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  1. Article ; Online: The HSV-1 pUL37 protein promotes cell invasion by regulating the kinesin-1 motor.

    Kim, DongHo / Cianfrocco, Michael A / Verhey, Kristen J / Smith, Gregory A

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

    2024  Volume 121, Issue 19, Page(s) e2401341121

    Abstract: Neurotropic alphaherpesviruses, including herpes simplex virus type 1 (HSV-1), recruit microtubule motor proteins to invade cells. The incoming viral particle traffics to nuclei in a two-step process. First, the particle uses the dynein-dynactin motor to ...

    Abstract Neurotropic alphaherpesviruses, including herpes simplex virus type 1 (HSV-1), recruit microtubule motor proteins to invade cells. The incoming viral particle traffics to nuclei in a two-step process. First, the particle uses the dynein-dynactin motor to sustain transport to the centrosome. In neurons, this step is responsible for long-distance retrograde axonal transport and is an important component of the neuroinvasive property shared by these viruses. Second, a kinesin-dependent mechanism redirects the particle from the centrosome to the nucleus. We have reported that the kinesin motor used during the second step of invasion is assimilated into nascent virions during the previous round of infection. Here, we report that the HSV-1 pUL37 tegument protein suppresses the assimilated kinesin-1 motor during retrograde axonal transport. Region 2 (R2) of pUL37 was required for suppression and functioned independently of the autoinhibitory mechanism native to kinesin-1. Furthermore, the motor domain and proximal coiled coil of kinesin-1 were sufficient for HSV-1 assimilation, pUL37 suppression, and nuclear trafficking. pUL37 localized to the centrosome, the site of assimilated kinesin-1 activation during infection, when expressed in cells in the absence of other viral proteins; however, pUL37 did not suppress kinesin-1 in this context. These results indicate that the pUL37 tegument protein spatially and temporally regulates kinesin-1 via the amino-terminal motor region in the context of the incoming viral particle.
    MeSH term(s) Kinesins/metabolism ; Herpesvirus 1, Human/physiology ; Herpesvirus 1, Human/metabolism ; Humans ; Animals ; Axonal Transport/physiology ; Chlorocebus aethiops ; Centrosome/metabolism ; Neurons/metabolism ; Neurons/virology ; Vero Cells ; Cell Nucleus/metabolism ; Cell Nucleus/virology ; Viral Structural Proteins
    Chemical Substances Kinesins (EC 3.6.4.4) ; UL37 protein, Human herpesvirus 1 ; Viral Structural Proteins
    Language English
    Publishing date 2024-05-02
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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.2401341121
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
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  2. Article: Cloud computing platforms to support cryo-EM structure determination.

    Li, Yilai / Cianfrocco, Michael A

    Trends in biochemical sciences

    2021  Volume 47, Issue 2, Page(s) 103–105

    Abstract: Leveraging the power of single-particle cryo-electron microscopy (cryo-EM) requires robust and accessible computational infrastructure. Here, we summarize the cloud computing landscape and picture the outlook of a hybrid cryo-EM computing workflow, and ... ...

    Abstract Leveraging the power of single-particle cryo-electron microscopy (cryo-EM) requires robust and accessible computational infrastructure. Here, we summarize the cloud computing landscape and picture the outlook of a hybrid cryo-EM computing workflow, and make suggestions to the community to facilitate a future for cryo-EM that integrates into cloud computing infrastructure.
    MeSH term(s) Cloud Computing ; Cryoelectron Microscopy
    Language English
    Publishing date 2021-12-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2021.11.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models.

    Cianfrocco, Michael A / Kellogg, Elizabeth H

    Journal of chemical information and modeling

    2020  Volume 60, Issue 5, Page(s) 2458–2469

    Abstract: Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an ... ...

    Abstract Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an increased number of microscopes, cryo-EM facilities, and scientists eager to leverage the ability to determine protein structures without crystallization. However, numerous pitfalls and considerations beset the path toward high-resolution structures and are not necessarily obvious from literature surveys. Here, we detail the most common misconceptions when initiating a cryo-EM project and common technical hurdles, as well as their solutions, and we conclude with a vision for the future of this exciting field.
    MeSH term(s) Cryoelectron Microscopy ; Proteins ; Software
    Chemical Substances Proteins
    Language English
    Publishing date 2020-03-09
    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 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.9b01178
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1230: Show issues Location:
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  4. Article: Cloud computing platforms to support cryo-EM structure determination

    Li, Yilai / Cianfrocco, Michael A.

    Trends in biochemical sciences. 2022 Feb., v. 47, no. 2

    2022  

    Abstract: Leveraging the power of single-particle cryo-electron microscopy (cryo-EM) requires robust and accessible computational infrastructure. Here, we summarize the cloud computing landscape and picture the outlook of a hybrid cryo-EM computing workflow, and ... ...

    Abstract Leveraging the power of single-particle cryo-electron microscopy (cryo-EM) requires robust and accessible computational infrastructure. Here, we summarize the cloud computing landscape and picture the outlook of a hybrid cryo-EM computing workflow, and make suggestions to the community to facilitate a future for cryo-EM that integrates into cloud computing infrastructure.
    Keywords cryo-electron microscopy ; infrastructure ; landscapes
    Language English
    Dates of publication 2022-02
    Size p. 103-105.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2021.11.005
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Autoinhibited kinesin-1 adopts a hierarchical folding pattern.

    Tan, Zhenyu / Yue, Yang / da Veiga Leprevost, Felipe / Haynes, Sarah E / Basrur, Venkatesha / Nesvizhskii, Alexey I / Verhey, Kristen J / Cianfrocco, Michael A

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 ... ...

