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  1. Article ; Online: Structures, Distributions, and Conformations of SARS-CoV-2 Spike Proteins on Intact Virions by Cryo-EM and Cryo-ET.

    Ke, Zunlong / Oton, Joaquin / Qu, Kun / Scheres, Sjors H W / Briggs, John A G

    Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

    2023  Volume 29, Issue 29 Suppl 1, Page(s) 902–903

    Language English
    Publishing date 2023-08-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 1385710-1
    ISSN 1435-8115 ; 1431-9276
    ISSN (online) 1435-8115
    ISSN 1431-9276
    DOI 10.1093/micmic/ozad067.448
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  2. Article ; Online: Workflow for High-resolution Sub-volume Averaging from Heterogenous Viral and Virus-like Assemblies.

    Sibert, Bryan S / Kim, Joseph Y / Yang, Jae E / Hannon-Hatfield, Adam / Ke, Zunlong / Garfinkel, David J / Wright, Elizabeth R

    Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

    2023  Volume 29, Issue 29 Suppl 1, Page(s) 943–944

    Language English
    Publishing date 2023-08-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1385710-1
    ISSN 1435-8115 ; 1431-9276
    ISSN (online) 1435-8115
    ISSN 1431-9276
    DOI 10.1093/micmic/ozad067.470
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  3. Article ; Online: Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

    Alexander J. Pak / Alvin Yu / Zunlong Ke / John A. G. Briggs / Gregory A. Voth

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 12

    Abstract: Simulations reveal concerted interactions between the SARS-CoV-2 spike trimers and ACE2 receptors that result in cooperative spike binding and shedding, and further suggest that variant efficacy is promoted by increased RBD opening or S1/S2 cleavage ... ...

    Abstract Simulations reveal concerted interactions between the SARS-CoV-2 spike trimers and ACE2 receptors that result in cooperative spike binding and shedding, and further suggest that variant efficacy is promoted by increased RBD opening or S1/S2 cleavage efficiency.
    Keywords Science ; Q
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core.

    Pak, Alexander J / Yu, Alvin / Ke, Zunlong / Briggs, John A G / Voth, Gregory A

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 1002

    Abstract: The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 ... ...

    Abstract The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
    MeSH term(s) Algorithms ; Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/metabolism ; COVID-19/virology ; Host-Pathogen Interactions ; Humans ; Membrane Fusion ; Molecular Dynamics Simulation ; Protein Binding ; Protein Domains ; Protein Multimerization ; Receptors, Virus/chemistry ; Receptors, Virus/metabolism ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Attachment ; Virus Internalization
    Chemical Substances Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-02-22
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-28654-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core.

    Pak, Alexander J / Yu, Alvin / Ke, Zunlong / Briggs, John A G / Voth, Gregory A

    bioRxiv : the preprint server for biology

    2021  

    Abstract: The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 ... ...

    Abstract The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
    Language English
    Publishing date 2021-06-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.05.24.445443
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Anti-Ebola virus mAb 3A6 with unprecedented potency protects highly viremic animals from fatal outcome and physically lifts its glycoprotein target from the virion membrane.

    Saphire, Erica / Salie, Zhe Li / Ke, Zunlong / Halfmann, Peter / DeWald, Lisa Evans / McArdle, Sara / Grinyo, Ariadna / Davidson, Edgar / Schendel, Sharon / Hariharan, Chitra / Norris, Michael / Yu, Xiaoying / Chennareddy, Chakravarthy / Xiong, Xiaoli / Heinrich, Megan / Holbrook, Michael / Doranz, Benjamin / Crozier, Ian / Hastie, Kathryn /
    Kawaoka, Yoshihiro / Branco, Luis / Kuhn, Jens / Briggs, John / Worwa, Gabriella / Davis, Carl / Ahmed, Rafi

    Research square

    2023  

    Abstract: Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein ( ... ...

    Abstract Monoclonal antibodies (mAbs) against Ebola virus (EBOV) glycoprotein (GP
    Language English
    Publishing date 2023-12-22
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3722563/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Flagellar Structures from the Bacterium Caulobacter crescentus and Implications for Phage

    Montemayor, Eric J / Ploscariu, Nicoleta T / Sanchez, Juan C / Parrell, Daniel / Dillard, Rebecca S / Shebelut, Conrad W / Ke, Zunlong / Guerrero-Ferreira, Ricardo C / Wright, Elizabeth R

    Journal of bacteriology

    2021  Volume 203, Issue 5

    Abstract: Caulobacter ... ...

