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Pichkur EB, Vorovitch MF, Ivanova AL, Protopopova EV, Loktev VB, Osolodkin DI, Ishmukhametov AA, Samygina VR. The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution. Emerg Microbes Infect 2024; 13:2313849. [PMID: 38465849 DOI: 10.1080/22221751.2024.2313849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin-Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.
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Affiliation(s)
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
| | - Elena V Protopopova
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russian Federation
| | - Valery B Loktev
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russian Federation
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
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2
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Ruehle MD, Li S, Agard DA, Pearson CG. Poc1 bridges basal body inner junctions to promote triplet microtubule integrity and connections. J Cell Biol 2024; 223:e202311104. [PMID: 38743010 PMCID: PMC11094743 DOI: 10.1083/jcb.202311104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/15/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Basal bodies (BBs) are conserved eukaryotic structures that organize cilia. They are comprised of nine, cylindrically arranged, triplet microtubules (TMTs) connected to each other by inter-TMT linkages which stabilize the structure. Poc1 is a conserved protein important for BB structural integrity in the face of ciliary forces transmitted to BBs. To understand how Poc1 confers BB stability, we identified the precise position of Poc1 in the Tetrahymena BB and the effect of Poc1 loss on BB structure. Poc1 binds at the TMT inner junctions, stabilizing TMTs directly. From this location, Poc1 also stabilizes inter-TMT linkages throughout the BB, including the cartwheel pinhead and the inner scaffold. The full localization of the inner scaffold protein Fam161A requires Poc1. As ciliary forces are increased, Fam161A is reduced, indicative of a force-dependent molecular remodeling of the inner scaffold. Thus, while not essential for BB assembly, Poc1 promotes BB interconnections that establish an architecture competent to resist ciliary forces.
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Affiliation(s)
- Marisa D. Ruehle
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sam Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Institute for Advanced Biological Imaging, Redwood Shores, CA, USA
| | - Chad G. Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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3
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Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024; 384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
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Affiliation(s)
| | | | | | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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4
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Pflüger T, Gschell M, Zhang L, Shnitsar V, Zabadné AJ, Zierep P, Günther S, Einsle O, Andrade SLA. How sensor Amt-like proteins integrate ammonium signals. SCIENCE ADVANCES 2024; 10:eadm9441. [PMID: 38838143 DOI: 10.1126/sciadv.adm9441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/30/2024] [Indexed: 06/07/2024]
Abstract
Unlike aquaporins or potassium channels, ammonium transporters (Amts) uniquely discriminate ammonium from potassium and water. This feature has certainly contributed to their repurposing as ammonium receptors during evolution. Here, we describe the ammonium receptor Sd-Amt1, where an Amt module connects to a cytoplasmic diguanylate cyclase transducer module via an HAMP domain. Structures of the protein with and without bound ammonium were determined to 1.7- and 1.9-Ångstrom resolution, depicting the ON and OFF states of the receptor and confirming the presence of a binding site for two ammonium cations that is pivotal for signal perception and receptor activation. The transducer domain was disordered in the crystals, and an AlphaFold2 prediction suggests that the helices linking both domains are flexible. While the sensor domain retains the trimeric fold formed by all Amt family members, the HAMP domains interact as pairs and serve to dimerize the transducer domain upon activation.
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Affiliation(s)
- Tobias Pflüger
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Mathias Gschell
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Lin Zhang
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Volodymyr Shnitsar
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Annas J Zabadné
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Paul Zierep
- Faculty of Chemistry and Pharmacy, Institute for Pharmaceutical Sciences, University Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Stefan Günther
- Faculty of Chemistry and Pharmacy, Institute for Pharmaceutical Sciences, University Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Oliver Einsle
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University Freiburg, Schänzlerstr. 1, 79104 Freiburg, Germany
| | - Susana L A Andrade
- Faculty of Chemistry and Pharmacy, Institute for Biochemistry, University Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University Freiburg, Schänzlerstr. 1, 79104 Freiburg, Germany
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5
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Guo X, Li H, Yan C, Lei J, Zhou R, Shi Y. Molecular mechanism of substrate recognition and cleavage by human γ-secretase. Science 2024; 384:1091-1095. [PMID: 38843321 DOI: 10.1126/science.adn5820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
Successive cleavages of amyloid precursor protein C-terminal fragment with 99 residues (APP-C99) by γ-secretase result in amyloid-β (Aβ) peptides of varying lengths. Most cleavages have a step size of three residues. To elucidate the underlying mechanism, we determined the atomic structures of human γ-secretase bound individually to APP-C99, Aβ49, Aβ46, and Aβ43. In all cases, the substrate displays the same structural features: a transmembrane α-helix, a three-residue linker, and a β-strand that forms a hybrid β-sheet with presenilin 1 (PS1). Proteolytic cleavage occurs just ahead of the substrate β-strand. Each cleavage is followed by unwinding and translocation of the substrate α-helix by one turn and the formation of a new β-strand. This mechanism is consistent with existing biochemical data and may explain the cleavages of other substrates by γ-secretase.
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Affiliation(s)
- Xuefei Guo
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haotian Li
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rui Zhou
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Westlake Laboratory of Life Science and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang, China
- Research Center for Industries of the Future; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang, China
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6
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Rieger B, Droste I, Gerritsma F, Ten Brink T, Stallinga S. Single image Fourier ring correlation. OPTICS EXPRESS 2024; 32:21767-21782. [PMID: 38859523 DOI: 10.1364/oe.524683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/21/2024] [Indexed: 06/12/2024]
Abstract
We address resolution assessment for (light super-resolution) microscopy imaging. In modalities where imaging is not diffraction limited, correlation between two noise independent images is the standard way to infer the resolution. Here we take away the need for two noise independent images by computationally splitting one image acquisition into two noise independent realizations. This procedure generates two Poisson noise distributed images if the input is Poissonian distributed. As most modern cameras are shot-noise limited this procedure is directly applicable. However, also in the presence of readout noise we can compute the resolution faithfully via a correction factor. We evaluate our method on simulations and experimental data of widefield microscopy, STED microscopy, rescan confocal microscopy, image scanning microscopy, conventional confocal microscopy, and transmission electron microscopy. In all situations we find that using one image instead of two results in the same computed image resolution.
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7
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Lin TY, Chung SC. CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm. Bioinformatics 2024; 40:btae345. [PMID: 38837333 PMCID: PMC11167209 DOI: 10.1093/bioinformatics/btae345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
MOTIVATION Cryo-electron microscopy (cryo-EM) is a powerful technique for studying macromolecules and holds the potential for identifying kinetically preferred transition sequences between conformational states. Typically, these sequences are explored within two-dimensional energy landscapes. However, due to the complexity of biomolecules, representing conformational changes in two dimensions can be challenging. Recent advancements in reconstruction models have successfully extracted structural heterogeneity from cryo-EM images using higher-dimension latent space. Nonetheless, creating high-dimensional conformational landscapes in the latent space and then searching for preferred paths continues to be a formidable task. RESULTS This study introduces an innovative framework for identifying preferred trajectories within high-dimensional conformational landscapes. Our method encompasses the search for the minimum energy path in the graph, where edge weights are determined based on the energy estimation at each node using local density. The effectiveness of this approach is demonstrated by identifying accurate transition states in both synthetic and real-world datasets featuring continuous conformational changes. AVAILABILITY AND IMPLEMENTATION The CLEAPA package is available at https://github.com/tengyulin/energy_aware_pathfinding/.
