1
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Liu J, McRae EKS, Zhang M, Geary C, Andersen ES, Ren G. Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography. Nat Commun 2024; 15:9084. [PMID: 39433544 PMCID: PMC11494099 DOI: 10.1038/s41467-024-52914-1] [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: 12/22/2023] [Accepted: 09/23/2024] [Indexed: 10/23/2024] Open
Abstract
Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e-Å-2, achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.
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Affiliation(s)
- Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000, Aarhus, Denmark
- Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000, Aarhus, Denmark
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, 69120, Heidelberg, Germany
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000, Aarhus, Denmark.
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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2
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Hayes BK, Harper M, Venugopal H, Lewis JM, Wright A, Lee HC, Steele JR, Steer DL, Schittenhelm RB, Boyce JD, McGowan S. Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery. Nat Commun 2024; 15:8709. [PMID: 39379370 PMCID: PMC11461821 DOI: 10.1038/s41467-024-52950-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: 11/18/2023] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins into adjacent cells. Here we present the structure of Tse15, a T6SS Rhs effector from the nosocomial pathogen Acinetobacter baumannii. Tse15 forms a triple layered β-cocoon Rhs domain with an N-terminal α-helical clade domain and an unfolded C-terminal toxin domain inside the Rhs cage. Tse15 is cleaved into three domains, through independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for N-terminal clade cleavage. Proteomic analyses identified that significantly more peptides from the N-terminal clade and toxin domains were secreted than from the Rhs cage, suggesting toxin delivery often occurs without the cage. We propose the clade domain acts as an internal chaperone to mediate toxin tethering to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggests this may be a common mechanism for delivery.
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Affiliation(s)
- Brooke K Hayes
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Marina Harper
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Jessica M Lewis
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Amy Wright
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Han-Chung Lee
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Joel R Steele
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David L Steer
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - John D Boyce
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia.
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia.
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia.
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia.
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3
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Alvarez Viar G, Klena N, Martino F, Nievergelt AP, Bolognini D, Capasso P, Pigino G. Protofilament-specific nanopatterns of tubulin post-translational modifications regulate the mechanics of ciliary beating. Curr Biol 2024; 34:4464-4475.e9. [PMID: 39270640 PMCID: PMC11466076 DOI: 10.1016/j.cub.2024.08.021] [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: 10/23/2023] [Revised: 06/18/2024] [Accepted: 08/14/2024] [Indexed: 09/15/2024]
Abstract
Controlling ciliary beating is essential for motility and signaling in eukaryotes. This process relies on the regulation of various axonemal proteins that assemble in stereotyped patterns onto individual microtubules of the ciliary structure. Additionally, each axonemal protein interacts exclusively with determined tubulin protofilaments of the neighboring microtubule to carry out its function. While it is known that tubulin post-translational modifications (PTMs) are important for proper ciliary motility, the mode and extent to which they contribute to these interactions remain poorly understood. Currently, the prevailing understanding is that PTMs can confer functional specialization at the level of individual microtubules. However, this paradigm falls short of explaining how the tubulin code can manage the complexity of the axonemal structure where functional interactions happen in defined patterns at the sub-microtubular scale. Here, we combine immuno-cryo-electron tomography (cryo-ET), expansion microscopy, and mutant analysis to show that, in motile cilia, tubulin glycylation and polyglutamylation form mutually exclusive protofilament-specific nanopatterns at a sub-microtubular scale. These nanopatterns are consistent with the distributions of axonemal dyneins and nexin-dynein regulatory complexes, respectively, and are indispensable for their regulation during ciliary beating. Our findings offer a new paradigm for understanding how different tubulin PTMs, such as glycylation, glutamylation, acetylation, tyrosination, and detyrosination, can coexist within the ciliary structure and specialize individual protofilaments for the regulation of diverse protein complexes. The identification of a ciliary tubulin nanocode by cryo-ET suggests the need for high-resolution studies to better understand the molecular role of PTMs in other cellular compartments beyond the cilium.
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Affiliation(s)
| | - Nikolai Klena
- Human Technopole, V.le Rita Levi-Montalcini 1, Milan 20157, Italy
| | - Fabrizio Martino
- Human Technopole, V.le Rita Levi-Montalcini 1, Milan 20157, Italy
| | - Adrian Pascal Nievergelt
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, Dresden 01307, Germany
| | - Davide Bolognini
- Human Technopole, V.le Rita Levi-Montalcini 1, Milan 20157, Italy
| | - Paola Capasso
- Human Technopole, V.le Rita Levi-Montalcini 1, Milan 20157, Italy
| | - Gaia Pigino
- Human Technopole, V.le Rita Levi-Montalcini 1, Milan 20157, Italy.
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4
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Marcelot O, Marcelot C, Rolando S. Limitations and drawbacks of DQE estimation methods applied to electron detectors. Microscopy (Oxf) 2024; 73:405-413. [PMID: 38498372 DOI: 10.1093/jmicro/dfae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/27/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024] Open
Abstract
The detective quantum efficiency (DQE) is generally accepted as the main figure of merit for the comparison between electron detectors, and most of the time given as a unique number at the Nyquist frequency while it is known to vary with electron dose. It is usually estimated, thanks to a method improved by McMullan in 2009. The purpose of this work is to analyze and to criticize this DQE extraction method on the basis of measurement and model results, and to give recommendations for fair comparison between detectors, wondering if the DQE is the right figure of merit for electron detectors.
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5
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Pierson JA, Yang JE, Wright ER. Recent advances in correlative cryo-light and electron microscopy. Curr Opin Struct Biol 2024; 89:102934. [PMID: 39366119 DOI: 10.1016/j.sbi.2024.102934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 10/06/2024]
Abstract
Correlative light and electron microscopy (CLEM) pipelines serve to integrate the imaging modalities of fluorescence light microscopy (FLM) and cryogenic electron microscopy (cryo-EM) to produce contextually relevant high-resolution structural snapshots of biological systems. Innovations in sample preparation, instrumentation, imaging, and data processing have advanced the field of cryo-EM. This review focuses on prior work and recent developments in the field of cryo- EM that support further integration of technologies for correlative microscopy workflows.
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Affiliation(s)
- Joshua A Pierson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA.
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6
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Marx V. 20 years of Nature Methods: how some papers shaped science and careers. Nat Methods 2024; 21:1786-1791. [PMID: 39384985 DOI: 10.1038/s41592-024-02452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2024]
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7
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Zhang H, Zhou C, Mohammad Z, Zhao J. Structural basis of human 20S proteasome biogenesis. Nat Commun 2024; 15:8184. [PMID: 39294158 PMCID: PMC11410832 DOI: 10.1038/s41467-024-52513-0] [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: 09/21/2023] [Accepted: 09/11/2024] [Indexed: 09/20/2024] Open
Abstract
New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. Here, to understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observe an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
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Affiliation(s)
- Hanxiao Zhang
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA
| | - Chenyu Zhou
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA
| | - Zarith Mohammad
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA
| | - Jianhua Zhao
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, USA.
