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  1. Article ; Conference proceedings ; Online: A ComputationalTool for Structural Biology

    Brünger, Axel T.

    Crystallographic Refinement by Simulated Annealing

    2023  

    Abstract: Conventional refinementof biological macromolecules involvesa series of steps, each of which consists ofa few cyclesofrestrained least-squares refinement with stereochemical and internal packingconstraints orrestraints that are followed by rebuilding the ...

    Abstract Conventional refinementof biological macromolecules involvesa series of steps, each of which consists ofa few cyclesofrestrained least-squares refinement with stereochemical and internal packingconstraints orrestraints that are followed by rebuilding the modelstructure with interactive computer graphics. Duringthefinal stages of refinement solvent molecules are usually included and alternative conformations for some atomsor residues in the protein may be introduced.
    Language English
    Publishing date 2023-11-03
    Publisher GBF Gesellschaft für Biotechnologische Forschung mbH, Braunschweig
    Publishing country de
    Document type Article ; Conference proceedings ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: The Core Complex of the Ca

    Brunger, Axel T / Leitz, Jeremy

    Journal of molecular biology

    2022  Volume 435, Issue 1, Page(s) 167853

    Abstract: Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon the arrival of an action potential. Critical to this ...

    Abstract Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon the arrival of an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca
    MeSH term(s) Calcium/metabolism ; Membrane Fusion ; Neurons/metabolism ; SNARE Proteins/metabolism ; Synaptic Transmission/physiology ; Synaptic Vesicles/metabolism ; Synaptotagmins/metabolism
    Chemical Substances Calcium (SY7Q814VUP) ; SNARE Proteins ; Synaptotagmins (134193-27-4)
    Language English
    Publishing date 2022-10-13
    Publishing country Netherlands
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2022.167853
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    Zs.A 867: Show issues Location:
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  3. Article ; Online: A new method for isolation and purification of fusion-competent inhibitory synaptic vesicles.

    Gopal, Nisha / Leitz, Jeremy / Wang, Chuchu / Esquivies, Luis / Pfuetzner, Richard A / Brunger, Axel T

    Current research in physiology

    2024  Volume 7, Page(s) 100121

    Abstract: Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to ... ...

    Abstract Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to isolate and purify GABA synaptic vesicles from mouse brains. GABA synaptic vesicles were immunoisolated from mouse brain tissue using an engineered fragment antigen-binding region (Fab) against the vesicular GABA transporter (vGAT) and purified. Western blot analysis confirmed that the GABA synaptic vesicles were specifically enriched for vGAT and largely depleted of contaminants from other synaptic vesicle types, such as vesicular glutamate transporter (vGLUT1), and other cellular organelles. This degree of purity was achieved despite the relatively low abundance of vGAT vesicles compared to the total synaptic vesicle pool in mammalian brains. Cryo-electron microscopy images of these isolated GABA synaptic vesicles revealed intact morphology with circular shape and protruding proteinaceous densities. The GABA synaptic vesicles are functional, as assessed by a hybrid (
    Language English
    Publishing date 2024-02-23
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2665-9441
    ISSN (online) 2665-9441
    DOI 10.1016/j.crphys.2024.100121
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  4. Article ; Online: Discovery of a drug to treat airway mucus hypersecretion.

    Dickey, Burton F / Lai, Ying / Frick, Manfred / Brunger, Axel T

    Clinical and translational medicine

    2022  Volume 12, Issue 8, Page(s) e972

    MeSH term(s) Mucus ; Respiratory System
    Language English
    Publishing date 2022-07-30
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2697013-2
    ISSN 2001-1326 ; 2001-1326
    ISSN (online) 2001-1326
    ISSN 2001-1326
    DOI 10.1002/ctm2.972
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  5. Article ; Online: The protein-folding problem: Not yet solved.

    Moore, Peter B / Hendrickson, Wayne A / Henderson, Richard / Brunger, Axel T

    Science (New York, N.Y.)

    2022  Volume 375, Issue 6580, Page(s) 507

    MeSH term(s) Protein Conformation ; Protein Folding
    Language English
    Publishing date 2022-02-03
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abn9422
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    Zs.MG 77: Show issues

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  6. Article ; Online: Discovery of a drug to treat airway mucus hypersecretion

    Burton F. Dickey / Ying Lai / Manfred Frick / Axel T. Brunger

    Clinical and Translational Medicine, Vol 12, Iss 8, Pp n/a-n/a (2022)

    2022  

    Keywords Medicine (General) ; R5-920
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher Wiley
    Document type Article ; Online
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  7. Article ; Online: The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines.

    Khan, Yousuf A / White, K Ian / Brunger, Axel T

    Critical reviews in biochemistry and molecular biology

    2021  Volume 57, Issue 2, Page(s) 156–187

    Abstract: ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. ... ...

    Abstract ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
    MeSH term(s) AAA Proteins/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/chemistry ; N-Ethylmaleimide-Sensitive Proteins/chemistry ; N-Ethylmaleimide-Sensitive Proteins/genetics ; N-Ethylmaleimide-Sensitive Proteins/metabolism ; SNARE Proteins/chemistry ; SNARE Proteins/metabolism
    Chemical Substances SNARE Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Adenosine Triphosphatases (EC 3.6.1.-) ; AAA Proteins (EC 3.6.4.-) ; N-Ethylmaleimide-Sensitive Proteins (EC 3.6.4.6)
    Language English
    Publishing date 2021-10-11
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1000977-2
    ISSN 1549-7798 ; 1381-3455 ; 1040-9238
    ISSN (online) 1549-7798
    ISSN 1381-3455 ; 1040-9238
    DOI 10.1080/10409238.2021.1979460
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    Zs.A 1024: Show issues Location:
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  8. Article ; Online: Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor.