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Affiliation(s)
- Teng-Yu Lin
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Szu-Chi Chung
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung 804, Taiwan
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8
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Brotherton DH, Nijjar S, Savva CG, Dale N, Cameron AD. Structures of wild-type and a constitutively closed mutant of connexin26 shed light on channel regulation by CO 2. eLife 2024; 13:RP93686. [PMID: 38829031 PMCID: PMC11147507 DOI: 10.7554/elife.93686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Connexins allow intercellular communication by forming gap junction channels (GJCs) between juxtaposed cells. Connexin26 (Cx26) can be regulated directly by CO2. This is proposed to be mediated through carbamylation of K125. We show that mutating K125 to glutamate, mimicking the negative charge of carbamylation, causes Cx26 GJCs to be constitutively closed. Through cryo-EM we observe that the K125E mutation pushes a conformational equilibrium towards the channel having a constricted pore entrance, similar to effects seen on raising the partial pressure of CO2. In previous structures of connexins, the cytoplasmic loop, important in regulation and where K125 is located, is disordered. Through further cryo-EM studies we trap distinct states of Cx26 and observe density for the cytoplasmic loop. The interplay between the position of this loop, the conformations of the transmembrane helices and the position of the N-terminal helix, which controls the aperture to the pore, provides a mechanism for regulation.
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Affiliation(s)
| | - Sarbjit Nijjar
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Christos G Savva
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of LeicesterLeicesterUnited Kingdom
| | - Nicholas Dale
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
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9
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Parkhurst JM, Varslot T, Dumoux M, Siebert CA, Darrow M, Basham M, Kirkland A, Grange M, Evans G, Naismith JH. Pillar data-acquisition strategies for cryo-electron tomography of beam-sensitive biological samples. Acta Crystallogr D Struct Biol 2024; 80:421-438. [PMID: 38829361 PMCID: PMC11154591 DOI: 10.1107/s2059798324004546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024] Open
Abstract
For cryo-electron tomography (cryo-ET) of beam-sensitive biological specimens, a planar sample geometry is typically used. As the sample is tilted, the effective thickness of the sample along the direction of the electron beam increases and the signal-to-noise ratio concomitantly decreases, limiting the transfer of information at high tilt angles. In addition, the tilt range where data can be collected is limited by a combination of various sample-environment constraints, including the limited space in the objective lens pole piece and the possible use of fixed conductive braids to cool the specimen. Consequently, most tilt series are limited to a maximum of ±70°, leading to the presence of a missing wedge in Fourier space. The acquisition of cryo-ET data without a missing wedge, for example using a cylindrical sample geometry, is hence attractive for volumetric analysis of low-symmetry structures such as organelles or vesicles, lysis events, pore formation or filaments for which the missing information cannot be compensated by averaging techniques. Irrespective of the geometry, electron-beam damage to the specimen is an issue and the first images acquired will transfer more high-resolution information than those acquired last. There is also an inherent trade-off between higher sampling in Fourier space and avoiding beam damage to the sample. Finally, the necessity of using a sufficient electron fluence to align the tilt images means that this fluence needs to be fractionated across a small number of images; therefore, the order of data acquisition is also a factor to consider. Here, an n-helix tilt scheme is described and simulated which uses overlapping and interleaved tilt series to maximize the use of a pillar geometry, allowing the entire pillar volume to be reconstructed as a single unit. Three related tilt schemes are also evaluated that extend the continuous and classic dose-symmetric tilt schemes for cryo-ET to pillar samples to enable the collection of isotropic information across all spatial frequencies. A fourfold dose-symmetric scheme is proposed which provides a practical compromise between uniform information transfer and complexity of data acquisition.
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Affiliation(s)
- James M. Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Trond Varslot
- Thermo Fisher Scientific, Vlastimila Pecha, Brno, Czechia
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - C. Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Michele Darrow
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Electron Physical Science Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - Michael Grange
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James H. Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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10
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Yang Z, Fan J, Wang J, Fan X, Ouyang Z, Wang HW, Zhou X. Electrospray-assisted cryo-EM sample preparation to mitigate interfacial effects. Nat Methods 2024; 21:1023-1032. [PMID: 38664529 PMCID: PMC11166575 DOI: 10.1038/s41592-024-02247-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/17/2024] [Indexed: 06/13/2024]
Abstract
Addressing interfacial effects during specimen preparation in cryogenic electron microscopy remains challenging. Here we introduce ESI-cryoPrep, a specimen preparation method based on electrospray ionization in native mass spectrometry, designed to alleviate issues associated with protein denaturation or preferred orientation induced by macromolecule adsorption at interfaces. Through fine-tuning spraying parameters, we optimized protein integrity preservation and achieved the desired ice thickness for analyzing target macromolecules. With ESI-cryoPrep, we prepared high-quality cryo-specimens of five proteins and obtained three-dimensional reconstructions at near-atomic resolution. Our findings demonstrate that ESI-cryoPrep effectively confines macromolecules within the middle of the thin layer of amorphous ice, facilitating the preparation of blotting-free vitreous samples. The protective mechanism, characterized by the uneven distribution of charged biomolecules of varying sizes within charged droplets, prevents the adsorption of target biomolecules at air-water or graphene-water interfaces, thereby avoiding structural damage to the protein particles or the introduction of dominant orientation issues.
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Affiliation(s)
- Zi Yang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jingjin Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.
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11
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Choi SH, Lee SS, Lee HY, Kim S, Kim JW, Jin MS. Cryo-EM structure of cadmium-bound human ABCB6. Commun Biol 2024; 7:672. [PMID: 38822018 PMCID: PMC11143254 DOI: 10.1038/s42003-024-06377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy structures of human ABCB6 bound to a cadmium Cd(II) ion in the presence of antioxidant thiol peptides glutathione (GSH) and phytochelatin 2 (PC2) at resolutions of 3.2 and 3.1 Å, respectively. The overall folding of the two structures resembles the inward-facing apo state but with less separation between the two halves of the transporter. Two GSH molecules are symmetrically bound to the Cd(II) ion in a bent conformation, with the central cysteine protruding towards the metal. The N-terminal glutamate and C-terminal glycine of GSH do not directly interact with Cd(II) but contribute to neutralizing positive charges of the binding cavity by forming hydrogen bonds and van der Waals interactions with nearby residues. In the presence of PC2, Cd(II) binding to ABCB6 is similar to that observed with GSH, except that two cysteine residues of each PC2 molecule participate in Cd(II) coordination to form a tetrathiolate. Structural comparison of human ABCB6 and its homologous Atm-type transporters indicate that their distinct substrate specificity might be attributed to variations in the capping residues situated at the top of the substrate-binding cavity.
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Affiliation(s)
- Seung Hun Choi
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Sang Soo Lee
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Hyeon You Lee
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Subin Kim
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Ji Won Kim
- Department of Life Sciences, POSTECH, 77 Cheongam-Ro, Nam-gu, Pohang, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea.