    Abstract Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
    Language English
    Publishing date 2023-09-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.26.525761
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Autoinhibited kinesin-1 adopts a hierarchical folding pattern.

    Tan, Zhenyu / Yue, Yang / Leprevost, Felipe / Haynes, Sarah / Basrur, Venkatesha / Nesvizhskii, Alexey I / Verhey, Kristen J / Cianfrocco, Michael A

    eLife

    2023  Volume 12

    Abstract: Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 ... ...

    Abstract Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine crosslinking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer (kinesin-1 heavy chain [KHC]) and kinesin-1 heterotetramer (KHC bound to kinesin light chain 1 [KLC1]). Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled-coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
    MeSH term(s) Kinesins ; Microtubule-Associated Proteins ; Biological Transport ; Consensus ; Mass Spectrometry
    Chemical Substances Kinesins (EC 3.6.4.4) ; Microtubule-Associated Proteins
    Language English
    Publishing date 2023-11-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.86776
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  7. Article: Structural and dynamic changes in P-Rex1 upon activation by PIP

    Ravala, Sandeep K / Adame-Garcia, Sendi Rafael / Li, Sheng / Chen, Chun-Liang / Cianfrocco, Michael A / Gutkind, J Silvio / Cash, Jennifer N / Tesmer, John J G

    bioRxiv : the preprint server for biology

    2024  

    Abstract: ... ...

    Abstract PIP
    Language English
    Publishing date 2024-04-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.15.557836
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: High-resolution cryo-EM using beam-image shift at 200 keV.

    Cash, Jennifer N / Kearns, Sarah / Li, Yilai / Cianfrocco, Michael A

    IUCrJ

    2020  Volume 7, Issue Pt 6, Page(s) 1179–1187

    Abstract: Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it remains unknown how well beam-image-shift data collection ... ...

    Abstract Recent advances in single-particle cryo-electron microscopy (cryo-EM) data collection utilize beam-image shift to improve throughput. Despite implementation on 300 keV cryo-EM instruments, it remains unknown how well beam-image-shift data collection affects data quality on 200 keV instruments and the extent to which aberrations can be computationally corrected. To test this, a cryo-EM data set for aldolase was collected at 200 keV using beam-image shift and analyzed. This analysis shows that the instrument beam tilt and particle motion initially limited the resolution to 4.9 Å. After particle polishing and iterative rounds of aberration correction in
    Language English
    Publishing date 2020-10-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252520013482
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  9. Article ; Online: High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines.

    Li, Yilai / Cash, Jennifer N / Tesmer, John J G / Cianfrocco, Michael A

    Structure (London, England : 1993)

    2020  Volume 28, Issue 7, Page(s) 858–869.e3

    Abstract: Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation devices herald a future where users will collect ... ...

    Abstract Single-particle cryoelectron microscopy (cryo-EM) continues to grow into a mainstream structural biology technique. Recent developments in data collection strategies alongside new sample preparation devices herald a future where users will collect multiple datasets per microscope session. To make cryo-EM data processing more automatic and user-friendly, we have developed an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep-learning and image-analysis tools. We have verified the performance of this pipeline on a number of datasets and extended its scope to include sample screening by the user-free assessment of the qualities of a series of datasets under different conditions. We propose that our workflow provides a decision-free solution for cryo-EM, making data preprocessing more generalized and robust in the high-throughput era as well as more convenient for users from a range of backgrounds.
    MeSH term(s) Cryoelectron Microscopy/methods ; Cryoelectron Microscopy/standards ; Deep Learning ; High-Throughput Screening Assays/methods ; High-Throughput Screening Assays/standards ; Image Processing, Computer-Assisted/methods ; Image Processing, Computer-Assisted/standards ; Protein Conformation
    Language English
    Publishing date 2020-04-14
    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 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2020.03.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4141: Show issues Location:
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  10. Article ; Online: Miro: A molecular switch at the center of mitochondrial regulation.

    Eberhardt, Emily L / Ludlam, Anthony V / Tan, Zhenyu / Cianfrocco, Michael A

    Protein science : a publication of the Protein Society

    2020  Volume 29, Issue 6, Page(s) 1269–1284

    Abstract: The orchestration of mitochondria within the cell represents a critical aspect of cell biology. At the center of this process is the outer mitochondrial membrane protein, Miro. Miro coordinates diverse cellular processes by regulating connections between ...

    Abstract The orchestration of mitochondria within the cell represents a critical aspect of cell biology. At the center of this process is the outer mitochondrial membrane protein, Miro. Miro coordinates diverse cellular processes by regulating connections between organelles and the cytoskeleton that range from mediating contacts between the endoplasmic reticulum and mitochondria to the regulation of both actin and microtubule motor proteins. Recently, a number of cell biological, biochemical, and protein structure studies have helped to characterize the myriad roles played by Miro. In addition to answering questions regarding Miro's function, these studies have opened the door to new avenues in the study of Miro in the cell. This review will focus on summarizing recent findings for Miro's structure, function, and activity while highlighting key questions that remain unanswered.
    MeSH term(s) Animals ; Humans ; Mitochondria/chemistry ; Mitochondria/metabolism ; Mitochondrial Membranes/chemistry ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry ; Mitochondrial Proteins/metabolism ; Models, Molecular ; rho GTP-Binding Proteins/chemistry ; rho GTP-Binding Proteins/metabolism
    Chemical Substances Mitochondrial Proteins ; RHOT1 protein, human (EC 3.6.1.-) ; rho GTP-Binding Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2020-02-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.3839
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.MO 1: Show issues

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