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8
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Rizvi A, Favetta B, Jaber N, Lee YK, Jiang J, Idris NS, Schuster BS, Dai W, Patterson JP. Revealing nanoscale structure and interfaces of protein and polymer condensates via cryo-electron microscopy. NANOSCALE 2024; 16:16706-16717. [PMID: 39171763 PMCID: PMC11392623 DOI: 10.1039/d4nr01877j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Liquid-liquid phase separation (LLPS) is a ubiquitous demixing phenomenon observed in various molecular solutions, including in polymer and protein solutions. Demixing of solutions results in condensed, phase separated droplets which exhibit a range of liquid-like properties driven by transient intermolecular interactions. Understanding the organization within these condensates is crucial for deciphering their material properties and functions. This study explores the distinct nanoscale networks and interfaces in the condensate samples using a modified cryo-electron microscopy (cryo-EM) method. The method involves initiating condensate formation on electron microscopy grids to limit droplet growth as large droplet sizes are not ideal for cryo-EM imaging. The versatility of this method is demonstrated by imaging three different classes of condensates. We further investigate the condensate structures using cryo-electron tomography which provides 3D reconstructions, uncovering porous internal structures, unique core-shell morphologies, and inhomogeneities within the nanoscale organization of protein condensates. Comparison with dry-state transmission electron microscopy emphasizes the importance of preserving the hydrated structure of condensates for accurate structural analysis. We correlate the internal structure of protein condensates with their amino acid sequences and material properties by performing viscosity measurements that support that more viscous condensates exhibit denser internal assemblies. Our findings contribute to a comprehensive understanding of nanoscale condensate structure and its material properties. Our approach here provides a versatile tool for exploring various phase-separated systems and their nanoscale structures for future studies.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
| | - Bruna Favetta
- Department of Biomedical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Nora Jaber
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yun-Kyung Lee
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jennifer Jiang
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Nehal S Idris
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA.
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, CA 92697-2025, USA
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9
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Whedon SD, Lee K, Wang ZA, Zahn E, Lu C, Yapa-Abeywardana M, Fairall L, Nam E, Dubois-Coyne S, Ioannes PD, Sheng X, Andrei A, Lundberg E, Jiang J, Armache KJ, Zhao Y, Schwabe JWR, Wu M, Garcia BA, Cole PA. A circular engineered sortase for interrogating histone H3 in chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612318. [PMID: 39372790 PMCID: PMC11451751 DOI: 10.1101/2024.09.10.612318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Reversible modification of the histone H3 N-terminal tail is critical in regulating chromatin structure, gene expression, and cell states, while its dysregulation contributes to disease pathogenesis. Understanding the crosstalk between H3 tail modifications in nucleosomes constitutes a central challenge in epigenetics. Here we describe an engineered sortase transpeptidase, cW11, that displays highly favorable properties for introducing scarless H3 tails onto nucleosomes. This approach significantly accelerates the production of both symmetrically and asymmetrically modified nucleosomes. We demonstrate the utility of asymmetrically modified nucleosomes produced in this way in dissecting the impact of multiple modifications on eraser enzyme processing and molecular recognition by a reader protein. Moreover, we show that cW11 sortase is very effective at cutting and tagging histone H3 tails from endogenous histones, facilitating multiplex "cut-and-paste" middle down proteomics with tandem mass tags. This cut-and- paste proteomics approach permits the quantitative analysis of histone H3 modification crosstalk after treatment with different histone deacetylase inhibitors. We propose that these chemoenzymatic tail isolation and modification strategies made possible with cW11 sortase will broadly power epigenetics discovery and therapeutic development.
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Affiliation(s)
- Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Emily Zahn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Congcong Lu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Maheeshi Yapa-Abeywardana
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Eunju Nam
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sarah Dubois-Coyne
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Pablo De Ioannes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, United States
| | - Xinlei Sheng
- The Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, United States
| | - Adelina Andrei
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Emily Lundberg
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jennifer Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, United States
| | - Yingming Zhao
- The Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, United States
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou 310030, China
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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10
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Guo J, Li S, Bai L, Zhao H, Shang W, Zhong Z, Maimaiti T, Gao X, Ji N, Chao Y, Li Z, Du D. Structural transition of GP64 triggered by a pH-sensitive multi-histidine switch. Nat Commun 2024; 15:7668. [PMID: 39227374 PMCID: PMC11372198 DOI: 10.1038/s41467-024-51799-4] [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: 04/15/2024] [Accepted: 08/16/2024] [Indexed: 09/05/2024] Open
Abstract
The fusion of viruses with cellular membranes is a critical step in the life cycle of enveloped viruses. This process is facilitated by viral fusion proteins, many of which are conformationally pH-sensitive. The specifics of how changes in pH initiate this fusion have remained largely elusive. This study presents the cryo-electron microscopy (cryo-EM) structures of a prototype class III fusion protein, GP64, in its prefusion and early intermediate states, revealing the structural intermediates accompanying the membrane fusion process. The structures identify the involvement of a pH-sensitive switch, comprising H23, H245, and H304, in sensing the low pH that triggers the initial step of membrane fusion. The pH sensing role of this switch is corroborated by assays of cell-cell syncytium formation and dual dye-labeling. The findings demonstrate that coordination between multiple histidine residues acts as a pH sensor and activator. The involvement of a multi-histidine switch in viral fusion is applicable to fusogens of human-infecting thogotoviruses and other viruses, which could lead to strategies for developing anti-viral therapies and vaccines.
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Affiliation(s)
- Jinliang Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shangrong Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lisha Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huimin Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenyu Shang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhaojun Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Xueyan Gao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ning Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanjie Chao
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Zhaofei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Dijun Du
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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11
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Chiu PL, Orjuela JD, de Groot BL, Aponte Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 2024; 12:RP90851. [PMID: 39222068 PMCID: PMC11368405 DOI: 10.7554/elife.90851] [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: 09/04/2024] Open
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
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Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Juan D Orjuela
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Biomedical Engineering Department, Universidad de los AndesBogotáColombia
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Camilo Aponte Santamaría
- Max Planck Tandem Group in Computational Biophysics, Universidad de los AndesBogotáColombia
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical StudiesHeidelbergGermany
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
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12
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Chong X, Leung H, Li Q, Yao J, Zhou N. Deep Spatio-Temporal Network for Low-SNR Cryo-EM Movie Frame Enhancement. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:1299-1310. [PMID: 38526906 DOI: 10.1109/tcbb.2024.3380410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Cryo-EM in single particle analysis is known to have low SNR and requires to utilize several frames of the same particle sample to restore one high-quality image for visualizing that particle. However, the low SNR of cryo-EM movie and motion caused by beam striking make the task very challenging. Video enhancement algorithms in computer vision shed new light on tackling such tasks by utilizing deep neural networks. However, they are designed for natural images with high SNR. Meanwhile, the lack of ground truth in cryo-EM movie seems to be one major limiting factor of the progress. Hence, we present a synthetic cryo-EM movie generation pipeline, which can produce realistic diverse cryo-EM movie datasets with low-SNR movie frames and multiple ground truth values. Then we propose a deep spatio-temporal network (DST-Net) for cryo-EM movie frame enhancement trained on our synthetic data. Spatial and temporal features are first extracted from each frame. Spatio-temporal fusion and high-resolution re-constructor are designed to obtain the enhanced output. For evaluation, we train our model on seven synthetic cryo-EM movie datasets and infer on real cryo-EM data. The experimental results show that DST-Net can achieve better enhancement performance both quantitatively and qualitatively compared with others.
