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Zhang H, Zheng D, Wu Q, Yan N, Peng H, Hu Q, Peng Y, Yan Z, Shi Z, Bao C, Hu M. CryoPROS: Correcting misalignment caused by preferred orientation using AI-generated auxiliary particles. Nat Commun 2025; 16:4565. [PMID: 40379674 PMCID: PMC12084624 DOI: 10.1038/s41467-025-59797-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 05/03/2025] [Indexed: 05/19/2025] Open
Abstract
The preferred orientation phenomenon is a common issue in cryo-EM, posing a persistent challenge to conventional reconstruction methods. In this study, we introduce cryoPROS, a computational framework designed to correct misalignment caused by preferred orientation through co-refining the raw and auxiliary particles. These auxiliary particles, generated using a self-supervised deep generative model, enhance the alignment accuracy of particles in datasets affected by preferred orientation. CryoPROS achieved near-atomic resolution with the untilted HA-trimer dataset and successfully resolved high-resolution structures from three experimental datasets, including P001-Y, NaX, and hormone-sensitive lipase dimer, all affected by preferred orientation issues. Extensive experiments validate the robustness of cryoPROS and its minimal risk of introducing model bias. These findings suggest that in many cases thought to suffer from preferred orientation, addressing misalignment issues can lead to significant improvements in the density map.
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Affiliation(s)
- Hui Zhang
- Qiuzhen College, Tsinghua University, Beijing, China
| | - Dihan Zheng
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Qiurong Wu
- Beijing Frontier Research Center for Biological Structure (Tsinghua University), Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structure (Tsinghua University), Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, China
| | - Han Peng
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Qi Hu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ying Peng
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhaofeng Yan
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zuoqiang Shi
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China
| | - Chenglong Bao
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
| | - Mingxu Hu
- Beijing Frontier Research Center for Biological Structure (Tsinghua University), Beijing, China.
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen, China.
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2
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Mertz KL, Jordahl, Hemme CA, Probasco MD, Forbes DS, Ducos PL, Salome AZ, Westphall MS, Quarmby ST, Grant T, Coon JJ. Laser-Induced Rehydration of Cryo-Landed Proteins Restores Native Structure. Mol Cell Proteomics 2025:100987. [PMID: 40349920 DOI: 10.1016/j.mcpro.2025.100987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2025] [Revised: 05/05/2025] [Accepted: 05/06/2025] [Indexed: 05/14/2025] Open
Abstract
The use of native mass spectrometry (MS) to land biological molecules for subsequent cryogenic electron microscopy (cryoEM) imaging and three-dimensional reconstruction has gained momentum in recent years as a means to overcome longstanding challenges posed by traditional cryoEM sample preparation. However, recent results obtained with this approach have been constrained by low resolution and the compaction of cryo-landed particles, likely due to dehydration during exposure to vacuum. Here, we describe a new sample preparation method that uses a laser integrated into a cryogenic soft-landing apparatus to liquefy precisely deposited amorphous ice, rehydrating particles and restoring their solution structure prior to rapid revitrification via the thermal mass of the grid. With this technique, we demonstrate the reconstruction of cryo-landed, rehydrated, and revitrified β-galactosidase that is comparable in resolution to that achieved with plunge freezing. Further, these particles are not compacted, matching the known structure and conformation obtained with traditionally plunge-frozen particles. These results establish the viability of coupling native MS with cryoEM for high-resolution structural determination without the limitations imposed by conventional sample preparation, and they open a path to solving previously inaccessible molecules and to integrating MS capabilities such as gas-phase purification to complex samples such as cell lysates.
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Affiliation(s)
- Keaton L Mertz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jordahl
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Colin A Hemme
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | | | - Dylan S Forbes
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Peter L Ducos
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Scott T Quarmby
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States.
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States; Morgridge Institute for Research, Madison, Wisconsin 53515, United States.
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3
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Stautz J, Griwatz D, Kaltwasser S, Mehdipour AR, Ketter S, Thiel C, Wunnicke D, Schrecker M, Mills DJ, Hummer G, Vonck J, Hänelt I. A short intrinsically disordered region at KtrB's N-terminus facilitates allosteric regulation of K + channel KtrAB. Nat Commun 2025; 16:4252. [PMID: 40335548 PMCID: PMC12059179 DOI: 10.1038/s41467-025-59546-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/25/2025] [Indexed: 05/09/2025] Open
Abstract
K+ homeostasis is crucial for bacterial survival. The bacterial K+ channel KtrAB is regulated by the binding of ADP and ATP to the cytosolic RCK subunits KtrA. While the ligand-induced conformational changes in KtrA are well described, the transmission to the gating regions within KtrB is not understood. Here, we present a cryo-EM structure of the ADP-bound, inactive KtrAB complex from Vibrio alginolyticus, which resolves part of KtrB's N termini. They are short intrinsically disordered regions (IDRs) located at the interface of KtrA and KtrB. We reveal that these IDRs play a decisive role in ATP-mediated channel opening, while the closed ADP-bound state does not depend on the N-termini. We propose an allosteric mechanism, in which ATP-induced conformational changes within KtrA trigger an interaction of KtrB's N-terminal IDRs with the membrane, stabilizing the active and conductive state of KtrAB.