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12
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Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O. Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature 2024:10.1038/s41586-024-07497-8. [PMID: 38811740 DOI: 10.1038/s41586-024-07497-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
The prime editor system composed of Streptococcus pyogenes Cas9 nickase (nSpCas9) and engineered Moloney murine leukaemia virus reverse transcriptase (M-MLV RT) collaborates with a prime editing guide RNA (pegRNA) to facilitate a wide variety of precise genome edits in living cells1. However, owing to a lack of structural information, the molecular mechanism of pegRNA-guided reverse transcription by the prime editor remains poorly understood. Here we present cryo-electron microscopy structures of the SpCas9-M-MLV RTΔRNaseH-pegRNA-target DNA complex in multiple states. The termination structure, along with our functional analysis, reveals that M-MLV RT extends reverse transcription beyond the expected site, resulting in scaffold-derived incorporations that cause undesired edits at the target loci. Furthermore, structural comparisons among the pre-initiation, initiation and elongation states show that M-MLV RT remains in a consistent position relative to SpCas9 during reverse transcription, whereas the pegRNA-synthesized DNA heteroduplex builds up along the surface of SpCas9. On the basis of our structural insights, we rationally engineered pegRNA variants and prime-editor variants in which M-MLV RT is fused within SpCas9. Collectively, our findings provide structural insights into the stepwise mechanism of prime editing, and will pave the way for the development of a versatile prime editing toolbox.
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Affiliation(s)
- Yutaro Shuto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryoya Nakagawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Shiyou Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mizuki Hoki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi N Omura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hisato Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuzuru Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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13
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Zhong Y, Feng J, Koh AF, Kotecha A, Greber BJ, Ataide S. Cryo-EM structure of SRP68/72 reveals an extended dimerization domain with RNA-binding activity. Nucleic Acids Res 2024; 52:5285-5300. [PMID: 38366771 PMCID: PMC11109942 DOI: 10.1093/nar/gkae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
The signal recognition particle (SRP) is a critical component in protein sorting pathways in all domains of life. Human SRP contains six proteins bound to the 7S RNA and their structures and functions have been mostly elucidated. The SRP68/72 dimer is the largest SRP component and is essential for SRP function. Although the structures of the SRP68/72 RNA binding and dimerization domains have been previously reported, the structure and function of large portions of the SRP68/72 dimer remain unknown. Here, we analyse full-length SRP68/72 using cryo-EM and report that SRP68/72 depend on each other for stability and form an extended dimerization domain. This newly observed dimerization domain is both a protein- and RNA-binding domain. Comparative analysis with current structural models suggests that this dimerization domain undergoes dramatic translocation upon SRP docking onto SRP receptor and eventually comes close to the Alu domain. We propose that the SRP68/72 dimerization domain functions by binding and detaching the Alu domain and SRP9/14 from the ribosomal surface, thus releasing elongation arrest upon docking onto the ER membrane.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Junjie Feng
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Adrian F Koh
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 Eindhoven, The Netherlands
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 Eindhoven, The Netherlands
| | - Basil J Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Sandro F Ataide
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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14
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Wakabayashi T, Oide M, Nakasako M. CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase. Sci Rep 2024; 14:11165. [PMID: 38750092 PMCID: PMC11096400 DOI: 10.1038/s41598-024-61793-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis-Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.
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Grants
- JPMJPR22E2 Japan Science and Technology Agency
- jp13480214 Japan Society for the Promotion of Science
- jp19204042 Japan Society for the Promotion of Science
- jp22244054 Japan Society for the Promotion of Science
- jp21H01050 Japan Society for the Promotion of Science
- jp26800227 Japan Society for the Promotion of Science
- 18J11653 Japan Society for the Promotion of Science
- jp15076210 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp20050030 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp22018027 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp23120525, jp25120725 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp15H01647 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp17H05891 Ministry of Education, Culture, Sports, Science and Technology of Japan
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Affiliation(s)
- Taiki Wakabayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo, 679-5148, Japan
| | - Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo, 679-5148, Japan
- PRESTO, Japan Science and Technology Agency, Chiyoda-Ku, Tokyo, 102-0076, Japan
- Protein Research Institute, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo, 679-5148, Japan.
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15
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Wang R, Cong Y, Qian D, Yan C, Gong D. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 2024:gkae395. [PMID: 38742627 DOI: 10.1093/nar/gkae395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
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Affiliation(s)
- Runhao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Ye Cong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Dandan Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Deshun Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
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16
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Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol 2024; 7:557. [PMID: 38730276 PMCID: PMC11087493 DOI: 10.1038/s42003-024-06204-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.
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Affiliation(s)
- Lisa Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Technical Biogeochemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany.
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Gerd Hause
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Christian Ihling
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany
| | - Milton T Stubbs
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany.
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
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17
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Chien DCC, Limjunyawong N, Cao C, Meixiong J, Peng Q, Ho CY, Fay JF, Roth BL, Dong X. MRGPRX4 mediates phospho-drug-associated pruritus in a humanized mouse model. Sci Transl Med 2024; 16:eadk8198. [PMID: 38718132 DOI: 10.1126/scitranslmed.adk8198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 04/12/2024] [Indexed: 05/30/2024]
Abstract
The phosphate modification of drugs is a common chemical strategy to increase solubility and allow for parenteral administration. Unfortunately, phosphate modifications often elicit treatment- or dose-limiting pruritus through an unknown mechanism. Using unbiased high-throughput drug screens, we identified the Mas-related G protein-coupled receptor X4 (MRGPRX4), a primate-specific, sensory neuron receptor previously implicated in itch, as a potential target for phosphate-modified compounds. Using both Gq-mediated calcium mobilization and G protein-independent GPCR assays, we found that phosphate-modified compounds potently activate MRGPRX4. Furthermore, a humanized mouse model expressing MRGPRX4 in sensory neurons exhibited robust phosphomonoester prodrug-evoked itch. To characterize and confirm this interaction, we further determined the structure of MRGPRX4 in complex with a phosphate-modified drug through single-particle cryo-electron microscopy (cryo-EM) and identified critical amino acid residues responsible for the binding of the phosphate group. Together, these findings explain how phosphorylated drugs can elicit treatment-limiting itch and identify MRGPRX4 as a potential therapeutic target to suppress itch and to guide future drug design.
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Affiliation(s)
- Daphne Chun-Che Chien
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nathachit Limjunyawong
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Can Cao
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - James Meixiong
- Department of Dermatology, University of California San Francisco, San Francisco, CA 94115, USA
| | - Qi Peng
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cheng-Ying Ho
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jonathan F Fay
- Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, Baltimore, MD 21201, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Xinzhong Dong
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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18
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Ibáñez de Opakua A, Pantoja CF, Cima-Omori MS, Dienemann C, Zweckstetter M. Impact of distinct FG nucleoporin repeats on Nup98 self-association. Nat Commun 2024; 15:3797. [PMID: 38714656 PMCID: PMC11076500 DOI: 10.1038/s41467-024-48194-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/24/2024] [Indexed: 05/10/2024] Open
Abstract
Nucleoporins rich in phenylalanine/glycine (FG) residues form the permeability barrier within the nuclear pore complex and are implicated in several pathological cellular processes, including oncogenic fusion condensates. The self-association of FG-repeat proteins and interactions between FG-repeats play a critical role in these activities by forming hydrogel-like structures. Here we show that mutation of specific FG repeats of Nup98 can strongly decrease the protein's self-association capabilities. We further present a cryo-electron microscopy structure of a Nup98 peptide fibril with higher stability per residue compared with previous Nup98 fibril structures. The high-resolution structure reveals zipper-like hydrophobic patches which contain a GLFG motif and are less compatible for binding to nuclear transport receptors. The identified distinct molecular properties of different regions of the nucleoporin may contribute to spatial variations in the self-association of FG-repeats, potentially influencing transport processes through the nuclear pore.