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13
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Savva CG, Sobhy MA, De Biasio A, Hamdan SM. Structure of Aquifex aeolicus lumazine synthase by cryo-electron microscopy to 1.42 Å resolution. IUCRJ 2024; 11:723-729. [PMID: 38965901 PMCID: PMC11364023 DOI: 10.1107/s2052252524005530] [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: 04/02/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) has become an essential structural determination technique with recent hardware developments making it possible to reach atomic resolution, at which individual atoms, including hydrogen atoms, can be resolved. In this study, we used the enzyme involved in the penultimate step of riboflavin biosynthesis as a test specimen to benchmark a recently installed microscope and determine if other protein complexes could reach a resolution of 1.5 Å or better, which so far has only been achieved for the iron carrier ferritin. Using state-of-the-art microscope and detector hardware as well as the latest software techniques to overcome microscope and sample limitations, a 1.42 Å map of Aquifex aeolicus lumazine synthase (AaLS) was obtained from a 48 h microscope session. In addition to water molecules and ligands involved in the function of AaLS, we can observe positive density for ∼50% of the hydrogen atoms. A small improvement in the resolution was achieved by Ewald sphere correction which was expected to limit the resolution to ∼1.5 Å for a molecule of this diameter. Our study confirms that other protein complexes can be solved to near-atomic resolution. Future improvements in specimen preparation and protein complex stabilization may allow more flexible macromolecules to reach this level of resolution and should become a priority of study in the field.
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Affiliation(s)
- Christos G. Savva
- Biological and Environmental Science and EngineeringKing Abdullah University of Science and Technology4700 KAUSTThuwal23955Saudi Arabia
| | - Mohamed A. Sobhy
- Biological and Environmental Science and EngineeringKing Abdullah University of Science and Technology4700 KAUSTThuwal23955Saudi Arabia
| | - Alfredo De Biasio
- Biological and Environmental Science and EngineeringKing Abdullah University of Science and Technology4700 KAUSTThuwal23955Saudi Arabia
| | - Samir M. Hamdan
- Biological and Environmental Science and EngineeringKing Abdullah University of Science and Technology4700 KAUSTThuwal23955Saudi Arabia
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14
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Czarnik C, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. J Struct Biol 2024; 216:108108. [PMID: 38944401 DOI: 10.1016/j.jsb.2024.108108] [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: 02/14/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these energies, specifically a ∼ 4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope fitted with a non-standard SP-Twin lens. We also achieved a ∼ 3.2 Å resolution reconstruction of a 115 kDa asymmetric protein complex, proving Alpine's effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ∼ 3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hev Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States.
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States.
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. SCIENCE ADVANCES 2024; 10:eadp0975. [PMID: 39196936 PMCID: PMC11352909 DOI: 10.1126/sciadv.adp0975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
During tumor development, promoter CpG islands that are normally silenced by Polycomb repressive complexes (PRCs) become DNA-hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) [DNMT(s)] catalyze CpG methylation at PRC-regulated regions remains unclear. Here, we report a cryo-electron microscopy structure of the DNMT3A long isoform (DNMT3A1) amino-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine-119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 amino terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Further, aberrant redistribution of DNMT3A1 to Polycomb target genes recapitulates the cancer-associated DNA hypermethylation signature and inhibits their transcriptional activation during cell differentiation. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for mediating promoter CpG island DNA hypermethylation, a major molecular hallmark of cancer.
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Affiliation(s)
- Kristjan H. Gretarsson
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Daniel N. Weinberg
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | - Varun Sahu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Xinjing Xu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Natalie Lipieta
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel Flashner
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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16
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Liu Y, Li Y, Wu J, Zhang X, Nan P, Wang P, Sun D, Wang Y, Zhu J, Ge B, Francisco JS. Direct Visualization of Molecular Stacking in Quasi-2D Hexagonal Ice. J Am Chem Soc 2024; 146:23598-23605. [PMID: 39165248 DOI: 10.1021/jacs.4c08313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Understanding ice nucleation and growth is of great interest to researchers due to its importance in the biological, cryopreservation, and environmental fields. However, microstructural investigations of ice on the molecular scale are still lacking. In this paper, a simple method is proposed to prepare quasi-2-dimensional ice Ih films, which have been characterized via cryogenic transmission electron microscope. The intersecting stacking faults of basal (BSF) and prismatic (PSF) types have been directly visualized and resolved with a notable first-time report of PSF in ice Ih. Moreover, the possible growth pathways of BSF, namely, the Ic phase, were elucidated by the theoretical calculations and the chair conformation of H2O molecules. This study offers valuable insights that can enhance researchers' understanding of the growth kinetics of crystalline ice.
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Affiliation(s)
- Yangrui Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Leibniz International Joint Research Center of Materials Sciences of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yun Li
- Shenzhen Key Laboratory of Natural Gas Hydrate, Department of Physics & Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Jing Wu
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xinyu Zhang
- Shenzhen Key Laboratory of Natural Gas Hydrate, Department of Physics & Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
| | - Pengfei Nan
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Leibniz International Joint Research Center of Materials Sciences of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Pengfei Wang
- Shenzhen Key Laboratory of Natural Gas Hydrate, Department of Physics & Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Dapeng Sun
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yumei Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jinlong Zhu
- Shenzhen Key Laboratory of Natural Gas Hydrate, Department of Physics & Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen 518055, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
- Quantum Science Center of Guangdong-Hong Kong-Macao Greater Bay Area (Guangdong), Shenzhen 518045, China
| | - Binghui Ge
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Leibniz International Joint Research Center of Materials Sciences of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Joseph S Francisco
- Department of Earth and Environmental Science, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6316, United States
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17
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Zhou P, Bibek GC, Hu B, Wu C. Development of SacB-based Counterselection for Efficient Allelic Exchange in Fusobacterium nucleatum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.16.608263. [PMID: 39229080 PMCID: PMC11370447 DOI: 10.1101/2024.08.16.608263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Fusobacterium nucleatum , prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare defined allelic exchange mutants. The sacB gene from Bacillus subtilis , encoding levansucrase, is a widely used counterselective marker partly due to the easy availability of sucrose. Yet, its potential application in F. nucleatum genetic study remains untested. We demonstrated that F. nucleatum cells expressing sacB in either a shuttle or suicide plasmid exhibit a lethal sensitivity to supplemental sucrose. Utilizing sucrose counterselection, we created an in-frame deletion of the F. nucleatum tonB gene, a critical gene for energy-dependent transport processes in Gram-negative bacteria, and a precise knockin of the luciferase gene immediately following the stop codon of the hslO gene, the last gene of a five-gene operon possible related to the natural competence of F. nucleatum . Post counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. This sacB -based counterselection technique provides a reliable method for isolating unmarked gene mutations in wild-type F. nucleatum , enriching the toolkit for fusobacterial research. IMPORTANCE Investigations into Fusobacterium nucleatum 's role in related diseases significantly benefit from the strategies of creating unmarked gene mutations, which hinge on using a counterselective marker. Previously, the galk -based allelic exchange method, while effective, faced an inherent limitation - the need for a modified host. This study aims to surmount this limitation by substituting galK with sacB for gene modification in F. nucleatum . Our application of the sacB -based methodology successfully yielded a tonB in-frame deletion mutant and a luciferase gene knockin at the precise chromosomal location in the wild-type background. The new method augments the existing toolkit for F. nucleatum research and has far-reaching implications due to the easy accessibility to the counterselection compound sucrose. We anticipate its broader adoption in further exploration, thereby reinforcing its critical role in propelling our understanding of F. nucleatum .
