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  1. Article ; Online: Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils.

    Miller, Alyssa / Chia, Sean / Klimont, Ewa / Knowles, Tuomas P J / Vendruscolo, Michele / Ruggeri, Francesco Simone

    Communications biology

    2024  Volume 7, Issue 1, Page(s) 153

    Abstract: Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile ... ...

    Abstract Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.
    MeSH term(s) Humans ; Amyloid/metabolism ; Protein Conformation, beta-Strand ; Microscopy, Atomic Force
    Chemical Substances Amyloid
    Language English
    Publishing date 2024-02-06
    Publishing country England
    Document type Journal Article
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-024-05858-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils

    Miller, Alyssa / Chia, Sean / Klimont, Ewa / Knowles, Tuomas P.J. / Vendruscolo, Michele / Ruggeri, Francesco Simone

    Communications Biology

    2024  Volume 7

    Abstract: Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile ... ...

    Abstract Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.
    Keywords Life Science
    Language English
    Publishing country nl
    Document type Article ; Online
    ISSN 2399-3642
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Spontaneous nucleation and fast aggregate-dependent proliferation of α-synuclein aggregates within liquid condensates at neutral pH.

    Dada, Samuel T / Hardenberg, Maarten C / Toprakcioglu, Zenon / Mrugalla, Lena K / Cali, Mariana P / McKeon, Mollie O / Klimont, Ewa / Michaels, Thomas C T / Knowles, Tuomas P J / Vendruscolo, Michele

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 9, Page(s) e2208792120

    Abstract: The aggregation of α-synuclein into amyloid fibrils has been under scrutiny in recent years because of its association with Parkinson's disease. This process can be triggered by a lipid-dependent nucleation process, and the resulting aggregates can ... ...

    Abstract The aggregation of α-synuclein into amyloid fibrils has been under scrutiny in recent years because of its association with Parkinson's disease. This process can be triggered by a lipid-dependent nucleation process, and the resulting aggregates can proliferate through secondary nucleation under acidic pH conditions. It has also been recently reported that the aggregation of α-synuclein may follow an alternative pathway, which takes place within dense liquid condensates formed through phase separation. The microscopic mechanism of this process, however, remains to be clarified. Here, we used fluorescence-based assays to enable a kinetic analysis of the microscopic steps underlying the aggregation process of α-synuclein within liquid condensates. Our analysis shows that at pH 7.4, this process starts with spontaneous primary nucleation followed by rapid aggregate-dependent proliferation. Our results thus reveal the microscopic mechanism of α-synuclein aggregation within condensates through the accurate quantification of the kinetic rate constants for the appearance and proliferation of α-synuclein aggregates at physiological pH.
    MeSH term(s) Humans ; alpha-Synuclein/metabolism ; Kinetics ; Parkinson Disease ; Amyloid ; Hydrogen-Ion Concentration ; Cell Proliferation ; Protein Aggregates
    Chemical Substances alpha-Synuclein ; Amyloid ; Protein Aggregates
    Language English
    Publishing date 2023-02-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2208792120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Bifunctional fluorescent probes for detection of amyloid aggregates and reactive oxygen species.

    Needham, Lisa-Maria / Weber, Judith / Fyfe, James W B / Kabia, Omaru M / Do, Dung T / Klimont, Ewa / Zhang, Yu / Rodrigues, Margarida / Dobson, Christopher M / Ghandi, Sonia / Bohndiek, Sarah E / Snaddon, Thomas N / Lee, Steven F

    Royal Society open science

    2018  Volume 5, Issue 2, Page(s) 171399

    Abstract: Protein aggregation into amyloid deposits and oxidative stress are key features of many neurodegenerative disorders including Parkinson's and Alzheimer's disease. We report here the creation of four highly sensitive bifunctional fluorescent probes, ... ...

    Abstract Protein aggregation into amyloid deposits and oxidative stress are key features of many neurodegenerative disorders including Parkinson's and Alzheimer's disease. We report here the creation of four highly sensitive bifunctional fluorescent probes, capable of H
    Language English
    Publishing date 2018-02-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.171399
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Correction to 'Bifunctional fluorescent probes for detection of amyloid aggregates and reactive oxygen species'.

    Needham, Lisa-Maria / Weber, Judith / Fyfe, James W B / Kabia, Omaru M / Do, Dung T / Klimont, Ewa / Zhang, Yu / Rodrigues, Margarida / Dobson, Christopher M / Gandhi, Sonia / Bohndiek, Sarah E / Snaddon, Thomas N / Lee, Steven F

    Royal Society open science

    2018  Volume 5, Issue 3, Page(s) 180308

    Abstract: This corrects the article DOI: 10.1098/rsos.171399.]. ...

    Abstract [This corrects the article DOI: 10.1098/rsos.171399.].
    Language English
    Publishing date 2018-03-28
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.180308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Structure of the AcrAB-TolC multidrug efflux pump.

    Du, Dijun / Wang, Zhao / James, Nathan R / Voss, Jarrod E / Klimont, Ewa / Ohene-Agyei, Thelma / Venter, Henrietta / Chiu, Wah / Luisi, Ben F

    Nature

    2014  Volume 509, Issue 7501, Page(s) 512–515

    Abstract: The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent 'pumps' that span ... ...

    Abstract The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent 'pumps' that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component. A model system for such a pump is the acridine resistance complex of Escherichia coli. This pump assembly comprises the outer-membrane channel TolC, the secondary transporter AcrB located in the inner membrane, and the periplasmic AcrA, which bridges these two integral membrane proteins. The AcrAB-TolC efflux pump is able to transport vectorially a diverse array of compounds with little chemical similarity, thus conferring resistance to a broad spectrum of antibiotics. Homologous complexes are found in many Gram-negative species, including in animal and plant pathogens. Crystal structures are available for the individual components of the pump and have provided insights into substrate recognition, energy coupling and the transduction of conformational changes associated with the transport process. However, how the subunits are organized in the pump, their stoichiometry and the details of their interactions are not known. Here we present the pseudo-atomic structure of a complete multidrug efflux pump in complex with a modulatory protein partner from E. coli. The model defines the quaternary organization of the pump, identifies key domain interactions, and suggests a cooperative process for channel assembly and opening. These findings illuminate the basis for drug resistance in numerous pathogenic bacterial species.
    MeSH term(s) Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/metabolism ; Carrier Proteins/chemistry ; Carrier Proteins/metabolism ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Drug Resistance, Bacterial ; Escherichia coli/chemistry ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Lipoproteins/chemistry ; Lipoproteins/metabolism ; Membrane Transport Proteins/chemistry ; Membrane Transport Proteins/metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins/chemistry ; Multidrug Resistance-Associated Proteins/metabolism ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Protein Subunits/metabolism
    Chemical Substances AcrA protein, E coli ; AcrB protein, E coli ; AcrZ protein, E coli ; Bacterial Outer Membrane Proteins ; Carrier Proteins ; Escherichia coli Proteins ; Lipoproteins ; Membrane Transport Proteins ; Multidrug Resistance-Associated Proteins ; Protein Subunits ; tolC protein, E coli
    Language English
    Publishing date 2014-04-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature13205
    Database MEDical Literature Analysis and Retrieval System OnLINE

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