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  1. Book: Activity-based proteomics

    Overkleeft, Herman S. / Florea, Bogdan I.

    methods and protocols

    (Methods in molecular biology ; 1491 ; Springer protocols)

    2017  

    Author's details edited by Herman S. Overkleeft and Bogdan I. Florea
    Series title Methods in molecular biology ; 1491
    Springer protocols
    Collection
    Keywords activity-based protein ; activity-based proteomics ; analytical chemistry ; annotate enzyme families ; bioorthogonal chemistry
    Language English
    Size xi, 222 Seiten, Illustrationen, 25.4 cm x 17.8 cm, 0 g
    Publisher Humana Press
    Publishing place New York
    Publishing country United States
    Document type Book
    HBZ-ID HT019108973
    ISBN 978-1-4939-6437-6 ; 1-4939-6437-2 ; 9781493964390 ; 1493964399
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -1491- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Synthesis and application of bacterial exopolysaccharides.

    Ruijgrok, Gijs / Wu, Dung-Yeh / Overkleeft, Herman S / Codée, Jeroen D C

    Current opinion in chemical biology

    2023  Volume 78, Page(s) 102418

    Abstract: Exopolysaccharides are produced and excreted by bacteria in the generation of biofilms to provide a protective environment. These polysaccharides are generally generated as heterogeneous polymers of varying length, featuring diverse substitution patterns. ...

    Abstract Exopolysaccharides are produced and excreted by bacteria in the generation of biofilms to provide a protective environment. These polysaccharides are generally generated as heterogeneous polymers of varying length, featuring diverse substitution patterns. To obtain well-defined fragments of these polysaccharides, organic synthesis often is the method of choice, as it allows for full control over chain length and the installation of a pre-determined substitution pattern. This review presents several recent syntheses of exopolysaccharide fragments of Pseudomonas aeruginosa and Staphylococcus aureus and illustrates how these have been used to study biosynthesis enzymes and generate synthetic glycoconjugate vaccines.
    MeSH term(s) Polysaccharides, Bacterial ; Biofilms ; Pseudomonas aeruginosa
    Chemical Substances Polysaccharides, Bacterial
    Language English
    Publishing date 2023-12-21
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1439176-4
    ISSN 1879-0402 ; 1367-5931
    ISSN (online) 1879-0402
    ISSN 1367-5931
    DOI 10.1016/j.cbpa.2023.102418
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes.

    McGregor, Nicholas G S / Overkleeft, Herman S / Davies, Gideon J

    Methods in enzymology

    2022  Volume 664, Page(s) 103–134

    Abstract: The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and ... ...

    Abstract The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.
    MeSH term(s) Catalysis ; Cyclohexanols ; Glycoside Hydrolases/metabolism
    Chemical Substances Cyclohexanols ; cyclophellitol (126661-83-4) ; Glycoside Hydrolases (EC 3.2.1.-)
    Language English
    Publishing date 2022-02-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2022.01.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Assembly of a Library of Pel-Oligosaccharides Featuring

    Zhang, Yongzhen / Wang, Liming / Overkleeft, Herman S / van der Marel, Gijsbert A / Codée, Jeroen D C

    Frontiers in chemistry

    2022  Volume 10, Page(s) 842238

    Abstract: Pseudomonas ... ...

    Abstract Pseudomonas aeruginosa
    Language English
    Publishing date 2022-01-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2022.842238
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Synthetic Dual Cysteine-ADP Ribosylated Peptides from the Androgen Receptor are Recognized by the DTX3L/PARP9 Complex.

    Wijngaarden, Sven / Yang, Chunsong / Vela-Rodríguez, Carlos / Lehtiö, Lari / Overkleeft, Herman S / Paschal, Bryce M / Filippov, Dmitri V

    ACS chemical biology

    2023  Volume 18, Issue 11, Page(s) 2377–2384

    Abstract: Androgen signaling in prostate cancer cells involves multisite cysteine ADP-ribosylation of the androgen receptor (AR) by PARP7. The AR modification is read by ADP-ribosyl binding macrodomains in PARP9, but the reason that multiple cysteines are modified ...

    Abstract Androgen signaling in prostate cancer cells involves multisite cysteine ADP-ribosylation of the androgen receptor (AR) by PARP7. The AR modification is read by ADP-ribosyl binding macrodomains in PARP9, but the reason that multiple cysteines are modified is unknown. Here, we use synthetic peptides to show that dual ADP-ribosylation of closely spaced cysteines mediates recognition by the DTX3L/PARP9 complex. Mono and dual ADP-ribosylated cysteine peptides were prepared using a novel solid-phase synthetic strategy utilizing a key, Boc-protected, ribofuranosylcysteine building block. This synthetic strategy allowed us to synthesize fluorescently labeled peptides containing a dual ADP-ribosylation motif. It was found that the DTX3L/PARP9 complex recognizes the dual ADP-ribosylated AR peptide (
    MeSH term(s) Male ; Humans ; Cysteine/metabolism ; Receptors, Androgen/metabolism ; ADP-Ribosylation ; Peptides/chemistry ; Prostatic Neoplasms ; Adenosine Diphosphate Ribose/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Neoplasm Proteins/metabolism ; Poly(ADP-ribose) Polymerases/metabolism
    Chemical Substances Cysteine (K848JZ4886) ; Receptors, Androgen ; Peptides ; Adenosine Diphosphate Ribose (20762-30-5) ; DTX3L protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; PARP9 protein, human ; Neoplasm Proteins ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30)
    Language English
    Publishing date 2023-11-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.3c00305
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing.