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Zhang H, Zhou C, Mohammad Z, Zhao J. Structural basis of human 20S proteasome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607236. [PMID: 39211201 PMCID: PMC11361150 DOI: 10.1101/2024.08.08.607236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. To understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observed an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
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19
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Egelman EH. The myth of high-resolution liquid phase biological electron microscopy. Protein Sci 2024; 33:e5125. [PMID: 39037286 PMCID: PMC11261809 DOI: 10.1002/pro.5125] [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: 06/18/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Cryo-electron microscopy (cryo-EM) has transformed structural biology over the past 12 years, with it now being routine rather than exceptional to reach a near-atomic level of resolution for proteins and macromolecular complexes. Samples are immobilized by vitrification and this sample can be maintained at liquid nitrogen temperatures in the vacuum of the electron microscope with negligible sublimation. Due to the low electron doses needed to avoid radiation damage, averaging over tens of thousands to hundreds of thousands of particle images is used to achieve a high signal-to-noise ratio. An alternative approach has been proposed where samples are at room temperature in the liquid state, maintained in the vacuum of the electron microscope by thin film enclosures that are relatively transparent to electrons while preventing evaporation of the liquid. A paper has argued that using this liquid-phase approach, higher resolution (3.2 Å) can be achieved than using cryo-EM (3.4 Å) when imaging and reconstructing adeno-associated virus particles. I show here that these assertions are untrue, and that basic principles in mathematics and physics would need to be violated to achieve the stated resolution in the liquid state. Thus, high resolution liquid phase EM of macromolecules remains science fiction.
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Affiliation(s)
- Edward H. Egelman
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
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20
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Aidukas T, Phillips NW, Diaz A, Poghosyan E, Müller E, Levi AFJ, Aeppli G, Guizar-Sicairos M, Holler M. High-performance 4-nm-resolution X-ray tomography using burst ptychography. Nature 2024; 632:81-88. [PMID: 39085541 DOI: 10.1038/s41586-024-07615-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 05/28/2024] [Indexed: 08/02/2024]
Abstract
Advances in science, medicine and engineering rely on breakthroughs in imaging, particularly for obtaining multiscale, three-dimensional information from functional systems such as integrated circuits or mammalian brains. Achieving this goal often requires combining electron- and photon-based approaches. Whereas electron microscopy provides nanometre resolution through serial, destructive imaging of surface layers1, ptychographic X-ray computed tomography2 offers non-destructive imaging and has recently achieved resolutions down to seven nanometres for a small volume3. Here we implement burst ptychography, which overcomes experimental instabilities and enables much higher performance, with 4-nanometre resolution at a 170-times faster acquisition rate, namely, 14,000 resolution elements per second. Another key innovation is tomographic back-propagation reconstruction4, allowing us to image samples up to ten times larger than the conventional depth of field. By combining the two innovations, we successfully imaged a state-of-the-art (seven-nanometre node) commercial integrated circuit, featuring nanostructures made of low- and high-density materials such as silicon and metals, which offer good radiation stability and contrast at the selected X-ray wavelength. These capabilities enabled a detailed study of the chip's design and manufacturing, down to the level of individual transistors. We anticipate that the combination of nanometre resolution and higher X-ray flux at next-generation X-ray sources will have a revolutionary impact in fields ranging from electronics to electrochemistry and neuroscience.
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Affiliation(s)
| | - Nicholas W Phillips
- Paul Scherrer Institute, Villigen, Switzerland
- Mineral Resources, CSIRO, Clayton, Victoria, Australia
| | - Ana Diaz
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | - A F J Levi
- Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Gabriel Aeppli
- Paul Scherrer Institute, Villigen, Switzerland
- Department of Physics, Eidgenössische Technische Hochschule Zürich (ETH Zürich), Zurich, Switzerland
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Quantum Center, Eidgenössische Technische Hochschule Zürich (ETH Zürich), Zurich, Switzerland
| | - Manuel Guizar-Sicairos
- Paul Scherrer Institute, Villigen, Switzerland
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Hirst IJ, Thomas WJ, Davies RA, Muench SP. CryoEM grid preparation: a closer look at advancements and impact of preparation mode and new approaches. Biochem Soc Trans 2024; 52:1529-1537. [PMID: 38864435 PMCID: PMC11346429 DOI: 10.1042/bst20231553] [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: 04/25/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
Sample preparation can present a significant hurdle within single particle cryo-electron microscopy (cryoEM), resulting in issues with reproducibility, data quality or an inability to visualise the sample. There are several factors which can influence this, including sample or buffer composition, grid type, route of sample preparation and interactions with the air-water interface (AWI). Here, we review some of the current routes for sample preparation and the associated challenges. We discuss a range of approaches for overcoming these challenges, such as minimising the grid preparation time, surfactants, grid type and biochemical approaches such as nanomagnetic beads. Finally, we discuss how a set of commercially available protein samples may serve as a benchmark suite for future technologies. This provides a route to compare techniques' abilities not just to generate high-resolution structures but also to overcome the challenges traditionally associated with cryoEM. As the field continues to produce new approaches to sample preparation and we start to better understand the underlying principles behind the behaviour of proteins within a thin film and in response to different environments, especially grid composition, it is hoped that more universal solutions can be provided that make the intractable systems tractable, improve resolution and, importantly, speed up data collection and reduce the currently required dataset sizes.
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Affiliation(s)
- Isobel J. Hirst
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - William J.R. Thomas
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Rhiannon A. Davies
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P. Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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22
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Ai H, He Z, Deng Z, Chu GC, Shi Q, Tong Z, Li JB, Pan M, Liu L. Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. Nat Struct Mol Biol 2024:10.1038/s41594-024-01342-2. [PMID: 38918638 DOI: 10.1038/s41594-024-01342-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in transcription repression, is dynamically regulated by the opposing activities of Polycomb repressive complex 1 (PRC1) and nucleosome deubiquitinases including the primary human USP16 and Polycomb repressive deubiquitinase (PR-DUB) complex. Recently, the catalytic mechanism for the multi-subunit PR-DUB complex has been described, but how the single-subunit USP16 recognizes the H2AK119Ub nucleosome and cleaves the ubiquitin (Ub) remains unknown. Here we report the cryo-EM structure of USP16-H2AK119Ub nucleosome complex, which unveils a fundamentally distinct mode of H2AK119Ub deubiquitination compared to PR-DUB, encompassing the nucleosome recognition pattern independent of the H2A-H2B acidic patch and the conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail. Our work highlights the mechanism diversity of H2AK119Ub deubiquitination and provides a structural framework for understanding the disease-causing mutations of USP16.