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Affiliation(s)
- Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany
| | - Christian F Pantoja
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany
| | - Maria-Sol Cima-Omori
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Am Fassberg 11, Göttingen, Germany.
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19
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Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA. Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun 2024; 15:3775. [PMID: 38710701 PMCID: PMC11074143 DOI: 10.1038/s41467-024-48237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
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Affiliation(s)
- Oliver J Acton
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ailidh J O Burgess
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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20
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Arnold WR, Mancino A, Moss FR, Frost A, Julius D, Cheng Y. Structural basis of TRPV1 modulation by endogenous bioactive lipids. Nat Struct Mol Biol 2024:10.1038/s41594-024-01299-2. [PMID: 38698206 DOI: 10.1038/s41594-024-01299-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/28/2024] [Indexed: 05/05/2024]
Abstract
TRP ion channels are modulated by phosphoinositide lipids, but the underlying structural mechanisms remain unclear. The capsaicin- and heat-activated receptor, TRPV1, has served as a model for deciphering lipid modulation, which is relevant to understanding how pro-algesic agents enhance channel activity in the setting of inflammatory pain. Identification of a pocket within the TRPV1 transmembrane core has provided initial clues as to how phosphoinositide lipids bind to and regulate the channel. Here we show that this regulatory pocket in rat TRPV1 can accommodate diverse lipid species, including the inflammatory lipid lysophosphatidic acid, whose actions are determined by their specific modes of binding. Furthermore, we show that an empty-pocket channel lacking an endogenous phosphoinositide lipid assumes an agonist-like state, even at low temperature, substantiating the concept that phosphoinositide lipids serve as negative TRPV1 modulators whose ejection from the binding pocket is a critical step toward activation by thermal or chemical stimuli.
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Affiliation(s)
- William R Arnold
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Adamo Mancino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Frank R Moss
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Altos Labs, Redwood City, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - David Julius
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
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21
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Schneider S, Brandina I, Peter D, Lagad S, Fraudeau A, Portell-Montserrat J, Tholen J, Zhao J, Galej WP. Structure of the human 20S U5 snRNP. Nat Struct Mol Biol 2024; 31:752-756. [PMID: 38467877 PMCID: PMC11102862 DOI: 10.1038/s41594-024-01250-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/14/2024] [Indexed: 03/13/2024]
Abstract
The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process.
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Affiliation(s)
- Sarah Schneider
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | - Irina Brandina
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | - Daniel Peter
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Sonal Lagad
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | | | - Júlia Portell-Montserrat
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Jonas Tholen
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Jiangfeng Zhao
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France.
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22
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Wan W, Khavnekar S, Wagner J. STOPGAP: an open-source package for template matching, subtomogram alignment and classification. Acta Crystallogr D Struct Biol 2024; 80:336-349. [PMID: 38606666 PMCID: PMC11066880 DOI: 10.1107/s205979832400295x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
Cryo-electron tomography (cryo-ET) enables molecular-resolution 3D imaging of complex biological specimens such as viral particles, cellular sections and, in some cases, whole cells. This enables the structural characterization of molecules in their near-native environments, without the need for purification or separation, thereby preserving biological information such as conformational states and spatial relationships between different molecular species. Subtomogram averaging is an image-processing workflow that allows users to leverage cryo-ET data to identify and localize target molecules, determine high-resolution structures of repeating molecular species and classify different conformational states. Here, STOPGAP, an open-source package for subtomogram averaging that is designed to provide users with fine control over each of these steps, is described. In providing detailed descriptions of the image-processing algorithms that STOPGAP uses, this manuscript is also intended to serve as a technical resource to users as well as for further community-driven software development.
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Affiliation(s)
- William Wan
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
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23
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Zhao Q, Bertolli S, Park YJ, Tan Y, Cutler KJ, Srinivas P, Asfahl KL, Fonesca-García C, Gallagher LA, Li Y, Wang Y, Coleman-Derr D, DiMaio F, Zhang D, Peterson SB, Veesler D, Mougous JD. Streptomyces umbrella toxin particles block hyphal growth of competing species. Nature 2024; 629:165-173. [PMID: 38632398 PMCID: PMC11062931 DOI: 10.1038/s41586-024-07298-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Streptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive1. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species1,2. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-electron microscopy structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, which led us to name them umbrella particles. Streptomyces coelicolor encodes three umbrella particles with distinct toxin and lectin composition. Notably, supernatant containing these toxins specifically and potently inhibits the growth of select Streptomyces species from among a diverse collection of bacteria screened. For one target, Streptomyces griseus, inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative hyphal growth. Our data show that Streptomyces umbrella particles mediate competition among vegetative mycelia of related species, a function distinct from small-molecule antibiotics, which are produced at the onset of reproductive growth and act broadly3,4. Sequence analyses suggest that this role of umbrella particles extends beyond Streptomyces, as we identified umbrella loci in nearly 1,000 species across Actinobacteria.
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Affiliation(s)
- Qinqin Zhao
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Savannah Bertolli
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Yongjun Tan
- Department of Biology, St Louis University, St Louis, MO, USA
| | - Kevin J Cutler
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Pooja Srinivas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kyle L Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Citlali Fonesca-García
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Larry A Gallagher
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaqiao Li
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Devin Coleman-Derr
- Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dapeng Zhang
- Department of Biology, St Louis University, St Louis, MO, USA
- Program of Bioinformatic and Computational Biology, St Louis University, St Louis, MO, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA.
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24
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Gomes JV, Singh-Bhagania S, Cenci M, Chacon Cordon C, Singh M, Butterwick JA. The molecular basis of sugar detection by an insect taste receptor. Nature 2024; 629:228-234. [PMID: 38447670 PMCID: PMC11062906 DOI: 10.1038/s41586-024-07255-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024]
Abstract
Animals crave sugars because of their energy potential and the pleasurable sensation of tasting sweetness. Yet all sugars are not metabolically equivalent, requiring mechanisms to detect and differentiate between chemically similar sweet substances. Insects use a family of ionotropic gustatory receptors to discriminate sugars1, each of which is selectively activated by specific sweet molecules2-6. Here, to gain insight into the molecular basis of sugar selectivity, we determined structures of Gr9, a gustatory receptor from the silkworm Bombyx mori (BmGr9), in the absence and presence of its sole activating ligand, D-fructose. These structures, along with structure-guided mutagenesis and functional assays, illustrate how D-fructose is enveloped by a ligand-binding pocket that precisely matches the overall shape and pattern of chemical groups in D-fructose. However, our computational docking and experimental binding assays revealed that other sugars also bind BmGr9, yet they are unable to activate the receptor. We determined the structure of BmGr9 in complex with one such non-activating sugar, L-sorbose. Although both sugars bind a similar position, only D-fructose is capable of engaging a bridge of two conserved aromatic residues that connects the pocket to the pore helix, inducing a conformational change that allows the ion-conducting pore to open. Thus, chemical specificity does not depend solely on the selectivity of the ligand-binding pocket, but it is an emergent property arising from a combination of receptor-ligand interactions and allosteric coupling. Our results support a model whereby coarse receptor tuning is derived from the size and chemical characteristics of the pocket, whereas fine-tuning of receptor activation is achieved through the selective engagement of an allosteric pathway that regulates ion conduction.