    Reichart, Nicholas J / Steiger, Andrea K / Van Fossen, Elise M / McClure, Ryan / Overkleeft, Herman S / Wright, Aaron T

    ISME communications

    2023  Volume 3, Issue 1, Page(s) 106

    Abstract: Multi-omic analyses can provide information on the potential for activity within a microbial community but often lack specificity to link functions to cell, primarily offer potential for function or rely on annotated databases. Functional assays are ... ...

    Abstract Multi-omic analyses can provide information on the potential for activity within a microbial community but often lack specificity to link functions to cell, primarily offer potential for function or rely on annotated databases. Functional assays are necessary for understanding in situ microbial activity to better describe and improve microbiome biology. Targeting enzyme activity through activity-based protein profiling enhances the accuracy of functional studies. Here, we introduce a pipeline of coupling activity-based probing with fluorescence-activated cell sorting, culturing, and downstream activity assays to isolate and examine viable populations of cells expressing a function of interest. We applied our approach to a soil microbiome using two activity-based probes to enrich for communities with elevated activity for lignocellulose-degradation phenotypes as determined by four fluorogenic kinetic assays. Our approach efficiently separated and identified microbial members with heightened activity for glycosyl hydrolases, and by expanding this workflow to various probes for other function, this process can be applied to unique phenotype targets of interest.
    Language English
    Publishing date 2023-09-30
    Publishing country England
    Document type Journal Article
    ISSN 2730-6151
    ISSN (online) 2730-6151
    DOI 10.1038/s43705-023-00305-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Solid-Phase Synthesis and Biological Evaluation of Peptides ADP-Ribosylated at Histidine.

    Minnee, Hugo / Rack, Johannes G M / van der Marel, Gijsbert A / Overkleeft, Herman S / Codée, Jeroen D C / Ahel, Ivan / Filippov, Dmitri V

    Angewandte Chemie (International ed. in English)

    2023  Volume 63, Issue 4, Page(s) e202313317

    Abstract: The transfer of an adenosine diphosphate (ADP) ribose moiety to a nucleophilic side chain by consumption of nicotinamide adenine dinucleotide is referred to as ADP-ribosylation, which allows for the spatiotemporal regulation of vital processes such as ... ...

    Abstract The transfer of an adenosine diphosphate (ADP) ribose moiety to a nucleophilic side chain by consumption of nicotinamide adenine dinucleotide is referred to as ADP-ribosylation, which allows for the spatiotemporal regulation of vital processes such as apoptosis and DNA repair. Recent mass-spectrometry based analyses of the "ADP-ribosylome" have identified histidine as ADP-ribose acceptor site. In order to study this modification, a fully synthetic strategy towards α-configured N(τ)- and N(π)-ADP-ribosylated histidine-containing peptides has been developed. Ribofuranosylated histidine building blocks were obtained via Mukaiyama-type glycosylation and the building blocks were integrated into an ADP-ribosylome derived peptide sequence using fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase peptide synthesis. On-resin installation of the ADP moiety was achieved using phosphoramidite chemistry, and global deprotection provided the desired ADP-ribosylated oligopeptides. The stability under various chemical conditions and resistance against (ADP-ribosyl) hydrolase-mediated degradation has been investigated to reveal that the constructs are stable under various chemical conditions and non-degradable by any of the known ADP-ribosylhydrolases.
    MeSH term(s) Histidine/metabolism ; Solid-Phase Synthesis Techniques ; Peptides/chemistry ; ADP-Ribosylation ; Adenosine Diphosphate/metabolism ; Adenosine Diphosphate Ribose/chemistry
    Chemical Substances Histidine (4QD397987E) ; Peptides ; Adenosine Diphosphate (61D2G4IYVH) ; Adenosine Diphosphate Ribose (20762-30-5)
    Language English
    Publishing date 2023-11-14
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202313317
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  8. Article: Solid-Phase Synthesis and Biological Evaluation of Peptides ADP-Ribosylated at Histidine.

    Minnee, Hugo / Rack, Johannes G M / van der Marel, Gijsbert A / Overkleeft, Herman S / Codée, Jeroen D C / Ahel, Ivan / Filippov, Dmitri V

    Angewandte Chemie (Weinheim an der Bergstrasse, Germany)

    2023  Volume 136, Issue 4, Page(s) e202313317

    Abstract: The transfer of an adenosine diphosphate (ADP) ribose moiety to a nucleophilic side chain by consumption of nicotinamide adenine dinucleotide is referred to as ADP-ribosylation, which allows for the spatiotemporal regulation of vital processes such as ... ...

