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  1. Article ; Online: Characterization of α-synuclein oligomers formed in the presence of lipid vesicles.

    Dasari, Anvesh K R / Sengupta, Urmi / Viverette, Elizabeth / Borgnia, Mario J / Kayed, Rakez / Lim, Kwang Hun

    Biochemistry and biophysics reports

    2024  Volume 38, Page(s) 101687

    Abstract: Aggregation of α-synuclein into oligomers and fibrils is associated with numerous neurodegenerative diseases such as Parkinson's disease (PD). Although the identity of the pathogenic species formed during the aggregation process is still under active ... ...

    Abstract Aggregation of α-synuclein into oligomers and fibrils is associated with numerous neurodegenerative diseases such as Parkinson's disease (PD). Although the identity of the pathogenic species formed during the aggregation process is still under active debate, mounting evidence suggests that small oligomeric species rather than fibrillar aggregates are real toxic species. Isolation and characterization of small oligomers is essential to developing therapeutic strategies to prevent oligomer formation. Preparation of misfolded oligomeric species for biophysical characterization is, however, a great challenge due to their heterogenous, transient nature. Here we report the preparation of toxic and non-toxic α-synuclein oligomeric species formed at different pH values in the presence of lipid vesicles that mimic mitochondria membranes containing cardiolipin. Biophysical characterization of the lipid-induced α-synuclein oligomeric assemblies revealed that α-synuclein oligomers formed at pH 7.4 have higher surface hydrophobicity than the aggregates formed at pH 6.0. In addition, the high-pH oligomers were shown to exhibit higher toxicity than the low-pH aggregates. Structural, dynamic properties of the oligomers were also investigated by using circular dichroism (CD) and NMR spectroscopy. Our CD analyses revealed that the two oligomeric species have distinct molecular conformations, and 2D
    Language English
    Publishing date 2024-03-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2831046-9
    ISSN 2405-5808 ; 2405-5808
    ISSN (online) 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2024.101687
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Automated systematic evaluation of cryo-EM specimens with SmartScope.

    Bouvette, Jonathan / Huang, Qinwen / Riccio, Amanda A / Copeland, William C / Bartesaghi, Alberto / Borgnia, Mario J

    eLife

    2022  Volume 11

    Abstract: Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has significantly increased the speed of data collection, ... ...

    Abstract Finding the conditions to stabilize a macromolecular target for imaging remains the most critical barrier to determining its structure by cryo-electron microscopy (cryo-EM). While automation has significantly increased the speed of data collection, specimens are still screened manually, a laborious and subjective task that often determines the success of a project. Here, we present SmartScope, the first framework to streamline, standardize, and automate specimen evaluation in cryo-EM. SmartScope employs deep-learning-based object detection to identify and classify features suitable for imaging, allowing it to perform thorough specimen screening in a fully automated manner. A web interface provides remote control over the automated operation of the microscope in real time and access to images and annotation tools. Manual annotations can be used to re-train the feature recognition models, leading to improvements in performance. Our automated tool for systematic evaluation of specimens streamlines structure determination and lowers the barrier of adoption for cryo-EM.
    MeSH term(s) Automation ; Cryoelectron Microscopy/methods ; Macromolecular Substances
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2022-08-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural ; 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.80047
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  3. Article: Molecular basis of polyspecific drug binding and transport by OCT1 and OCT2.

    Suo, Yang / Wright, Nicholas J / Guterres, Hugo / Fedor, Justin G / Butay, Kevin John / Borgnia, Mario J / Im, Wonpil / Lee, Seok-Yong

    bioRxiv : the preprint server for biology

    2023  

    Abstract: A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their ... ...

    Abstract A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.15.532610
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Structures of trehalose-6-phosphate synthase, Tps1, from the fungal pathogen

    Washington, Erica J / Zhou, Ye / Hsu, Allen L / Petrovich, Matthew / Borgnia, Mario J / Bartesaghi, Alberto / Brennan, Richard G

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Invasive fungal diseases are a major threat to human health, resulting in more than 1.5 million deaths worldwide each year. Yet the arsenal of antifungal therapeutics remains limited and is in dire need of novel drugs that target additional fungal- ... ...

    Abstract Invasive fungal diseases are a major threat to human health, resulting in more than 1.5 million deaths worldwide each year. Yet the arsenal of antifungal therapeutics remains limited and is in dire need of novel drugs that target additional fungal-specific biosynthetic pathways. One such pathway involves the biosynthesis of trehalose. Trehalose is a non-reducing disaccharide composed of two molecules of glucose that is required for pathogenic fungi, including
    Language English
    Publishing date 2023-03-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.14.530545
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Expanding the Reach of Cryo-EM through Open Design Robotics and Remote Screening.

    Zhang, Steven / Peele, Wyatt / Bouvette, Jonathan / Huang, Qinwen / Bartesaghi, Alberto / Dandey, Venkata / Borgnia, Mario J

    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) 1019

    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/ozad067.515
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  6. Article ; Online: Molecular basis of polyspecific drug and xenobiotic recognition by OCT1 and OCT2.

    Suo, Yang / Wright, Nicholas J / Guterres, Hugo / Fedor, Justin G / Butay, Kevin John / Borgnia, Mario J / Im, Wonpil / Lee, Seok-Yong

    Nature structural & molecular biology

    2023  Volume 30, Issue 7, Page(s) 1001–1011

    Abstract: A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition. In mammals, organic cation transporter (OCT) subtypes 1 and 2 (OCT1 and OCT2, also known as SLC22A1 and ... ...