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Affiliation(s)
- João Victor Gomes
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Matthew Cenci
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos Chacon Cordon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Manjodh Singh
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Joel A Butterwick
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
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25
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Zhang X, Zhan X, Bian T, Yang F, Li P, Lu Y, Xing Z, Fan R, Zhang QC, Shi Y. Structural insights into branch site proofreading by human spliceosome. Nat Struct Mol Biol 2024; 31:835-845. [PMID: 38196034 DOI: 10.1038/s41594-023-01188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2023] [Indexed: 01/11/2024]
Abstract
Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5.
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Affiliation(s)
- Xiaofeng Zhang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Xiechao Zhan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Tong Bian
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Fenghua Yang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Pan Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yichen Lu
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Zhihan Xing
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Rongyan Fan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Qiangfeng Cliff Zhang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China.
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26
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Liang CC, Greenhough LA, Masino L, Maslen S, Bajrami I, Tuppi M, Skehel M, Taylor IA, West SC. Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Nature 2024; 629:697-703. [PMID: 38658755 PMCID: PMC11096129 DOI: 10.1038/s41586-024-07347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
RAD52 is important for the repair of DNA double-stranded breaks1,2, mitotic DNA synthesis3-5 and alternative telomere length maintenance6,7. Central to these functions, RAD52 promotes the annealing of complementary single-stranded DNA (ssDNA)8,9 and provides an alternative to BRCA2/RAD51-dependent homologous recombination repair10. Inactivation of RAD52 in homologous-recombination-deficient BRCA1- or BRCA2-defective cells is synthetically lethal11,12, and aberrant expression of RAD52 is associated with poor cancer prognosis13,14. As a consequence, RAD52 is an attractive therapeutic target against homologous-recombination-deficient breast, ovarian and prostate cancers15-17. Here we describe the structure of RAD52 and define the mechanism of annealing. As reported previously18-20, RAD52 forms undecameric (11-subunit) ring structures, but these rings do not represent the active form of the enzyme. Instead, cryo-electron microscopy and biochemical analyses revealed that ssDNA annealing is driven by RAD52 open rings in association with replication protein-A (RPA). Atomic models of the RAD52-ssDNA complex show that ssDNA sits in a positively charged channel around the ring. Annealing is driven by the RAD52 N-terminal domains, whereas the C-terminal regions modulate the open-ring conformation and RPA interaction. RPA associates with RAD52 at the site of ring opening with critical interactions occurring between the RPA-interacting domain of RAD52 and the winged helix domain of RPA2. Our studies provide structural snapshots throughout the annealing process and define the molecular mechanism of ssDNA annealing by the RAD52-RPA complex.
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Affiliation(s)
| | | | | | | | | | - Marcel Tuppi
- The Francis Crick Institute, London, UK
- Abcam, Cambridge Biomedical Campus, Cambridge, UK
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27
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Tuijtel MW, Cruz-León S, Kreysing JP, Welsch S, Hummer G, Beck M, Turoňová B. Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. SCIENCE ADVANCES 2024; 10:eadk6285. [PMID: 38669330 PMCID: PMC11051657 DOI: 10.1126/sciadv.adk6285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Cryo-electron tomography (cryo-ET) is a powerful method to elucidate subcellular architecture and to structurally analyze biomolecules in situ by subtomogram averaging, yet data quality critically depends on specimen thickness. Cells that are too thick for transmission imaging can be thinned into lamellae by cryo-focused ion beam (cryo-FIB) milling. Despite being a crucial parameter directly affecting attainable resolution, optimal lamella thickness has not been systematically investigated nor the extent of structural damage caused by gallium ions used for FIB milling. We thus systematically determined how resolution is affected by these parameters. We find that ion-induced damage does not affect regions more than 30 nanometers from either lamella surface and that up to ~180-nanometer lamella thickness does not negatively affect resolution. This shows that there is no need to generate very thin lamellae and lamella thickness can be chosen such that it captures cellular features of interest, thereby opening cryo-ET also for studies of large complexes.
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Affiliation(s)
- Maarten W. Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute of Biochemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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28
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Sun C, He B, Gao Y, Wang X, Liu X, Sun L. Structural insights into the calcium-coupled zinc export of human ZnT1. SCIENCE ADVANCES 2024; 10:eadk5128. [PMID: 38669333 PMCID: PMC11051671 DOI: 10.1126/sciadv.adk5128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
Cellular zinc (Zn2+) homeostasis is essential to human health and is under tight regulations. Human zinc transporter 1 (hZnT1) is a plasma membrane-localized Zn2+ exporter belonging to the ZnT family, and its functional aberration is associated with multiple diseases. Here, we show that hZnT1 works as a Zn2+/Ca2+ exchanger. We determine the structure of hZnT1 using cryo-electron microscopy (cryo-EM) single particle analysis. hZnT1 adopts a homodimeric structure, and each subunit contains a transmembrane domain consisting of six transmembrane segments, a cytosolic domain, and an extracellular domain. The transmembrane region displays an outward-facing conformation. On the basis of structural and functional analysis, we propose a model for the hZnT1-mediated Zn2+/Ca2+ exchange. Together, these results facilitate our understanding of the biological functions of hZnT1 and provide a basis for further investigations of the ZnT family transporters.
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Affiliation(s)
- Chunqiao Sun
- Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Bangguo He
- Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Yongxiang Gao
- Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Cryo-EM Center, Core Facility Center for Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xingbing Wang
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Xin Liu
- Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Linfeng Sun
- Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
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29
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Adams CS, Kim H, Burtner AE, Lee DS, Dobbins C, Criswell C, Coventry B, Kim HM, King NP. De novo design of protein minibinder agonists of TLR3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589973. [PMID: 38659926 PMCID: PMC11042314 DOI: 10.1101/2024.04.17.589973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Toll-like Receptor 3 (TLR3) is a pattern recognition receptor that initiates antiviral immune responses upon binding double-stranded RNA (dsRNA). Several nucleic acid-based TLR3 agonists have been explored clinically as vaccine adjuvants in cancer and infectious disease, but present substantial manufacturing and formulation challenges. Here, we use computational protein design to create novel miniproteins that bind to human TLR3 with nanomolar affinities. Cryo-EM structures of two minibinders in complex with TLR3 reveal that they bind the target as designed, although one partially unfolds due to steric competition with a nearby N-linked glycan. Multimeric forms of both minibinders induce NF-κB signaling in TLR3-expressing cell lines, demonstrating that they may have therapeutically relevant biological activity. Our work provides a foundation for the development of specific, stable, and easy-to-formulate protein-based agonists of TLRs and other pattern recognition receptors.