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Affiliation(s)
- Huasong Ai
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China
| | - Zaozhen He
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Guo-Chao Chu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Qiang Shi
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zebin Tong
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Man Pan
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China.
| | - Lei Liu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
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23
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Lin HH, Wang CH, Huang SH, Lin SY, Kato T, Namba K, Hosogi N, Song C, Murata K, Yen CH, Hsu TL, Wong CH, Wu YM, Tu IP, Chang WH. Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å. Sci Rep 2024; 14:14079. [PMID: 38890341 PMCID: PMC11189423 DOI: 10.1038/s41598-024-62045-8] [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: 06/28/2023] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of small domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating anti-tumor toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.
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Affiliation(s)
- Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Academia Sinica Cryo-EM Facility, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsin Huang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Sung-Yao Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
- Institute of Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
| | - Naoki Hosogi
- JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | | | - Tsui-Ling Hsu
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Huey Wong
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Min Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Cryo-EM Facility, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
- Genomic Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Physics, Academia Sinica, Taipei, Taiwan.
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24
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Eibauer M, Weber MS, Kronenberg-Tenga R, Beales CT, Boujemaa-Paterski R, Turgay Y, Sivagurunathan S, Kraxner J, Köster S, Goldman RD, Medalia O. Vimentin filaments integrate low-complexity domains in a complex helical structure. Nat Struct Mol Biol 2024; 31:939-949. [PMID: 38632361 PMCID: PMC11189308 DOI: 10.1038/s41594-024-01261-2] [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: 05/08/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.
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Affiliation(s)
- Matthias Eibauer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Charlie T Beales
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Yagmur Turgay
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Suganya Sivagurunathan
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Kraxner
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- MDC Berlin-Buch, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Robert D Goldman
- Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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25
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Liu N, Wang HW. Graphene in cryo-EM specimen optimization. Curr Opin Struct Biol 2024; 86:102823. [PMID: 38688075 DOI: 10.1016/j.sbi.2024.102823] [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: 02/03/2024] [Revised: 03/16/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Abstract
Specimen preparation is a critical but challenging step in high-resolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past decade, graphene has gained much recognition as the supporting substrate to optimize cryo-EM specimen preparation. It improves macromolecule embedding in ice, reduces beam-induced motion, while imposing negligible background noise. Various types of graphene-coated cryo-EM grids were implemented to improve the robustness and efficiency of specimen preparation. Graphene functionalization by different means has been proved specifically useful in addressing challenges related to the air-water interface (AWI), such as preferential orientation and sample denaturation. Graphene sandwich specimen preparation sets a new direction to explore in cryo-EM analysis of biological specimens. In this review, we discuss the current challenges and future prospects of graphene application in cryo-EM analysis of macromolecules.
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Affiliation(s)
- Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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26
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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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27
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Andersen JF, Lei H, Strayer EC, Pham V, Ribeiro JMC. Mechanism of complement inhibition by a mosquito protein revealed through cryo-EM. Commun Biol 2024; 7:649. [PMID: 38802531 PMCID: PMC11130238 DOI: 10.1038/s42003-024-06351-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: 11/06/2023] [Accepted: 05/17/2024] [Indexed: 05/29/2024] Open
Abstract
Salivary complement inhibitors occur in many of the blood feeding arthropod species responsible for transmission of pathogens. During feeding, these inhibitors prevent the production of proinflammatory anaphylatoxins, which may interfere with feeding, and limit formation of the membrane attack complex which could damage arthropod gut tissues. Salivary inhibitors are, in many cases, novel proteins which may be pharmaceutically useful or display unusual mechanisms that could be exploited pharmaceutically. Albicin is a potent inhibitor of the alternative pathway of complement from the saliva of the malaria transmitting mosquito, Anopheles albimanus. Here we describe the cryo-EM structure of albicin bound to C3bBb, the alternative C3 convertase, a proteolytic complex that is responsible for cleavage of C3 and amplification of the complement response. Albicin is shown to induce dimerization of C3bBb, in a manner similar to the bacterial inhibitor SCIN, to form an inactive complex unable to bind the substrate C3. Size exclusion chromatography and structures determined after 30 minutes of incubation of C3b, factor B (FB), factor D (FD) and albicin indicate that FBb dissociates from the inhibited dimeric complex leaving a C3b-albicin dimeric complex which apparently decays more slowly.
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Affiliation(s)
- John F Andersen
- NIH-NIAID, Laboratory of Malaria and Vector Research, Rockville, MD, USA.
| | - Haotian Lei
- NIH-NIAID, Research Technologies Branch, Bethesda, MD, USA
| | - Ethan C Strayer
- NIH-NIAID, Laboratory of Malaria and Vector Research, Rockville, MD, USA
- Biological and Biomedical Sciences Program, Yale University, New Haven, CT, USA
| | - Van Pham
- NIH-NIAID, Laboratory of Malaria and Vector Research, Rockville, MD, USA
| | - José M C Ribeiro
- NIH-NIAID, Laboratory of Malaria and Vector Research, Rockville, MD, USA
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28
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Schmiege P, Donnelly L, Elghobashi-Meinhardt N, Lee CH, Li X. Structure and inhibition of the human lysosomal transporter Sialin. Nat Commun 2024; 15:4386. [PMID: 38782953 PMCID: PMC11116495 DOI: 10.1038/s41467-024-48535-3] [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: 11/29/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Sialin, a member of the solute carrier 17 (SLC17) transporter family, is unique in its ability to transport not only sialic acid using a pH-driven mechanism, but also transport mono and diacidic neurotransmitters, such as glutamate and N-acetylaspartylglutamate (NAAG), into synaptic vesicles via a membrane potential-driven mechanism. While most transporters utilize one of these mechanisms, the structural basis of how Sialin transports substrates using both remains unclear. Here, we present the cryogenic electron-microscopy structures of human Sialin: apo cytosol-open, apo lumen-open, NAAG-bound, and inhibitor-bound. Our structures show that a positively charged cytosol-open vestibule accommodates either NAAG or the Sialin inhibitor Fmoc-Leu-OH, while its luminal cavity potentially binds sialic acid. Moreover, functional analyses along with molecular dynamics simulations identify key residues in binding sialic acid and NAAG. Thus, our findings uncover the essential conformational states in NAAG and sialic acid transport, demonstrating a working model of SLC17 transporters.
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Affiliation(s)
- Philip Schmiege
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Linda Donnelly
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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29
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Chiu PL, Orjuela JD, de Groot BL, Aponte-Santamaría C, Walz T. Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.16.540959. [PMID: 37292626 PMCID: PMC10245776 DOI: 10.1101/2023.05.16.540959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.
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30
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Hu H, Yang R, Zeng Z. Advances in Electrochemical Liquid-Phase Transmission Electron Microscopy for Visualizing Rechargeable Battery Reactions. ACS NANO 2024; 18:12598-12609. [PMID: 38723158 DOI: 10.1021/acsnano.4c03319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
This review presents an overview of the application of electrochemical liquid-phase transmission electron microscopy (ELP-TEM) in visualizing rechargeable battery reactions. The technique provides atomic-scale spatial resolution and real-time temporal resolution, enabling direct observation and analysis of battery materials and processes under realistic working conditions. The review highlights key findings and insights obtained by ELP-TEM on the electrochemical reaction mechanisms and discusses the current limitations and future prospects of ELP-TEM, including improvements in spatial and temporal resolution and the expansion of the scope of materials and systems that can be studied. Furthermore, the review underscores the critical role of ELP-TEM in understanding and optimizing the design and fabrication of high-performance, long-lasting rechargeable batteries.