    Abstract A wide range of endogenous and xenobiotic organic ions require facilitated transport systems to cross the plasma membrane for their disposition. In mammals, organic cation transporter (OCT) subtypes 1 and 2 (OCT1 and OCT2, also known as SLC22A1 and SLC22A2, respectively) are polyspecific transporters responsible for the uptake and clearance of structurally diverse cationic compounds in the liver and kidneys, respectively. Notably, it is well established that human OCT1 and OCT2 play central roles in the pharmacokinetics and drug-drug interactions of many prescription medications, including metformin. Despite their importance, the basis of polyspecific cationic drug recognition and the alternating access mechanism for OCTs have remained a mystery. Here we present four cryo-electron microscopy structures of apo, substrate-bound and drug-bound OCT1 and OCT2 consensus variants, in outward-facing and outward-occluded states. Together with functional experiments, in silico docking and molecular dynamics simulations, these structures uncover general principles of organic cation recognition by OCTs and provide insights into extracellular gate occlusion. Our findings set the stage for a comprehensive structure-based understanding of OCT-mediated drug-drug interactions, which will prove critical in the preclinical evaluation of emerging therapeutics.
    MeSH term(s) Animals ; Humans ; Organic Cation Transport Proteins/metabolism ; Organic Cation Transporter 2/metabolism ; Cryoelectron Microscopy ; Xenobiotics ; Organic Cation Transporter 1/metabolism ; Cations/metabolism ; Mammals/metabolism
    Chemical Substances Organic Cation Transport Proteins ; Organic Cation Transporter 2 ; Xenobiotics ; Organic Cation Transporter 1 ; Cations
    Language English
    Publishing date 2023-06-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-023-01017-4
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  7. Article: Method for the structural analysis of Twinkle mitochondrial DNA helicase by cryo-EM

    Riccio, Amanda A. / Bouvette, Jonathan / Longley, Matthew J. / Krahn, Juno M. / Borgnia, Mario J. / Copeland, William C.

    Methods. 2022 June 27,

    2022  

    Abstract: The mitochondrial replisome replicates the 16.6 kb mitochondria DNA (mtDNA). The proper functioning of this multicomponent protein complex is vital for the integrity of the mitochondrial genome. One of the critical protein components of the mitochondrial ...

    Abstract The mitochondrial replisome replicates the 16.6 kb mitochondria DNA (mtDNA). The proper functioning of this multicomponent protein complex is vital for the integrity of the mitochondrial genome. One of the critical protein components of the mitochondrial replisome is the Twinkle helicase, a member of the Superfamily 4 (SF4) helicases. Decades of research has uncovered common themes among SF4 helicases including self-assembly, ATP-dependent translocation, and formation of protein–protein complexes. Some of the molecular details of these processes are still unknown for the mitochondria SF4 helicase, Twinkle. Here, we describe a protocol for expression, purification, and single-particle cryo-electron microscopy of the Twinkle helicase clinical variant, W315L, which resulted in the first high-resolution structure of Twinkle helicase. The methods described here serve as an adaptable protocol to support future high-resolution studies of Twinkle helicase or other SF4 helicases.
    Keywords DNA helicases ; cryo-electron microscopy ; mitochondria ; mitochondrial DNA ; mitochondrial genome
    Language English
    Dates of publication 2022-0627
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2022.06.012
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  8. Article ; Online: Author Correction: Structural basis for pre-tRNA recognition and processing by the human tRNA splicing endonuclease complex.

    Hayne, Cassandra K / Butay, Kevin John U / Stewart, Zachary D / Krahn, Juno M / Perera, Lalith / Williams, Jason G / Petrovitch, Robert M / Deterding, Leesa J / Matera, A Gregory / Borgnia, Mario J / Stanley, Robin E

    Nature structural & molecular biology

    2024  Volume 31, Issue 2, Page(s) 390

    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-024-01213-w
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  9. Article ; Online: Antiviral drug recognition and elevator-type transport motions of CNT3.

    Wright, Nicholas J / Zhang, Feng / Suo, Yang / Kong, Lingyang / Yin, Ying / Fedor, Justin G / Sharma, Kedar / Borgnia, Mario J / Im, Wonpil / Lee, Seok-Yong

    Nature chemical biology

    2024  

    Abstract: Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with ... ...

    Abstract Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiviral drugs used in the treatment of coronavirus infections. We report high-resolution single-particle cryo-electron microscopy structures of bovine CNT3 complexed with antiviral nucleosides N
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-024-01559-8
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  10. Article ; Online: Heat-dependent opening of TRPV1 in the presence of capsaicin.

    Kwon, Do Hoon / Zhang, Feng / Suo, Yang / Bouvette, Jonathan / Borgnia, Mario J / Lee, Seok-Yong

    Nature structural & molecular biology

    2021  Volume 28, Issue 7, Page(s) 554–563

    Abstract: Transient receptor potential vanilloid member 1 (TRPV1) is a ... ...

    Abstract Transient receptor potential vanilloid member 1 (TRPV1) is a Ca
    MeSH term(s) Animals ; Capsaicin/metabolism ; Cell Line ; Cryoelectron Microscopy ; Enzyme Activation/physiology ; HEK293 Cells ; Hot Temperature ; Humans ; Nanostructures ; Protein Binding ; Protein Conformation ; Protein Domains ; Rats ; Signal Transduction/physiology ; TRPV Cation Channels/genetics ; TRPV Cation Channels/metabolism ; Thermosensing/physiology
    Chemical Substances TRPV Cation Channels ; Trpv1 protein, rat ; Capsaicin (S07O44R1ZM)
    Language English
    Publishing date 2021-07-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-021-00616-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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