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Affiliation(s)
- Chloe S. Adams
- Institute for Protein Design, University of Washington, Seattle, WA, 98195 USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195 USA
| | - Hyojin Kim
- Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, South Korea
| | - Abigail E. Burtner
- Institute for Protein Design, University of Washington, Seattle, WA, 98195 USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195 USA
| | - Dong Sun Lee
- Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, South Korea
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, 98195 USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195 USA
| | - Cameron Criswell
- Institute for Protein Design, University of Washington, Seattle, WA, 98195 USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195 USA
| | - Brian Coventry
- Institute for Protein Design, University of Washington, Seattle, WA, 98195 USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195 USA
| | - Ho Min Kim
- Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, South Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA, 98195 USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195 USA
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30
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Berkeley RF, Cook BD, Herzik MA. Machine learning approaches to cryoEM density modification differentially affect biomacromolecule and ligand density quality. Front Mol Biosci 2024; 11:1404885. [PMID: 38698773 PMCID: PMC11063317 DOI: 10.3389/fmolb.2024.1404885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
The application of machine learning to cryogenic electron microscopy (cryoEM) data analysis has added a valuable set of tools to the cryoEM data processing pipeline. As these tools become more accessible and widely available, the implications of their use should be assessed. We noticed that machine learning map modification tools can have differential effects on cryoEM densities. In this perspective, we evaluate these effects to show that machine learning tools generally improve densities for biomacromolecules while generating unpredictable results for ligands. This unpredictable behavior manifests both in quantitative metrics of map quality and in qualitative investigations of modified maps. The results presented here highlight the power and potential of machine learning tools in cryoEM, while also illustrating some of the risks of their unexamined use.
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31
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Bi M, Wang X, Wang J, Xu J, Sun W, Adediwura VA, Miao Y, Cheng Y, Ye L. Structure and function of an intermediate GPCR-Gαβγ complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587841. [PMID: 38617296 PMCID: PMC11014534 DOI: 10.1101/2024.04.02.587841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Unraveling the signaling roles of intermediate complexes is pivotal for G protein-coupled receptor (GPCR) drug development. Despite hundreds of GPCR-Gαβγ structures, these snapshots primarily capture the fully activated end-state complex. Consequently, a comprehensive understanding of the conformational transitions during GPCR activation and the roles of intermediate GPCR-G protein complexes in signaling remain elusive. Guided by a conformational landscape profiled by 19 F quantitative NMR ( 19 F-qNMR) and Molecular Dynamics (MD) simulations, we resolved the structure of an unliganded GPCR-G protein intermediate complex by blocking its transition to the fully activated end-state complex. More importantly, we presented direct evidence that the intermediate GPCR-Gαsβγ complex initiates a rate-limited nucleotide exchange without progressing to the fully activated end-state complex, thereby bridging a significant gap in our understanding the complexity of GPCR signaling. Understanding the roles of individual conformational states and their complexes in signaling efficacy and bias will help us to design drugs that discriminately target a disease-related conformation.
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32
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Yang XY, Shen Z, Xie J, Greenwald J, Marathe I, Lin Q, Xie WJ, Wysocki VH, Fu TM. Molecular basis of Gabija anti-phage supramolecular assemblies. Nat Struct Mol Biol 2024:10.1038/s41594-024-01283-w. [PMID: 38627580 DOI: 10.1038/s41594-024-01283-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 03/22/2024] [Indexed: 05/15/2024]
Abstract
As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of Bacillus cereus GajA and GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.
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Affiliation(s)
- Xiao-Yuan Yang
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Program of OSBP, The Ohio State University, Columbus, OH, USA
| | - Zhangfei Shen
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jiale Xie
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Program of OSBP, The Ohio State University, Columbus, OH, USA
| | - Jacelyn Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Ila Marathe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Qingpeng Lin
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Wen Jun Xie
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Program of OSBP, The Ohio State University, Columbus, OH, USA.
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33
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Wang Z, McCallum M, Yan L, Gibson CA, Sharkey W, Park YJ, Dang HV, Amaya M, Person A, Broder CC, Veesler D. Structure and design of Langya virus glycoprotein antigens. Proc Natl Acad Sci U S A 2024; 121:e2314990121. [PMID: 38593070 PMCID: PMC11032465 DOI: 10.1073/pnas.2314990121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse, and hamster target cells using a different, yet unknown, receptor than Nipah virus (NiV) and Hendra virus (HeV) and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryoelectron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing their conformational landscape and distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
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Affiliation(s)
- Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD20814
| | - Cecily A. Gibson
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - William Sharkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA98195
- HHMI, Seattle, WA98195
| | - Ha V. Dang
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD20814
| | - Ashley Person
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD20814
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- HHMI, Seattle, WA98195
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34
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Liu YT, Fan H, Hu JJ, Zhou ZH. Overcoming the preferred orientation problem in cryoEM with self-supervised deep-learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.588921. [PMID: 38645074 PMCID: PMC11030451 DOI: 10.1101/2024.04.11.588921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
While advances in single-particle cryoEM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the so-called "preferred" orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep-learning-based software to address the preferred orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's capability of generating near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, β-galactosidases, and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred orientation problem.
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Affiliation(s)
- Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Hongcheng Fan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Jason J. Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
- Current address: Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
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35
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Bigelyte G, Duchovska B, Zedaveinyte R, Sasnauskas G, Sinkunas T, Dalgediene I, Tamulaitiene G, Silanskas A, Kazlauskas D, Valančauskas L, Madariaga-Marcos J, Seidel R, Siksnys V, Karvelis T. Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing. Nucleic Acids Res 2024; 52:3234-3248. [PMID: 38261981 PMCID: PMC11013384 DOI: 10.1093/nar/gkae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/20/2023] [Accepted: 01/10/2024] [Indexed: 01/25/2024] Open
Abstract
Cas9 and Cas12 nucleases of class 2 CRISPR-Cas systems provide immunity in prokaryotes through RNA-guided cleavage of foreign DNA. Here we characterize a set of compact CRISPR-Cas12m (subtype V-M) effector proteins and show that they provide protection against bacteriophages and plasmids through the targeted DNA binding rather than DNA cleavage. Biochemical assays suggest that Cas12m effectors can act as roadblocks inhibiting DNA transcription and/or replication, thereby triggering interference against invaders. Cryo-EM structure of Gordonia otitidis (Go) Cas12m ternary complex provided here reveals the structural mechanism of DNA binding ensuring interference. Harnessing GoCas12m innate ability to bind DNA target we fused it with adenine deaminase TadA-8e and showed an efficient A-to-G editing in Escherichia coli and human cells. Overall, this study expands our understanding of the functionally diverse Cas12 protein family, revealing DNA-binding dependent interference mechanism of Cas12m effectors that could be harnessed for engineering of compact base-editing tools.
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Affiliation(s)
- Greta Bigelyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Brigita Duchovska
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Rimante Zedaveinyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Indre Dalgediene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Lukas Valančauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Julene Madariaga-Marcos
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Tautvydas Karvelis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
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36
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Vayssières M, Marechal N, Yun L, Lopez Duran B, Murugasamy NK, Fogg JM, Zechiedrich L, Nadal M, Lamour V. Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Science 2024; 384:227-232. [PMID: 38603484 PMCID: PMC11108255 DOI: 10.1126/science.adl5899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the other, remains elusive owing to structures derived solely from single linear duplex DNAs lacking topological constraints. Using cryo-electron microscopy, we solved the structure of Escherichia coli DNA gyrase bound to a negatively supercoiled minicircle DNA. We show how DNA gyrase captures a DNA crossover, revealing both conserved molecular grooves that accommodate the DNA helices. Together with molecular tweezer experiments, the structure shows that the DNA crossover is of positive chirality, reconciling the binding step of gyrase-mediated DNA relaxation and supercoiling in a single structure.