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Affiliation(s)
- Honglu Hu
- Department of Materials Science and Engineering and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, People's Republic of China
| | - Ruijie Yang
- Department of Materials Science and Engineering and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, People's Republic of China
- Department of Chemical and Petroleum Engineering, University of Calgary, 2500 University Drive, NW, Calgary, Alberta T2N 1N4, Canada
| | - Zhiyuan Zeng
- Department of Materials Science and Engineering and State Key Laboratory of Marine Pollution, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, People's Republic of China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, People's Republic of China
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31
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Unwin N. Influence of lipid bilayer on the structure of the muscle-type nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A 2024; 121:e2319913121. [PMID: 38683987 PMCID: PMC11087746 DOI: 10.1073/pnas.2319913121] [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: 11/14/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
The muscle-type nicotinic acetylcholine receptor is a transmitter-gated ion channel residing in the plasma membrane of electrocytes and striated muscle cells. It is present predominantly at synaptic junctions, where it effects rapid depolarization of the postsynaptic membrane in response to acetylcholine released into the synaptic cleft. Previously, cryo-EM of intact membrane from Torpedo revealed that the lipid bilayer surrounding the junctional receptor has a uniquely asymmetric and ordered structure, due to a high concentration of cholesterol. It is now shown that this special lipid environment influences the transmembrane (TM) folding of the protein. All five submembrane MX helices of the membrane-intact junctional receptor align parallel to the surface of the cholesterol-ordered lipids in the inner leaflet of the bilayer; also, the TM helices in the outer leaflet are splayed apart. However in the structure obtained from the same protein after extraction and incorporation in nanodiscs, the MX helices do not align to a planar surface, and the TM helices arrange compactly in the outer leaflet. Realignment of the MX helices of the nanodisc-solved structure to a planar surface converts their adjoining TM helices into an obligatory splayed configuration, characteristic of the junctional receptor. Thus, the form of the receptor sustained by the special lipid environment of the synaptic junction is the one that mediates fast synaptic transmission; whereas, the nanodisc-embedded protein may be like the extrajunctional form, existing in a disordered lipid environment.
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Affiliation(s)
- Nigel Unwin
- Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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32
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Nelson N. Investigating the Balance between Structural Conservation and Functional Flexibility in Photosystem I. Int J Mol Sci 2024; 25:5073. [PMID: 38791114 PMCID: PMC11121529 DOI: 10.3390/ijms25105073] [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: 02/27/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Photosynthesis, as the primary source of energy for all life forms, plays a crucial role in maintaining the global balance of energy, entropy, and enthalpy in living organisms. Among its various building blocks, photosystem I (PSI) is responsible for light-driven electron transfer, crucial for generating cellular reducing power. PSI acts as a light-driven plastocyanin-ferredoxin oxidoreductase and is situated in the thylakoid membranes of cyanobacteria and the chloroplasts of eukaryotic photosynthetic organisms. Comprehending the structure and function of the photosynthetic machinery is essential for understanding its mode of action. New insights are offered into the structure and function of PSI and its associated light-harvesting proteins, with a specific focus on the remarkable structural conservation of the core complex and high plasticity of the peripheral light-harvesting complexes.
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Affiliation(s)
- Nathan Nelson
- Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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33
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Liu J, Gore S, Heyer WD. Local structural dynamics of Rad51 protomers revealed by cryo-electron microscopy of Rad51-ssDNA filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592824. [PMID: 38766236 PMCID: PMC11100689 DOI: 10.1101/2024.05.06.592824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Homologous recombination (HR) is a high-fidelity repair mechanism for double-strand breaks. Rad51 is the key enzyme that forms filaments on single-stranded DNA (ssDNA) to catalyze homology search and DNA strand exchange in recombinational DNA repair. In this study, we employed single-particle cryo-electron microscopy (cryo-EM) to ascertain the density map of the budding yeast Rad51-ssDNA filament bound to ADP-AlF 3 , achieving a resolution of 2.35 Å without imposing helical symmetry. The model assigned 6 Rad51 protomers, 24 nt of DNA, and 6 bound ADP-AlF 3 . It shows 6-fold symmetry implying monomeric building blocks, unlike the structure of the Rad51-I345T mutant filament with three-fold symmetry implying dimeric building blocks, for which the structural comparisons provide a satisfying mechanistic explanation. This image analysis enables comprehensive comparisons of individual Rad51 protomers within the filament and reveals local conformational movements of amino acid side chains. Notably, Arg293 in Loop1 adopts multiple conformations to facilitate Leu296 and Val331 in separating and twisting the DNA triplets. We also analyzed the predicted structures of yeast Rad51-K342E and two tumor-derived human RAD51 variants, RAD51-Q268P and RAD51-Q272L, using the Rad51-ssDNA structure from this study as a reference.
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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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Malatesta M, Fornasier E, Di Salvo ML, Tramonti A, Zangelmi E, Peracchi A, Secchi A, Polverini E, Giachin G, Battistutta R, Contestabile R, Percudani R. One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse. Nat Commun 2024; 15:3199. [PMID: 38615009 PMCID: PMC11016064 DOI: 10.1038/s41467-024-47466-3] [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: 08/25/2023] [Accepted: 03/26/2024] [Indexed: 04/15/2024] Open
Abstract
The increasing availability of experimental and computational protein structures entices their use for function prediction. Here we develop an automated procedure to identify enzymes involved in metabolic reactions by assessing substrate conformations docked to a library of protein structures. By screening AlphaFold-modeled vitamin B6-dependent enzymes, we find that a metric based on catalytically favorable conformations at the enzyme active site performs best (AUROC Score=0.84) in identifying genes associated with known reactions. Applying this procedure, we identify the mammalian gene encoding hydroxytrimethyllysine aldolase (HTMLA), the second enzyme of carnitine biosynthesis. Upon experimental validation, we find that the top-ranked candidates, serine hydroxymethyl transferase (SHMT) 1 and 2, catalyze the HTMLA reaction. However, a mouse protein absent in humans (threonine aldolase; Tha1) catalyzes the reaction more efficiently. Tha1 did not rank highest based on the AlphaFold model, but its rank improved to second place using the experimental crystal structure we determined at 2.26 Å resolution. Our findings suggest that humans have lost a gene involved in carnitine biosynthesis, with HTMLA activity of SHMT partially compensating for its function.
