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  1. Article ; Online: A guided tour through α-helical peptide antibiotics and their targets.

    Preußke, Nils / Sönnichsen, Frank Dieter / Leippe, Matthias

    Bioscience reports

    2023  

    Abstract: Nowadays, not only biologists, but also researchers from other disciplines such as chemistry, pharmacy, material sciences, or physics are working with antimicrobial peptides. This review is written for researchers and students working in or interested in ...

    Abstract Nowadays, not only biologists, but also researchers from other disciplines such as chemistry, pharmacy, material sciences, or physics are working with antimicrobial peptides. This review is written for researchers and students working in or interested in the field of antimicrobial peptides - and especially those who do not have a profound biological background. To lay the ground for a thorough discussion on how AMPs act on cells, the architectures of mammalian and bacterial cell envelopes are described in detail because they are important targets of AMPs and provide the basis for their selectivity. The modes of action of α-helical AMPs (αAMPs) are not limited to different models of membrane permeabilization, but also include the disruption of intracellular processes, as well as the formation of fibrillary structures and their potential implications for antimicrobial activity. As biofilm-related infections are very difficult to treat with conventional antibiotics, they pose a major problem in the clinic. Therefore, this review also discusses the biological background of biofilm infections and the mode of actions of αAMPs against biofilms. The last chapter focusses on the design of αAMPs by providing an overview of historic milestones in αAMP design. It describes how modern αAMP design is aiming to produce peptides suitable to be applied in the clinic. Hence, the article concludes with a section on translational research discussing the prospects of αAMPs and remaining challenges on their way into the clinic.
    Language English
    Publishing date 2023-05-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 764946-0
    ISSN 1573-4935 ; 0144-8463
    ISSN (online) 1573-4935
    ISSN 0144-8463
    DOI 10.1042/BSR20230474
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1676: Show issues Location:
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  2. Article ; Online: Pore-forming toxins from pathogenic amoebae.

    Leippe, Matthias

    Applied microbiology and biotechnology

    2014  Volume 98, Issue 10, Page(s) 4347–4353

    Abstract: Some amoeboid protozoans are facultative or obligate parasites in humans and bear an enormous cytotoxic potential that can result in severe destruction of host tissues and fatal diseases. Pathogenic amoebae produce soluble pore-forming polypeptides that ... ...

    Abstract Some amoeboid protozoans are facultative or obligate parasites in humans and bear an enormous cytotoxic potential that can result in severe destruction of host tissues and fatal diseases. Pathogenic amoebae produce soluble pore-forming polypeptides that bind to prokaryotic and eukaryotic target cell membranes and generate pores upon insertion and oligomerization. This review summerizes the current knowledge of such small protein toxins from amoebae, compares them with related proteins from other species, focuses on their three-dimensional structures, and gives insights into divergent activation mechanisms. The potential use of pore-forming toxins in biotechnology will be briefly outlined.
    MeSH term(s) Amoeba/chemistry ; Animals ; Biotechnology/methods ; Humans ; Models, Molecular ; Pore Forming Cytotoxic Proteins/chemistry ; Pore Forming Cytotoxic Proteins/toxicity ; Protein Conformation ; Protozoan Proteins/chemistry ; Protozoan Proteins/toxicity
    Chemical Substances Pore Forming Cytotoxic Proteins ; Protozoan Proteins
    Language English
    Publishing date 2014-05
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-014-5673-z
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2229: Show issues Location:
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  3. Book ; Online ; Thesis: Utilizing the Trp-cage miniprotein in the design of light-responsive proteins and stable antimicrobial peptides

    Preußke, Nils Verfasser] / [Sönnichsen, Frank [Akademischer Betreuer] / Leippe, Matthias [Gutachter]

    2022  

    Author's details Nils Preußke ; Gutachter: Matthias Leippe ; Betreuer: Frank Sönnichsen
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek Kiel
    Publishing place Kiel
    Document type Book ; Online ; Thesis
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  4. Article: Digital Microfluidics Supported Microproteomics for Quantitative Proteome Analysis of Single Caenorhabditis elegans Nematodes

    Steinbach, Max K. / Leipert, Jan / Blurton, Christine / Leippe, Matthias / Tholey, Andreas

    Journal of proteome research. 2022 June 30, v. 21, no. 8

    2022  

    Abstract: Miniaturization of sample preparation, including omissible manual sample handling steps, is key for reproducible nanoproteomics, as material is often restricted to only hundreds of cells or single model organisms. Here, we demonstrate a highly sensitive ... ...