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Affiliation(s)
- Marlène Vayssières
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Nils Marechal
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Long Yun
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Brian Lopez Duran
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Naveen Kumar Murugasamy
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Jonathan M. Fogg
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Marc Nadal
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Life Sciences, Université Paris Cité, Paris, France
| | - Valérie Lamour
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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37
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Dai J, Ma M, Niu Q, Eisert RJ, Wang X, Das P, Lechtreck KF, Dutcher SK, Zhang R, Brown A. Mastigoneme structure reveals insights into the O-linked glycosylation code of native hydroxyproline-rich helices. Cell 2024; 187:1907-1921.e16. [PMID: 38552624 PMCID: PMC11015965 DOI: 10.1016/j.cell.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/06/2024] [Accepted: 03/05/2024] [Indexed: 04/14/2024]
Abstract
Hydroxyproline-rich glycoproteins (HRGPs) are a ubiquitous class of protein in the extracellular matrices and cell walls of plants and algae, yet little is known of their native structures or interactions. Here, we used electron cryomicroscopy (cryo-EM) to determine the structure of the hydroxyproline-rich mastigoneme, an extracellular filament isolated from the cilia of the alga Chlamydomonas reinhardtii. The structure demonstrates that mastigonemes are formed from two HRGPs (a filament of MST1 wrapped around a single copy of MST3) that both have hyperglycosylated poly(hydroxyproline) helices. Within the helices, O-linked glycosylation of the hydroxyproline residues and O-galactosylation of interspersed serine residues create a carbohydrate casing. Analysis of the associated glycans reveals how the pattern of hydroxyproline repetition determines the type and extent of glycosylation. MST3 possesses a PKD2-like transmembrane domain that forms a heteromeric polycystin-like cation channel with PKD2 and SIP, explaining how mastigonemes are tethered to ciliary membranes.
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Affiliation(s)
- Jin Dai
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Meisheng Ma
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Qingwei Niu
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA; Molecular Cell Biology (MCB) graduate program, Division of Biology & Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Robyn J Eisert
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Xiangli Wang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Poulomi Das
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Susan K Dutcher
- Department of Genetics, Washington University in St. Louis, St Louis, MO, USA
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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38
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Zyla DS, Wiegand T, Bachmann P, Zdanowicz R, Giese C, Meier BH, Waksman G, Hospenthal MK, Glockshuber R. The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili. Nat Commun 2024; 15:3032. [PMID: 38589417 PMCID: PMC11001860 DOI: 10.1038/s41467-024-47212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024] Open
Abstract
Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.
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Affiliation(s)
- Dawid S Zyla
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany
| | - Paul Bachmann
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK
| | - Manuela K Hospenthal
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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39
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Li Y, Guo Y, Bröer A, Dai L, Brӧer S, Yan R. Cryo-EM structure of the human Asc-1 transporter complex. Nat Commun 2024; 15:3036. [PMID: 38589439 PMCID: PMC11001984 DOI: 10.1038/s41467-024-47468-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
The Alanine-Serine-Cysteine transporter 1 (Asc-1 or SLC7A10) forms a crucial heterodimeric transporter complex with 4F2hc (SLC3A2) through a covalent disulfide bridge. This complex enables the sodium-independent transport of small neutral amino acids, including L-Alanine (L-Ala), Glycine (Gly), and D-Serine (D-Ser), within the central nervous system (CNS). D-Ser and Gly are two key endogenous glutamate co-agonists that activate N-methyl-d-aspartate (NMDA) receptors by binding to the allosteric site. Mice deficient in Asc-1 display severe symptoms such as tremors, ataxia, and seizures, leading to early postnatal death. Despite its physiological importance, the functional mechanism of the Asc-1-4F2hc complex has remained elusive. Here, we present cryo-electron microscopy (cryo-EM) structures of the human Asc-1-4F2hc complex in its apo state, D-Ser bound state, and L-Ala bound state, resolved at 3.6 Å, 3.5 Å, and 3.4 Å, respectively. Through detailed structural analysis and transport assays, we uncover a comprehensive alternating access mechanism that underlies conformational changes in the complex. In summary, our findings reveal the architecture of the Asc-1 and 4F2hc complex and provide valuable insights into substrate recognition and the functional cycle of this essential transporter complex.
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Affiliation(s)
- Yaning Li
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yingying Guo
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Angelika Bröer
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Lu Dai
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Stefan Brӧer
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
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40
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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401150. [PMID: 38582512 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325011, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Haihong Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Ximiao Hou
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
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41
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Sauer PV, Cupellini L, Sutter M, Bondanza M, Domínguez Martin MA, Kirst H, Bína D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polívka7 T, Mennucci B, Kerfeld CA. Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. SCIENCE ADVANCES 2024; 10:eadk7535. [PMID: 38578996 PMCID: PMC10997198 DOI: 10.1126/sciadv.adk7535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
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Affiliation(s)
- Paul V. Sauer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - María Agustina Domínguez Martin
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Bína
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Basil J. Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Polívka7
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Thermo Fisher Scientific, Eindhoven, Netherlands
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Sanchez-Garcia R, Gaullier G, Cuadra-Troncoso JM, Vargas J. Cryo-EM Map Anisotropy Can Be Attenuated by Map Post-Processing and a New Method for Its Estimation. Int J Mol Sci 2024; 25:3959. [PMID: 38612769 PMCID: PMC11012471 DOI: 10.3390/ijms25073959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection sphere. As a result, the overall quality of the reconstructed maps can be severely affected, as manifested by the presence of anisotropy in the map resolution. Several methods have been proposed to measure the directional resolution of maps in tandem with experimental protocols to address the problem of preferential orientations in cryo-EM. Following these works, in this manuscript we identified one potential limitation that may affect most of the existing methods and we proposed an alternative approach to evaluate the presence of preferential orientations in cryo-EM reconstructions. In addition, we also showed that some of the most recently proposed cryo-EM map post-processing algorithms can attenuate map anisotropy, thus offering alternative visualization opportunities for cases affected by moderate levels of preferential orientations.
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Affiliation(s)
- Ruben Sanchez-Garcia
- Department of Statistics, University of Oxford, 24–29 St Giles’, Oxford OX1 3LB, UK
| | - Guillaume Gaullier
- Department of Chemistry—Ångström, Uppsala University, Box 523, SE 751 20 Uppsala, Sweden;
| | - Jose Manuel Cuadra-Troncoso
- Departamento de Inteligencia Artificial, Universidad Nacional de Educación a Distancia, C. Juan del Rosal 16, 28040 Madrid, Spain;
| | - Javier Vargas
- Departamento de Óptica, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040 Madrid, Spain
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43
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Premageetha GT, Vinothkumar KR, Bose S. Exploring advances in single particle CryoEM with apoferritin: From blobs to true atomic resolution. Int J Biochem Cell Biol 2024; 169:106536. [PMID: 38307321 DOI: 10.1016/j.biocel.2024.106536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024]
Abstract
Deciphering the three-dimensional structures of macromolecules is of paramount importance for gaining insights into their functions and roles in human health and disease. Single particle cryoEM has emerged as a powerful technique that enables direct visualization of macromolecules and their complexes, and through subsequent averaging, achieve near atomic-level resolution. A major breakthrough was recently achieved with the determination of the apoferritin structure at true atomic resolution. In this review, we discuss the latest technological innovations across the entire single-particle workflow, which have been instrumental in driving the resolution revolution and in transforming cryoEM as a mainstream technique in structural biology. We illustrate these advancements using apoferritin as an example that has served as an excellent benchmark sample for assessing emerging technologies. We further explore whether the existing technology can routinely generate atomic structures of dynamic macromolecules that more accurately represent real-world samples, the limitations in the workflow, and the current approaches employed to overcome them.