    Abstract Caulobacter crescentus
    MeSH term(s) Amino Acid Sequence ; Bacteriophages/physiology ; Caulobacter crescentus/genetics ; Caulobacter crescentus/ultrastructure ; Caulobacter crescentus/virology ; Flagella/chemistry ; Flagellin/chemistry ; Flagellin/genetics ; Genes, Bacterial ; Protein Conformation, alpha-Helical ; Virus Attachment
    Chemical Substances Flagellin (12777-81-0)
    Language English
    Publishing date 2021-02-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2968-3
    ISSN 1098-5530 ; 0021-9193
    ISSN (online) 1098-5530
    ISSN 0021-9193
    DOI 10.1128/JB.00399-20
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0.

    Zivanov, Jasenko / Otón, Joaquín / Ke, Zunlong / von Kügelgen, Andriko / Pyle, Euan / Qu, Kun / Morado, Dustin / Castaño-Díez, Daniel / Zanetti, Giulia / Bharat, Tanmay A M / Briggs, John A G / Scheres, Sjors H W

    eLife

    2022  Volume 11

    Abstract: We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a ... ...

    Abstract We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
    MeSH term(s) Image Processing, Computer-Assisted/methods ; Bayes Theorem ; Electrons ; Cryoelectron Microscopy/methods ; Electron Microscope Tomography/methods
    Language English
    Publishing date 2022-12-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.83724
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  9. Article ; Online: Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

    Pak, Alexander J / Yu, Alvin / Ke, Zunlong / Briggs, John / Voth, Gregory A

    bioRxiv

    Abstract: The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 ... ...

    Abstract The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development and use of coarse-grained models and simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
    Keywords covid19
    Language English
    Publishing date 2021-05-24
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.05.24.445443
    Database COVID19

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  10. Article ; Online: Human Hepatitis B Virus Core Protein Inhibits IFNα-Induced IFITM1 Expression by Interacting with BAF200.

    Li, Tongya / Ke, Zunlong / Liu, Weiyong / Xiong, Ying / Zhu, Ying / Liu, Yingle

    Viruses

    2019  Volume 11, Issue 5

    Abstract: Human hepatitis B virus core protein (HBc) is a structural protein of the hepatitis B virus (HBV) and contributes to HBV regulation of host-cell transcription. However, the mechanisms of transcriptional regulation remain poorly characterized. To dissect ... ...

    Abstract Human hepatitis B virus core protein (HBc) is a structural protein of the hepatitis B virus (HBV) and contributes to HBV regulation of host-cell transcription. However, the mechanisms of transcriptional regulation remain poorly characterized. To dissect the function of HBc, a yeast two-hybrid was performed to identify HBc-binding proteins, and the C-terminal of BRG1/hBRM-associated factors 200 (BAF200C) was identified. Then, the existence of HBc interactions with BAF200C and full-length BAF200 was confirmed via co-immunoprecipitation assays in 293T, HepG2 and HepG2-NTCP cells. Furthermore, we show that the binding between HBc and BAF200 was of vital importance to HBc mediated downregulation of interferon-induced transmembrane protein 1 (IFITM1) expression, and the mechanisms for the downregulation were disclosed as follows. Basal level of IFITM1 expression depends on BAF200, rather than the JAK-STAT1 pathway. The interaction of HBc with BAF200 disturbs the stability of the polybromo-associated BAF (PBAF) complex and results in the suppression of IFTM1 transcription. Finally, the antiviral effects of IFITM1 on cell proliferation and HBV replication were found to be partially restored when HBc was co-transfected with BAF200. Collectively, our findings indicate that HBc plays a role in HBV resistance against the antiviral activities of IFNα, providing details about HBV evasion of host innate immunity.
    MeSH term(s) Antigens, Differentiation/genetics ; Antigens, Differentiation/metabolism ; Hep G2 Cells ; Hepatitis B/genetics ; Hepatitis B/metabolism ; Hepatitis B/virology ; Hepatitis B Core Antigens/genetics ; Hepatitis B Core Antigens/metabolism ; Hepatitis B virus/genetics ; Hepatitis B virus/metabolism ; Humans ; Interferon-alpha/genetics ; Interferon-alpha/metabolism ; Protein Binding ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances ARID2 protein, human ; Antigens, Differentiation ; Hepatitis B Core Antigens ; Interferon-alpha ; Transcription Factors ; leu-13 antigen
    Keywords covid19
    Language English
    Publishing date 2019-05-09
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v11050427
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