    Abstract Miniaturization of sample preparation, including omissible manual sample handling steps, is key for reproducible nanoproteomics, as material is often restricted to only hundreds of cells or single model organisms. Here, we demonstrate a highly sensitive digital microfluidics (DMF)-based sample preparation workflow making use of single-pot solid-phase enhanced sample preparation (SP3) in combination with high-field asymmetric-waveform ion mobility spectrometry (FAIMS), and fast and sensitive ion trap detection on an Orbitrap tribrid MS system. Compared to a manual in-tube SP3-supported sample preparation, the numbers of identified peptides and proteins were markedly increased, while lower standard deviations between replicates were observed. We repeatedly identified up to 5000 proteins from single nematodes. Moreover, label-free quantification of protein changes in single Caenorhabditis elegans treated with a heat stimulus yielded 45 differentially abundant proteins when compared to the untreated control, highlighting the potential of this technology for low-input proteomics studies. LC-MS data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD033143.
    Keywords Caenorhabditis elegans ; data collection ; heat ; microfluidic technology ; peptides ; proteome ; proteomics ; research
    Language English
    Dates of publication 2022-0630
    Size p. 1986-1996.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00274
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
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  5. Article: Validation of Top-Down Proteomics Data by Bottom-Up-Based N-Terminomics Reveals Pitfalls in Top-Down-Based Terminomics Workflows

    Winkels, Konrad / Koudelka, Tomas / Kaulich, Philipp T. / Leippe, Matthias / Tholey, Andreas

    Journal of proteome research. 2022 Aug. 16, v. 21, no. 9

    2022  

    Abstract: Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide ... ...

    Abstract Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide additional information about post-translational modifications and the respective C-termini. To evaluate the potential of TDP for terminomics, two established TDP workflows were employed for the proteome analysis of the nematode Caenorhabditis elegans. The N-termini of the identified proteoforms were validated using a BUP-based N-terminomics approach. The TDP workflows used here identified 1658 proteoforms, the N-termini of which were verified by BUP in 25% of entities only. Caveats in both the BUP- and TDP-based workflows were shown to contribute to this low overlap. In BUP, the use of trypsin prohibits the detection of arginine-rich or arginine-deficient N-termini, while in TDP, the formation of artificially generated termini was observed in particular in a workflow encompassing sample treatment with high acid concentrations. Furthermore, we demonstrate the applicability of reductive dimethylation in TDP to confirm biological N-termini. Overall, our study shows not only the potential but also current limitations of TDP for terminomics studies and also presents suggestions for future developments, for example, for data quality control, allowing improvement of the detection of protein termini by TDP.
    Keywords Caenorhabditis elegans ; data quality ; peptides ; proteome ; proteomics ; quality control ; research ; trypsin
    Language English
    Dates of publication 2022-0816
    Size p. 2185-2196.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00277
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    Zs.A 6189: Show issues Location:
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  6. Article ; Online: Preconditioning With Natural Microbiota Strain

    Petersen, Carola / Pees, Barbara / Martínez Christophersen, Christina / Leippe, Matthias

    Frontiers in cellular and infection microbiology

    2021  Volume 11, Page(s) 775634

    Abstract: In comparison with the standard monoxenic maintenance in the laboratory, rearing the ... ...

    Abstract In comparison with the standard monoxenic maintenance in the laboratory, rearing the nematode
    MeSH term(s) Animals ; Bacteria ; Caenorhabditis elegans ; Microbiota ; Ochrobactrum ; Virulence
    Language English
    Publishing date 2021-12-17
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2021.775634
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  7. Article ; Online: Validation of Top-Down Proteomics Data by Bottom-Up-Based N-Terminomics Reveals Pitfalls in Top-Down-Based Terminomics Workflows.

    Winkels, Konrad / Koudelka, Tomas / Kaulich, Philipp T / Leippe, Matthias / Tholey, Andreas

    Journal of proteome research

    2022  Volume 21, Issue 9, Page(s) 2185–2196

    Abstract: Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide ... ...

    Abstract Bottom-up proteomics (BUP)-based N-terminomics techniques have become standard to identify protein N-termini. While these methods rely on the identification of N-terminal peptides only, top-down proteomics (TDP) comes with the promise to provide additional information about post-translational modifications and the respective C-termini. To evaluate the potential of TDP for terminomics, two established TDP workflows were employed for the proteome analysis of the nematode
    MeSH term(s) Arginine ; DNA-Binding Proteins ; Protein Processing, Post-Translational ; Proteome/analysis ; Proteomics/methods ; Workflow
    Chemical Substances DNA-Binding Proteins ; Proteome ; Arginine (94ZLA3W45F)
    Language English
    Publishing date 2022-08-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00277
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
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  8. Article ; Online: Digital Microfluidics Supported Microproteomics for Quantitative Proteome Analysis of Single

    Steinbach, Max K / Leipert, Jan / Blurton, Christine / Leippe, Matthias / Tholey, Andreas

    Journal of proteome research

    2022  Volume 21, Issue 8, Page(s) 1986–1996

    Abstract: Miniaturization of sample preparation, including omissible manual sample handling steps, is key for reproducible nanoproteomics, as material is often restricted to only hundreds of cells or single model organisms. Here, we demonstrate a highly sensitive ... ...

