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  1. Article ; Online: Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake.

    Zinke, Maximilian / Lejeune, Maylis / Mechaly, Ariel / Bardiaux, Benjamin / Boneca, Ivo Gomperts / Delepelaire, Philippe / Izadi-Pruneyre, Nadia

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 331

    Abstract: Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner ...

    Abstract Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
    MeSH term(s) Peptidoglycan ; Protons ; Cell Wall ; Nutrients ; Bacteria
    Chemical Substances Peptidoglycan ; Protons
    Language English
    Publishing date 2024-01-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44606-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Major tail proteins of bacteriophages of the order Caudovirales.

    Zinke, Maximilian / Schröder, Gunnar F / Lange, Adam

    The Journal of biological chemistry

    2021  Volume 298, Issue 1, Page(s) 101472

    Abstract: Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form ...

    Abstract Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form or when packed within a crystal lattice. These hollow elongated protein structures, present in most bacteriophages of the order Caudovirales, connect the DNA-containing capsid with a receptor function at the distal end of the tail and consist of helical and polymerized major tail proteins. However, the resolution of cryo-EM data for these systems differs enormously between different tail tube types, partly inhibiting the building of high-fidelity models and barring a combination with further structural biology methods. Here, we review the structural biology efforts within this field and highlight the role of integrative structural biology approaches that have proved successful for some of these systems. Finally, we summarize the structural elements of major tail proteins and conceptualize how different amounts of tail tube flexibility confer heterogeneity within cryo-EM maps and, thus, limit high-resolution reconstructions.
    MeSH term(s) Bacteriophages/chemistry ; Bacteriophages/metabolism ; Capsid/chemistry ; Capsid/metabolism ; Capsid Proteins/metabolism ; Caudovirales/chemistry ; Caudovirales/metabolism ; Cryoelectron Microscopy ; Protein Conformation ; Virion/metabolism
    Chemical Substances Capsid Proteins
    Language English
    Publishing date 2021-12-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2021.101472
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake

    Maximilian Zinke / Maylis Lejeune / Ariel Mechaly / Benjamin Bardiaux / Ivo Gomperts Boneca / Philippe Delepelaire / Nadia Izadi-Pruneyre

    Nature Communications, Vol 15, Iss 1, Pp 1-

    2024  Volume 12

    Abstract: Abstract Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at ... ...

    Abstract Abstract Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel’s open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
    Keywords Science ; Q
    Subject code 612
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: Bonds and Bytes

    Hoff, Samuel / Zinke, Maximilian / Izadi-Pruneyre, Nadia / Bonomi, Massimiliano

    the Odyssey of Structural Biology

    2023  

    Abstract: Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method comprehensively ... ...

    Abstract Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method comprehensively reveals the behavior of biological systems across various spatio-temporal scales. Instead, we have a versatile toolkit of techniques, each contributing a piece to the overall puzzle. Integrative Structural Biology combines different techniques to create accurate and precise multi-scale models that expand our understanding of complex biological systems. This review outlines recent advancements in computational and experimental methods in Structural Biology, with special focus on recent Artificial Intelligence techniques, emphasizes integrative approaches that combine different types of data for precise spatio-temporal modeling, and provides an outlook into future directions of this field.

    Comment: 16 pages, 2 figures
    Keywords Quantitative Biology - Quantitative Methods
    Publishing date 2023-10-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake.

    Zinke, Maximilian / Lejeune, Maylis / Mechaly, Ariel / Bardiaux, Benjamin / Boneca, Ivo Gomperts / Delepelaire, Philippe / Izadi-Pruneyre, Nadia

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner ...

    Abstract Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By
    Language English
    Publishing date 2023-08-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.11.552980
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Conference proceedings: The PROPER Study: A pan-EU real-world study of SB5 biosimilar following transition from reference adalimumab; An interim analysis of patients from the German rheumatoid arthritis cohort

    Müller-Ladner, Ulf / Zinke, Silke / Liebhaber, Anke / Utzinger, Maximilian / Addison, Janet

    2020  , Page(s) RA.46

    Event/congress Deutscher Rheumatologiekongress 2020, 48. Kongress der Deutschen Gesellschaft für Rheumatologie (DGRh), 34. Jahrestagung der Deutschen Gesellschaft für Orthopädische Rheumatologie (DGORh); sine loco [digital]; ; Deutsche Gesellschaft für Orthopädische Rheumatologie; 2020
    Keywords Medizin, Gesundheit
    Publishing date 2020-09-09
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Conference proceedings
    DOI 10.3205/20dgrh142
    Database German Medical Science

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  7. Article ; Online: Architecture of the flexible tail tube of bacteriophage SPP1.

    Zinke, Maximilian / Sachowsky, Katrin A A / Öster, Carl / Zinn-Justin, Sophie / Ravelli, Raimond / Schröder, Gunnar F / Habeck, Michael / Lange, Adam

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 5759

    Abstract: Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, ... ...

    Abstract Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.
    MeSH term(s) Amino Acid Sequence ; Cryoelectron Microscopy ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Protein Structure, Secondary ; Siphoviridae/chemistry ; Siphoviridae/ultrastructure ; Thermodynamics ; Viral Proteins/chemistry ; Viral Proteins/ultrastructure
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2020-11-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-19611-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy.

    Zinke, Maximilian / Fricke, Pascal / Lange, Sascha / Zinn-Justin, Sophie / Lange, Adam

    Chemphyschem : a European journal of chemical physics and physical chemistry

    2018  Volume 19, Issue 19, Page(s) 2457–2460

    Abstract: Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect ... ...

    Abstract Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.
    MeSH term(s) Amino Acid Sequence ; Glycoproteins/chemistry ; Isoleucine/chemistry ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Tertiary ; Proteins/chemistry ; Protons
    Chemical Substances Glycoproteins ; Proteins ; Protons ; Isoleucine (04Y7590D77)
    Language English
    Publishing date 2018-06-27
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2025223-7
    ISSN 1439-7641 ; 1439-4235
    ISSN (online) 1439-7641
    ISSN 1439-4235
    DOI 10.1002/cphc.201800542
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Architecture of the flexible tail tube of bacteriophage SPP1

    Maximilian Zinke / Katrin A. A. Sachowsky / Carl Öster / Sophie Zinn-Justin / Raimond Ravelli / Gunnar F. Schröder / Michael Habeck / Adam Lange

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 9

    Abstract: Bacteriophages of the Siphoviridae family have a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, the authors present the atomic structure of the tail tube of one of these phages, showing a hollow flexible ... ...

    Abstract Bacteriophages of the Siphoviridae family have a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, the authors present the atomic structure of the tail tube of one of these phages, showing a hollow flexible tube formed by hexameric rings stacked by flexible linkers.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Architecture of the flexible tail tube of bacteriophage SPP1

    Maximilian Zinke / Katrin A. A. Sachowsky / Carl Öster / Sophie Zinn-Justin / Raimond Ravelli / Gunnar F. Schröder / Michael Habeck / Adam Lange

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 9

    Abstract: Bacteriophages of the Siphoviridae family have a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, the authors present the atomic structure of the tail tube of one of these phages, showing a hollow flexible ... ...

    Abstract Bacteriophages of the Siphoviridae family have a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, the authors present the atomic structure of the tail tube of one of these phages, showing a hollow flexible tube formed by hexameric rings stacked by flexible linkers.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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