    Abstract The transfer of an adenosine diphosphate (ADP) ribose moiety to a nucleophilic side chain by consumption of nicotinamide adenine dinucleotide is referred to as ADP-ribosylation, which allows for the spatiotemporal regulation of vital processes such as apoptosis and DNA repair. Recent mass-spectrometry based analyses of the "ADP-ribosylome" have identified histidine as ADP-ribose acceptor site. In order to study this modification, a fully synthetic strategy towards α-configured N(τ)- and N(π)-ADP-ribosylated histidine-containing peptides has been developed. Ribofuranosylated histidine building blocks were obtained via Mukaiyama-type glycosylation and the building blocks were integrated into an ADP-ribosylome derived peptide sequence using fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase peptide synthesis. On-resin installation of the ADP moiety was achieved using phosphoramidite chemistry, and global deprotection provided the desired ADP-ribosylated oligopeptides. The stability under various chemical conditions and resistance against (ADP-ribosyl) hydrolase-mediated degradation has been investigated to reveal that the constructs are stable under various chemical conditions and non-degradable by any of the known ADP-ribosylhydrolases.
    Language English
    Publishing date 2023-11-14
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 506609-8
    ISSN 1521-3757 ; 0044-8249 ; 0932-2140
    ISSN (online) 1521-3757
    ISSN 0044-8249 ; 0932-2140
    DOI 10.1002/ange.202313317
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Synthesis and Macrodomain Binding of Gln-carba-ADPr-peptide.

    Engelsma, Sander B / Nardozza, Aurelio Pio / de Saint Aulaire, Pieter / Overkleeft, Herman S / van der Marel, Gijsbert A / Ladurner, Andreas G / Filippov, Dmitri V

    Chembiochem : a European journal of chemical biology

    2024  Volume 25, Issue 8, Page(s) e202300865

    Abstract: Mono-ADP-ribosylation is a dynamic post-translational modification (PTM) with important roles in cell signalling. This modification occurs on a wide variety of amino acids, and one of the canonical modification sites within proteins is the side chain of ... ...

    Abstract Mono-ADP-ribosylation is a dynamic post-translational modification (PTM) with important roles in cell signalling. This modification occurs on a wide variety of amino acids, and one of the canonical modification sites within proteins is the side chain of glutamic acid. Given the transient nature of this modification (acylal linkage) and the high sensitivity of ADP-ribosylated glutamic acid, stabilized isosteres are required for structural and biochemical studies. Here, we report the synthesis of a mimic of ADP-ribosylated peptide derived from histone H2B that contains carba-ADP-ribosylated glutamine as a potential mimic for Glu-ADPr. We synthesized a cyclopentitol-ribofuranosyl derivative of 5'-phosphoribosylated Fmoc-glutamine and used this in the solid-phase synthesis of the carba-ADPr-peptide mimicking the ADP-ribosylated N-terminal tail of histone H2B. Binding studies with isothermal calorimetry demonstrate that the macrodomains of human MacroD2 and TARG1 bind to carba-ADPr-peptide in the same way as ADPr-peptides containing the native ADP-riboside moiety connected to the side chain of glutamine in the same peptide sequence.
    MeSH term(s) Humans ; Glutamine/chemistry ; Glutamine/metabolism ; Histones/metabolism ; Peptides/chemistry ; ADP-Ribosylation ; Glutamates/metabolism
    Chemical Substances Glutamine (0RH81L854J) ; Histones ; Peptides ; Glutamates
    Language English
    Publishing date 2024-03-20
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202300865
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book: Activity-based proteomics

    Overkleeft, Herman S / Florea, Bogdan I

    methods and protocols

    (Methods in molecular biology, ; 1491 ; Springer protocols)

    2017  

    Abstract: This volume focuses on explorative activity-based proteomics, biomedical applications of activity-based proteomics, and chemical strategies in activity-based proteomics providing a concise overview of activity-based protein profiling. Written in the ... ...

    Author's details edited by Herman S. Overkleeft and Bogdan I. Florea
    Series title Methods in molecular biology, ; 1491
    Springer protocols
    Abstract This volume focuses on explorative activity-based proteomics, biomedical applications of activity-based proteomics, and chemical strategies in activity-based proteomics providing a concise overview of activity-based protein profiling. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Activity-Based Proteomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.
    MeSH term(s) Proteogenomics/methods ; Structure-Activity Relationship
    Language English
    Size xi, 222 pages :, illustrations (some color) ;, 26 cm.
    Document type Book
    ISBN 9781493964376 ; 1493964372 ; 9781493964390 ; 1493964399
    Database Catalogue of the US National Library of Medicine (NLM)

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