    Abstract Miniaturization of sample preparation, including omissible manual sample handling steps, is key for reproducible nanoproteomics, as material is often restricted to only hundreds of cells or single model organisms. Here, we demonstrate a highly sensitive digital microfluidics (DMF)-based sample preparation workflow making use of single-pot solid-phase enhanced sample preparation (SP3) in combination with high-field asymmetric-waveform ion mobility spectrometry (FAIMS), and fast and sensitive ion trap detection on an Orbitrap tribrid MS system. Compared to a manual in-tube SP3-supported sample preparation, the numbers of identified peptides and proteins were markedly increased, while lower standard deviations between replicates were observed. We repeatedly identified up to 5000 proteins from single nematodes. Moreover, label-free quantification of protein changes in single
    MeSH term(s) Animals ; Caenorhabditis elegans ; Ion Mobility Spectrometry/methods ; Microfluidics ; Proteome/analysis ; Proteomics/methods
    Chemical Substances Proteome
    Language English
    Publishing date 2022-06-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00274
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
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  9. Article: Pore-forming toxins from pathogenic amoebae

    Leippe, Matthias

    Applied microbiology and biotechnology. 2014 May, v. 98, no. 10

    2014  

    Abstract: Some amoeboid protozoans are facultative or obligate parasites in humans and bear an enormous cytotoxic potential that can result in severe destruction of host tissues and fatal diseases. Pathogenic amoebae produce soluble pore-forming polypeptides that ... ...

    Abstract Some amoeboid protozoans are facultative or obligate parasites in humans and bear an enormous cytotoxic potential that can result in severe destruction of host tissues and fatal diseases. Pathogenic amoebae produce soluble pore-forming polypeptides that bind to prokaryotic and eukaryotic target cell membranes and generate pores upon insertion and oligomerization. This review summerizes the current knowledge of such small protein toxins from amoebae, compares them with related proteins from other species, focuses on their three-dimensional structures, and gives insights into divergent activation mechanisms. The potential use of pore-forming toxins in biotechnology will be briefly outlined.
    Keywords Protozoa ; biotechnology ; cell membranes ; humans ; parasites ; polypeptides ; proteins ; toxins
    Language English
    Dates of publication 2014-05
    Size p. 4347-4353.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 392453-1
    ISSN 1432-0614 ; 0171-1741 ; 0175-7598
    ISSN (online) 1432-0614
    ISSN 0171-1741 ; 0175-7598
    DOI 10.1007/s00253-014-5673-z
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    In stock of ZB MED Bonn / Germany

    Z 79/727: Show issues

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  10. Article ; Online: Digital Microfluidics and Magnetic Bead-Based Intact Proteoform Elution for Quantitative Top-down Nanoproteomics of Single C. elegans Nematodes.

    Leipert, Jan / Kaulich, Philipp T / Steinbach, Max K / Steer, Britta / Winkels, Konrad / Blurton, Christine / Leippe, Matthias / Tholey, Andreas

    Angewandte Chemie (International ed. in English)

    2023  Volume 62, Issue 28, Page(s) e202301969

    Abstract: While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up proteomics workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we established a ... ...

    Abstract While most nanoproteomics approaches for the analysis of low-input samples are based on bottom-up proteomics workflows, top-down approaches enabling proteoform characterization are still underrepresented. Using mammalian cell proteomes, we established a facile one-pot sample preparation protocol based on protein aggregation on magnetic beads and intact proteoform elution using 40 % formic acid. Performed on a digital microfluidics device, the workflow enabled sensitive analyses of single Caenorhabditis elegans nematodes, thereby increasing the number of proteoform identifications compared to in-tube sample preparation by 46 %. Label-free quantification of single nematodes grown under different conditions allowed to identify changes in the abundance of proteoforms not distinguishable by bottom-up proteomics. The presented workflow will facilitate proteoform-directed analysis on samples of limited availability.
    MeSH term(s) Animals ; Caenorhabditis elegans/metabolism ; Microfluidics ; Proteome/analysis ; Proteomics/methods ; Magnetic Phenomena ; Mammals/metabolism
    Chemical Substances Proteome
    Language English
    Publishing date 2023-05-31
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202301969
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