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Affiliation(s)
- Gowtham ThambraRajan Premageetha
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bangalore 560065, India; Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576104, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Post, Bangalore 560065, India
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bangalore 560065, India.
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44
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Egelman EH. Helical reconstruction, again. Curr Opin Struct Biol 2024; 85:102788. [PMID: 38401399 PMCID: PMC10923117 DOI: 10.1016/j.sbi.2024.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
Many protein and nucleoprotein complexes exist as helical polymers. As a result, much effort has been invested in developing methods for using electron microscopy to determine the structure of these assemblies. With the revolution in cryo-electron microscopy (cryo-EM), it has now become routine to reach a near-atomic level of resolution for these structures, and it is the exception when this is not possible. However, the greatest challenge is frequently determining the correct symmetry. This review focuses on why this can be so difficult and the current absence of a better approach than trial-and-error.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22903, USA.
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45
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Zhang JT, Wei XY, Cui N, Tian R, Jia N. Target ssDNA activates the NADase activity of prokaryotic SPARTA immune system. Nat Chem Biol 2024; 20:503-511. [PMID: 37932528 DOI: 10.1038/s41589-023-01479-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Argonaute proteins (Agos), which use small RNAs or DNAs as guides to recognize complementary nucleic acid targets, mediate RNA silencing in eukaryotes. In prokaryotes, Agos are involved in immunity: the short prokaryotic Ago/TIR-APAZ (SPARTA) immune system triggers cell death by degrading NAD+ in response to invading plasmids, but its molecular mechanisms remain unknown. Here we used cryo-electron microscopy to determine the structures of inactive monomeric and active tetrameric Crenotalea thermophila SPARTA complexes, revealing mechanisms underlying SPARTA assembly, RNA-guided recognition of target single-stranded DNA (ssDNA) and subsequent SPARTA tetramerization, as well as tetramerization-dependent NADase activation. The small RNA guides Ago to recognize its ssDNA target, inducing SPARTA tetramerization via both Ago- and TIR-mediated interactions and resulting in a two-stranded, parallel, head-to-tail TIR rearrangement primed for NAD+ hydrolysis. Our findings thus identify the molecular basis for target ssDNA-mediated SPARTA activation, which will facilitate the development of SPARTA-based biotechnological tools.
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Affiliation(s)
- Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xin-Yang Wei
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Ning Cui
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
- Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, China.
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46
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Wang X, Shen X, Qu Y, Zhang H, Wang C, Yang F, Shen H. Structural insights into ion selectivity and transport mechanisms of Oryza sativa HKT2;1 and HKT2;2/1 transporters. NATURE PLANTS 2024; 10:633-644. [PMID: 38570642 DOI: 10.1038/s41477-024-01665-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
Plant high-affinity K+ transporters (HKTs) play a pivotal role in maintaining the balance of Na+ and K+ ions in plants, thereby influencing plant growth under K+-depleted conditions and enhancing tolerance to salinity stress. Here we report the cryo-electron microscopy structures of Oryza sativa HKT2;1 and HKT2;2/1 at overall resolutions of 2.5 Å and 2.3 Å, respectively. Both transporters adopt a dimeric assembly, with each protomer enclosing an ion permeation pathway. Comparison between the selectivity filters of the two transporters reveals the critical roles of Ser88/Gly88 and Val243/Gly243 in determining ion selectivity. A constriction site along the ion permeation pathway is identified, consisting of Glu114, Asn273, Pro392, Pro393, Arg525, Lys517 and the carboxy-terminal Trp530 from the neighbouring protomer. The linker between domains II and III adopts a stable loop structure oriented towards the constriction site, potentially participating in the gating process. Electrophysiological recordings, yeast complementation assays and molecular dynamics simulations corroborate the functional importance of these structural features. Our findings provide crucial insights into the ion selectivity and transport mechanisms of plant HKTs, offering valuable structural templates for developing new salinity-tolerant cultivars and strategies to increase crop yields.
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Affiliation(s)
- Xiaohui Wang
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaoshuai Shen
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yannan Qu
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Heng Zhang
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Chu Wang
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Fan Yang
- Department of Biophysics and Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
| | - Huaizong Shen
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
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47
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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48
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Nakagawa T, Wang XT, Miguez-Cabello FJ, Bowie D. The open gate of the AMPA receptor forms a Ca 2+ binding site critical in regulating ion transport. Nat Struct Mol Biol 2024; 31:688-700. [PMID: 38409505 DOI: 10.1038/s41594-024-01228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptors (AMPARs) are cation-selective ion channels that mediate most fast excitatory neurotransmission in the brain. Although their gating mechanism has been studied extensively, understanding how cations traverse the pore has remained elusive. Here we investigated putative ion and water densities in the open pore of Ca2+-permeable AMPARs (rat GRIA2 flip-Q isoform) at 2.3-2.6 Å resolution. We show that the ion permeation pathway attains an extracellular Ca2+ binding site (site-G) when the channel gate moves into the open configuration. Site-G is highly selective for Ca2+ over Na+, favoring the movement of Ca2+ into the selectivity filter of the pore. Seizure-related N619K mutation, adjacent to site-G, promotes channel opening but attenuates Ca2+ binding and thus diminishes Ca2+ permeability. Our work identifies the importance of site-G, which coordinates with the Q/R site of the selectivity filter to ensure the preferential transport of Ca2+ through the channel pore.
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Affiliation(s)
- Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University, School of Medicine, Nashville, TN, USA.
| | - Xin-Tong Wang
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | | | - Derek Bowie
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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49
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Brown HG, Smith D, Wardle BC, Hanssen E. Square condenser apertures for square cameras in low-dose transmission electron microscopy. Nat Methods 2024; 21:566-568. [PMID: 38459386 DOI: 10.1038/s41592-024-02206-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin.
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Affiliation(s)
- Hamish G Brown
- Ian Holmes Imaging Centre and ARC Industrial Training Centre for Cryo Electron Microscopy of Membrane Proteins, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
| | - Dan Smith
- Melbourne Centre for Nanofabrication, Australian National Fabrication Facility, Clayton, Victoria, Australia
| | | | - Eric Hanssen
- Ian Holmes Imaging Centre and ARC Industrial Training Centre for Cryo Electron Microscopy of Membrane Proteins, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
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50
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Bloch Y, Felix J, Merceron R, Provost M, Symakani RA, De Backer R, Lambert E, Mehdipour AR, Savvides SN. Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23. Nat Struct Mol Biol 2024; 31:591-597. [PMID: 38287195 DOI: 10.1038/s41594-023-01190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/22/2023] [Indexed: 01/31/2024]
Abstract
Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.
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Affiliation(s)
- Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Hamburg, Germany
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Romain Merceron
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Eurofins DiscoverX Products France, Celle-Lévescault, France
| | - Mathias Provost
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Argenx, Ghent, Belgium
| | - Royan Alipour Symakani
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Robin De Backer
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Elisabeth Lambert
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Solvias, Basel, Switzerland
| | | | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
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