    Yang, Kailu / Wang, Chuchu / Kreutzberger, Alex J B / White, K Ian / Pfuetzner, Richard A / Esquivies, Luis / Kirchhausen, Tomas / Brunger, Axel T

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

    2023  Volume 120, Issue 13, Page(s) e2300360120

    Abstract: The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduced a relatively large number of mutations, including three mutations in the highly conserved heptad repeat 1 (HR1) region of the spike glycoprotein (S) critical ... ...

    Abstract The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduced a relatively large number of mutations, including three mutations in the highly conserved heptad repeat 1 (HR1) region of the spike glycoprotein (S) critical for its membrane fusion activity. We show that one of these mutations, N969K induces a substantial displacement in the structure of the heptad repeat 2 (HR2) backbone in the HR1HR2 postfusion bundle. Due to this mutation, fusion-entry peptide inhibitors based on the Wuhan strain sequence are less efficacious. Here, we report an Omicron-specific peptide inhibitor designed based on the structure of the Omicron HR1HR2 postfusion bundle. Specifically, we inserted an additional residue in HR2 near the Omicron HR1 K969 residue to better accommodate the N969K mutation and relieve the distortion in the structure of the HR1HR2 postfusion bundle it introduced. The designed inhibitor recovers the loss of inhibition activity of the original longHR2_42 peptide with the Wuhan strain sequence against the Omicron variant in both a cell-cell fusion assay and a vesicular stomatitis virus (VSV)-SARS-CoV-2 chimera infection assay, suggesting that a similar approach could be used to combat future variants. From a mechanistic perspective, our work suggests the interactions in the extended region of HR2 may mediate the initial landing of HR2 onto HR1 during the transition of the S protein from the prehairpin intermediate to the postfusion state.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Viral Envelope Proteins/genetics ; Amino Acid Sequence ; COVID-19 ; Protein Structure, Secondary ; Spike Glycoprotein, Coronavirus/metabolism ; Peptides/genetics ; Peptides/pharmacology ; Peptides/chemistry ; Anti-Retroviral Agents
    Chemical Substances Viral Envelope Proteins ; Spike Glycoprotein, Coronavirus ; Peptides ; Anti-Retroviral Agents ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2300360120
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    Zs.A 1148: Show issues Location:
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  9. Article ; Online: A feature-guided, focused 3D signal permutation method for subtomogram averaging.

    Peters, John Jacob / Leitz, Jeremy / Guo, Qiang / Beck, Florian / Baumeister, Wolfgang / Brunger, Axel T

    Journal of structural biology

    2022  Volume 214, Issue 2, Page(s) 107851

    Abstract: Advances in electron microscope instrumentation, cryo-electron tomography data collection, and subtomogram averaging have allowed for the in-situ visualization of molecules and their complexes in their native environment. Current data processing ... ...

    Abstract Advances in electron microscope instrumentation, cryo-electron tomography data collection, and subtomogram averaging have allowed for the in-situ visualization of molecules and their complexes in their native environment. Current data processing pipelines commonly extract subtomograms as a cubic subvolume with the key assumption that the selected object of interest is discrete from its surroundings. However, in instances when the object is in its native environment, surrounding densities may negatively affect the subsequent alignment and refinement processes, leading to loss of information due to misalignment. For example, the strong densities from surrounding membranes may dominate the alignment process for membrane proteins. Here, we developed methods for feature-guided subtomogram alignment and 3D signal permutation for subtomogram averaging. Our 3D signal permutation method randomizes and filters voxels outside a mask of any shape and blurs the boundary of the mask that encapsulates the object of interest. The randomization preserves global statistical properties such as mean density and standard deviation of voxel density values, effectively producing a featureless background surrounding the object of interest. This signal permutation process can be repeatedly applied with intervening alignments of the 3D signal-permuted subvolumes, recentering of the mask, and optional adjustments of the shape of the mask. We have implemented these methods in a new processing pipeline which starts from tomograms, contains feature-guided subtomogram extraction and alignment, 3D signal-permutation, and subtomogram visualization tools. As an example, feature-guided alignment and 3D signal permutation leads to improved subtomogram average maps for a dataset of synaptic protein complexes in their native environment.
    MeSH term(s) Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods ; Image Processing, Computer-Assisted/methods
    Language English
    Publishing date 2022-03-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1032718-6
    ISSN 1095-8657 ; 1047-8477
    ISSN (online) 1095-8657
    ISSN 1047-8477
    DOI 10.1016/j.jsb.2022.107851
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    Zs.A 1428: Show issues Location:
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  10. Article ; Online: Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.

    Yang, Kailu / Wang, Chuchu / White, K Ian / Pfuetzner, Richard A / Esquivies, Luis / Brunger, Axel T

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

    2022  Volume 119, Issue 16, Page(s) e2119467119

    Abstract: Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) ...

    Abstract Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
    MeSH term(s) COVID-19 ; Conserved Sequence ; Humans ; Protein Domains ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Virus Internalization
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2119467119
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