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Affiliation(s)
- Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Martino Luigi Di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Angela Tramonti
- Institute of Molecular Biology and Pathology, Italian National Research Council, Rome, Italy
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Eugenia Polverini
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Gabriele Giachin
- Department of Chemical Sciences, University of Padua, Padova, Italy
| | | | - Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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36
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Sharma R, Yang WCD. Perspective and prospects of in situ transmission/scanning transmission electron microscopy. Microscopy (Oxf) 2024; 73:79-100. [PMID: 38006307 DOI: 10.1093/jmicro/dfad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/01/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023] Open
Abstract
In situ transmission/scanning transmission electron microscopy (TEM/STEM) measurements have taken a central stage for establishing structure-chemistry-property relationship over the past couple of decades. The challenges for realizing 'a lab-in-gap', i.e. gap between the objective lens pole pieces, or 'a lab-on-chip', to be used to carry out experiments are being met through continuous instrumental developments. Commercially available TEM columns and sample holder, that have been modified for in situ experimentation, have contributed to uncover structural and chemical changes occurring in the sample when subjected to external stimulus such as temperature, pressure, radiation (photon, ions and electrons), environment (gas, liquid and magnetic or electrical field) or a combination thereof. Whereas atomic resolution images and spectroscopy data are being collected routinely using TEM/STEM, temporal resolution is limited to millisecond. On the other hand, better than femtosecond temporal resolution can be achieved using an ultrafast electron microscopy or dynamic TEM, but the spatial resolution is limited to sub-nanometers. In either case, in situ experiments generate large datasets that need to be transferred, stored and analyzed. The advent of artificial intelligence, especially machine learning platforms, is proving crucial to deal with this big data problem. Further developments are still needed in order to fully exploit our capability to understand, measure and control chemical and/or physical processes. We present the current state of instrumental and computational capabilities and discuss future possibilities.
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Affiliation(s)
- Renu Sharma
- Materials Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Wei-Chang David Yang
- Materials Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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37
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Zhou RQ, Jiang YL, Li H, Hou P, Kong WW, Deng JX, Chen Y, Zhou CZ, Zeng Q. Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. NATURE PLANTS 2024; 10:661-672. [PMID: 38589484 DOI: 10.1038/s41477-024-01660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.
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Affiliation(s)
- Rui-Qian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jia-Xin Deng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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38
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585588. [PMID: 38562823 PMCID: PMC10983913 DOI: 10.1101/2024.03.18.585588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of the DNMT3A long isoform (DNMT3A1) N-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine 119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional activation during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.
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39
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Durieux Trouilleton Q, Housset D, Tarillon P, Arragain B, Malet H. Structural characterization of the oligomerization of full-length Hantaan virus polymerase into symmetric dimers and hexamers. Nat Commun 2024; 15:2256. [PMID: 38480734 PMCID: PMC10937945 DOI: 10.1038/s41467-024-46601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
Hantaan virus is a dangerous human pathogen whose segmented negative-stranded RNA genome is replicated and transcribed by a virally-encoded multi-functional polymerase. Here we describe the complete cryo-electron microscopy structure of Hantaan virus polymerase in several oligomeric forms. Apo polymerase protomers can adopt two drastically different conformations, which assemble into two distinct symmetric homodimers, that can themselves gather to form hexamers. Polymerase dimerization induces the stabilization of most polymerase domains, including the C-terminal domain that contributes the most to dimer's interface, along with a lariat region that participates to the polymerase steadying. Binding to viral RNA induces significant conformational changes resulting in symmetric oligomer disruption and polymerase activation, suggesting the possible involvement of apo multimers as protecting systems that would stabilize the otherwise flexible C-terminal domains. Overall, these results provide insights into the multimerization capability of Hantavirus polymerase and may help to define antiviral compounds to counteract these life-threatening viruses.
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Affiliation(s)
| | - Dominique Housset
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Paco Tarillon
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France
| | - Benoît Arragain
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
- European Molecular Biology Laboratory (EMBL), Grenoble, France.
| | - Hélène Malet
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.
- Institut Universitaire de France (IUF), Paris, France.
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40
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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41
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Finci LI, Chakrabarti M, Gulten G, Finney J, Grose C, Fox T, Yang R, Nissley DV, McCormick F, Esposito D, Balius TE, Simanshu DK. Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements. Commun Biol 2024; 7:260. [PMID: 38431713 PMCID: PMC10908828 DOI: 10.1038/s42003-024-05959-3] [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: 02/22/2024] [Indexed: 03/05/2024] Open
Abstract
RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1's unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.
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Affiliation(s)
- Lorenzo I Finci
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mayukh Chakrabarti
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gulcin Gulten
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph Finney
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Carissa Grose
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tara Fox
- National Cryo-EM Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Renbin Yang
- Center for Molecular Microscopy, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Trent E Balius
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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42
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DeRonja J, Nowell M, Wright S, Kacher J. Generational assessment of EBSD detectors for cross-correlation-based analysis: From scintillators to direct detection. Ultramicroscopy 2024; 257:113913. [PMID: 38141535 DOI: 10.1016/j.ultramic.2023.113913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Introduced over ten years ago, cross-correlation-based electron backscatter diffraction has enabled high precision measurements of crystallographic rotations and elastic strain gradients at high spatial resolution. Since that time, there have been remarkable improvements in electron detector technology, including the advent of ultra-high speed detectors and the commercialization of direct detectors. In this study, we assess the efficacy of multiple generations of electron detectors for cross-correlation-based analysis using a single crystal Si sample as a reference. We show that, while improvements in precision are modest, there have been significant gains in the rate at which high-quality diffraction patterns can be collected. This has important implications in the size of datasets that can be collected and reduces the impact of drift and sample contamination.
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Affiliation(s)
| | | | | | - Josh Kacher
- Georgia Institute of Technology, Atlanta, GA 30332, United States.
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43
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Collier CP, Bolmatov D, Elkins JG, Katsaras J. Nanoscopic lipid domains determined by microscopy and neutron scattering. Methods 2024; 223:127-135. [PMID: 38331125 DOI: 10.1016/j.ymeth.2024.01.020] [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: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.
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Affiliation(s)
- Charles P Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Neutron Scattering Division, Oak Ridge National Laboratorry, Oak Ridege, TN, USA
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44
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Zhang Z, Moye AR, He F, Chen M, Agosto MA, Wensel TG. Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography. Life Sci Alliance 2024; 7:e202302409. [PMID: 38182160 PMCID: PMC10770417 DOI: 10.26508/lsa.202302409] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ciliopathies in humans. Key to their functions are structures at their base: the basal body, the transition zone, the "Y-shaped links," and the "ciliary necklace." We have used cryo-electron tomography with subtomogram averaging and conventional transmission electron microscopy to elucidate the structures associated with the basal region of the "connecting cilia" of rod outer segments in mouse retina. The longitudinal variations in microtubule (MT) structures and the lumenal scaffold complexes connecting them have been determined, as well as membrane-associated transition zone structures: Y-shaped links connecting MT to the membrane, and ciliary beads connected to them that protrude from the cell surface and form a necklace-like structure. These results represent a clearer structural scaffold onto which molecules identified by genetics, proteomics, and superresolution fluorescence can be placed in our emerging model of photoreceptor sensory cilia.
