLH) conjugate and screening for high affinity binders through phage display. The crystal structure of the bound-VHH to chloramphenicol was key to identifying a mutation in the binding pocket that resulted in a 16-fold improvement in binding affinity. In addition, the structure provides new insights into VHH-hapten interactions that can guide future engineering of VHHs against additional targets.
    MeSH term(s) Animals ; Single-Domain Antibodies ; Chloramphenicol ; Reproducibility of Results ; Camelids, New World ; Anti-Bacterial Agents ; Antibody Specificity
    Chemical Substances Single-Domain Antibodies ; Chloramphenicol (66974FR9Q1) ; Anti-Bacterial Agents
    Language English
    Publishing date 2022-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; 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.4457
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure.

    Nordeen, Sarah A / Andersen, Kasper R / Knockenhauer, Kevin E / Ingram, Jessica R / Ploegh, Hidde L / Schwartz, Thomas U

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 6179

    Abstract: Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric ... ...

    Abstract Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.
    MeSH term(s) Amino Acid Sequence ; Animals ; Antibody Affinity ; Antibody Specificity ; Binding Sites ; Camelids, New World ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Kinetics ; Models, Molecular ; Nuclear Pore/chemistry ; Nuclear Pore/metabolism ; Nuclear Pore/ultrastructure ; Nuclear Pore Complex Proteins/chemistry ; Nuclear Pore Complex Proteins/genetics ; Nuclear Pore Complex Proteins/metabolism ; Peptide Library ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Isoforms/chemistry ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Single-Domain Antibodies/chemistry ; Single-Domain Antibodies/genetics ; Single-Domain Antibodies/isolation & purification ; Single-Domain Antibodies/metabolism
    Chemical Substances NIC96 protein, S cerevisiae ; NUP84 protein, S cerevisiae ; Nuclear Pore Complex Proteins ; Peptide Library ; Protein Isoforms ; Recombinant Proteins ; Saccharomyces cerevisiae Proteins ; Single-Domain Antibodies
    Language English
    Publishing date 2020-12-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-19884-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Photocatalytic synthesis of dihydrobenzofurans by oxidative [3+2] cycloaddition of phenols.

    Blum, Travis R / Zhu, Ye / Nordeen, Sarah A / Yoon, Tehshik P

    Angewandte Chemie (International ed. in English)

    2014  Volume 53, Issue 41, Page(s) 11056–11059

    Abstract: We report a protocol for oxidative [3+2] cycloadditions of phenols and alkenes applicable to the modular synthesis of a large family of dihydrobenzofuran natural products. Visible-light-activated transition metal photocatalysis enables the use of ... ...

    Abstract We report a protocol for oxidative [3+2] cycloadditions of phenols and alkenes applicable to the modular synthesis of a large family of dihydrobenzofuran natural products. Visible-light-activated transition metal photocatalysis enables the use of ammonium persulfate as an easily handled, benign terminal oxidant. The broad range of organic substrates that are readily oxidized by photoredox catalysis suggests that this strategy may be applicable to a variety of useful oxidative transformations.
    MeSH term(s) Alkenes/chemistry ; Benzofurans/chemical synthesis ; Benzofurans/chemistry ; Biological Products/chemical synthesis ; Biological Products/chemistry ; Catalysis ; Cycloaddition Reaction ; Light ; Oxidation-Reduction ; Phenols/chemistry ; Ruthenium/chemistry
    Chemical Substances Alkenes ; Benzofurans ; Biological Products ; Phenols ; Ruthenium (7UI0TKC3U5) ; benzofuran (LK6946W774)
    Language English
    Publishing date 2014-08-25
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.201406393
    Database MEDical Literature Analysis and Retrieval System OnLINE

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