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Affiliation(s)
- Zhixian Zhang
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Abigail R Moye
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmic Genetics, Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Feng He
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Muyuan Chen
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Melina A Agosto
- Department of Physiology and Biophysics and Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Canada
| | - Theodore G Wensel
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
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45
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Korir PK, Iudin A, Somasundharam S, Weyand S, Salih O, Hartley M, Sarkans U, Patwardhan A, Kleywegt GJ. Ten recommendations for organising bioimaging data for archival. F1000Res 2024; 12:ELIXIR-1391. [PMID: 38486614 PMCID: PMC10938051 DOI: 10.12688/f1000research.129720.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Organised data is easy to use but the rapid developments in the field of bioimaging, with improvements in instrumentation, detectors, software and experimental techniques, have resulted in an explosion of the volumes of data being generated, making well-organised data an elusive goal. This guide offers a handful of recommendations for bioimage depositors, analysts and microscope and software developers, whose implementation would contribute towards better organised data in preparation for archival. Based on our experience archiving large image datasets in EMPIAR, the BioImage Archive and BioStudies, we propose a number of strategies that we believe would improve the usability (clarity, orderliness, learnability, navigability, self-documentation, coherence and consistency of identifiers, accessibility, succinctness) of future data depositions more useful to the bioimaging community (data authors and analysts, researchers, clinicians, funders, collaborators, industry partners, hardware/software producers, journals, archive developers as well as interested but non-specialist users of bioimaging data). The recommendations that may also find use in other data-intensive disciplines. To facilitate the process of analysing data organisation, we present bandbox, a Python package that provides users with an assessment of their data by flagging potential issues, such as redundant directories or invalid characters in file or folder names, that should be addressed before archival. We offer these recommendations as a starting point and hope to engender more substantial conversations across and between the various data-rich communities.
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Affiliation(s)
- Paul K. Korir
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Andrii Iudin
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | - Simone Weyand
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Osman Salih
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Matthew Hartley
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Ugis Sarkans
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Ardan Patwardhan
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
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46
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Gopal N, Leitz J, Wang C, Esquivies L, Pfuetzner RA, Brunger AT. A new method for isolation and purification of fusion-competent inhibitory synaptic vesicles. Curr Res Physiol 2024; 7:100121. [PMID: 38572021 PMCID: PMC10990708 DOI: 10.1016/j.crphys.2024.100121] [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: 10/13/2023] [Revised: 01/18/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to isolate and purify GABA synaptic vesicles from mouse brains. GABA synaptic vesicles were immunoisolated from mouse brain tissue using an engineered fragment antigen-binding region (Fab) against the vesicular GABA transporter (vGAT) and purified. Western blot analysis confirmed that the GABA synaptic vesicles were specifically enriched for vGAT and largely depleted of contaminants from other synaptic vesicle types, such as vesicular glutamate transporter (vGLUT1), and other cellular organelles. This degree of purity was achieved despite the relatively low abundance of vGAT vesicles compared to the total synaptic vesicle pool in mammalian brains. Cryo-electron microscopy images of these isolated GABA synaptic vesicles revealed intact morphology with circular shape and protruding proteinaceous densities. The GABA synaptic vesicles are functional, as assessed by a hybrid (ex vivo/in vitro) vesicle fusion assay, and they undergo synchronized fusion with synthetic plasma membrane mimic vesicles in response to Ca2+-triggering, but, as a negative control, not to Mg2+-triggering. Our immunoisolation method could also be applied to other types of vesicles.
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Affiliation(s)
- Nisha Gopal
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
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47
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580363. [PMID: 38405886 PMCID: PMC10888765 DOI: 10.1101/2024.02.14.580363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these voltages, specifically a ~4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope. We also achieved a ~3.2 Å resolution reconstruction for a 115 kDa asymmetric protein complex, proving its effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ~3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, possibly bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hevatib Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
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48
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Xu J, Gao X, Zheng L, Jia X, Xu K, Ma Y, Wei X, Liu N, Peng H, Wang HW. Graphene sandwich-based biological specimen preparation for cryo-EM analysis. Proc Natl Acad Sci U S A 2024; 121:e2309384121. [PMID: 38252835 PMCID: PMC10835136 DOI: 10.1073/pnas.2309384121] [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: 06/11/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
High-quality specimen preparation plays a crucial role in cryo-electron microscopy (cryo-EM) structural analysis. In this study, we have developed a reliable and convenient technique called the graphene sandwich method for preparing cryo-EM specimens. This method involves using two layers of graphene films that enclose macromolecules on both sides, allowing for an appropriate ice thickness for cryo-EM analysis. The graphene sandwich helps to mitigate beam-induced charging effect and reduce particle motion compared to specimens prepared using the traditional method with graphene support on only one side, therefore improving the cryo-EM data quality. These advancements may open new opportunities to expand the use of graphene in the field of biological electron microscopy.
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Affiliation(s)
- Jie Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Xiaoyin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Liming Zheng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Xia Jia
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Kui Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Yuwei Ma
- State Key Laboratory for Turbulence and Complex System, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing100871, China
| | - Xiaoding Wei
- State Key Laboratory for Turbulence and Complex System, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing100871, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Hailin Peng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
- Beijing Graphene Institute, Beijing100095, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
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49
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Liu J, Lu Y, Zhu L. A kinetic model for solving a combination optimization problem in ab-initio Cryo-EM 3D reconstruction. Brief Bioinform 2024; 25:bbad473. [PMID: 38261343 PMCID: PMC10805181 DOI: 10.1093/bib/bbad473] [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: 07/13/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Cryo-Electron Microscopy (cryo-EM) is a widely used and effective method for determining the three-dimensional (3D) structure of biological molecules. For ab-initio Cryo-EM 3D reconstruction using single particle analysis (SPA), estimating the projection direction of the projection image is a crucial step. However, the existing SPA methods based on common lines are sensitive to noise. The error in common line detection will lead to a poor estimation of the projection directions and thus may greatly affect the final reconstruction results. To improve the reconstruction results, multiple candidate common lines are estimated for each pair of projection images. The key problem then becomes a combination optimization problem of selecting consistent common lines from multiple candidates. To solve the problem efficiently, a physics-inspired method based on a kinetic model is proposed in this work. More specifically, hypothetical attractive forces between each pair of candidate common lines are used to calculate a hypothetical torque exerted on each projection image in the 3D reconstruction space, and the rotation under the hypothetical torque is used to optimize the projection direction estimation of the projection image. This way, the consistent common lines along with the projection directions can be found directly without enumeration of all the combinations of the multiple candidate common lines. Compared with the traditional methods, the proposed method is shown to be able to produce more accurate 3D reconstruction results from high noise projection images. Besides the practical value, the proposed method also serves as a good reference for solving similar combinatorial optimization problems.
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Affiliation(s)
- Jiaxuan Liu
- School of Information Science and Engineering, Lanzhou
| | - Yonggang Lu
- School of Information Science and Engineering, Lanzhou
| | - Li Zhu
- School of Life Sciences, Lanzhou University
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50
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Gambelli L, McLaren M, Conners R, Sanders K, Gaines MC, Clark L, Gold VAM, Kattnig D, Sikora M, Hanus C, Isupov MN, Daum B. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 2024; 13:e84617. [PMID: 38251732 PMCID: PMC10903991 DOI: 10.7554/elife.84617] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lewis Clark
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel Kattnig
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Frankfurt, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
- GHU Psychiatrie et Neurosciences de Paris, Paris, France
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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