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Affiliation(s)
- Janina Stautz
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - David Griwatz
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susann Kaltwasser
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ahmad Reza Mehdipour
- Center for Molecular Modeling, Ghent University, Zwijnaarde, Belgium
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Sophie Ketter
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Celina Thiel
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Dorith Wunnicke
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marina Schrecker
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deryck J Mills
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Inga Hänelt
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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4
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Soni K, Horvath A, Dybkov O, Schwan M, Trakansuebkul S, Flemming D, Wild K, Urlaub H, Fischer T, Sinning I. Structures of aberrant spliceosome intermediates on their way to disassembly. Nat Struct Mol Biol 2025; 32:914-925. [PMID: 39833470 PMCID: PMC12086092 DOI: 10.1038/s41594-024-01480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/19/2024] [Indexed: 01/22/2025]
Abstract
Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans. While key steps of the canonical spliceosome cycle have been revealed by combined structure-function analyses, structural information on an aberrant spliceosome committed to premature disassembly is not available. Here, we report two cryo-electron microscopy structures of post-Bact spliceosome intermediates from Schizosaccharomyces pombe primed for disassembly. We identify the DEAH-box helicase-G-patch protein pair (Gih35-Gpl1, homologous to human DHX35-GPATCH1) and show how it maintains catalytic dormancy. In both structures, Gpl1 recognizes a remodeled active site introduced by an overstabilization of the U5 loop I interaction with the 5' exon leading to a single-nucleotide insertion at the 5' splice site. Remodeling is communicated to the spliceosome surface and the Ntr1 complex that mediates disassembly is recruited. Our data pave the way for a targeted analysis of splicing quality control.
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Affiliation(s)
- Komal Soni
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
| | - Attila Horvath
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Merlin Schwan
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Sasanan Trakansuebkul
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Tamás Fischer
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
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5
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Chen X, Wang L, Xie J, Nowak JS, Luo B, Zhang C, Jia G, Zou J, Huang D, Glatt S, Yang Y, Su Z. RNA sample optimization for cryo-EM analysis. Nat Protoc 2025; 20:1114-1157. [PMID: 39548288 DOI: 10.1038/s41596-024-01072-1] [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: 08/04/2023] [Accepted: 09/12/2024] [Indexed: 11/17/2024]
Abstract
RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine these 3D structures due to their conformational heterogeneity and intrinsic dynamics. Cryogenic electron microscopy (cryo-EM) has recently played an emerging role in resolving dynamic conformational changes and understanding structure-function relationships of RNAs including ribozymes, riboswitches and bacterial and viral noncoding RNAs. A variety of methods and pipelines have been developed to facilitate cryo-EM structure determination of challenging RNA targets with small molecular weights at subnanometer to near-atomic resolutions. While a wide range of conditions have been used to prepare RNAs for cryo-EM analysis, correlations between the variables in these conditions and cryo-EM visualizations and reconstructions remain underexplored, which continue to hinder optimizations of RNA samples for high-resolution cryo-EM structure determination. Here we present a protocol that describes rigorous screenings and iterative optimizations of RNA preparation conditions that facilitate cryo-EM structure determination, supplemented by cryo-EM data processing pipelines that resolve RNA dynamics and conformational changes and RNA modeling algorithms that generate atomic coordinates based on moderate- to high-resolution cryo-EM density maps. The current protocol is designed for users with basic skills and experience in RNA biochemistry, cryo-EM and RNA modeling. The expected time to carry out this protocol may range from 3 days to more than 3 weeks, depending on the many variables described in the protocol. For particularly challenging RNA targets, this protocol could also serve as a starting point for further optimizations.
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Affiliation(s)
- Xingyu Chen
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Liu Wang
- The State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, Department of Cardiology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiahao Xie
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jakub S Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Dingming Huang
- The State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, Department of Cardiology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department for Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Yang Yang
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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6
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Ren Y, Fan P, Zhang X, Fang T, Chen Z, Yao Y, Chi X, Zhang G, Zhao X, Sun B, Li F, Liu Z, Song Z, Zhang B, Peng C, Li E, Yang Y, Li J, Chiu S, Yu C. Potent Cross-neutralizing Antibodies Reveal Vulnerabilities of Henipavirus Fusion Glycoprotein. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e2501996. [PMID: 40298900 DOI: 10.1002/advs.202501996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2025] [Revised: 04/02/2025] [Indexed: 04/30/2025]
Abstract
Hendra and Nipah viruses (HNVs), zoonotic paramyxoviruses with >50% case fatality rates, cause fatal encephalitis and respiratory disease, yet lack approved therapies. Here, nine rhesus-derived monoclonal antibodies (mAbs) targeting the fusion glycoprotein (F) prefusion conformation are developed. Four mAbs exhibit first-rate cross-neutralization against HNVs, with two showing synergistic potency when combined with attachment glycoprotein (G)-specific mAbs. Single-dose administration of mAbs confers robust protection against lethal Nipah virus challenge in hamsters. Structural insights reveal that 8 of the 9 potent mAbs adopt a human IGHV4-59-like framework with protruding CDRH3 loops, forming pushpin-shaped paratopes that stabilize the prefusion F-trimer by occupying vulnerable interprotomer cavities. Systematic mutational profiling identifies 14 prefusion-locking residues within the F ectodomain, classified as i) structural linchpins governing fusogenicity or ii) immunodominant hotspots targeted by cross-neutralizing mAbs. This work delivers promising therapeutic candidates against HNVs and provides blueprints for the rational design of antibodies and vaccines targeting viral fusion machinery.
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Affiliation(s)
- Yi Ren
- School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Pengfei Fan
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Xinghai Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Ting Fang
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Zhengshan Chen
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Yanfeng Yao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Xiangyang Chi
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Guanying Zhang
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Xiaofan Zhao
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Bingjie Sun
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Fangxu Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Zixuan Liu
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Zhenwei Song
- School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Baoyue Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430207, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Entao Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yilong Yang
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Jianmin Li
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Changming Yu
- School of Medicine, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Advanced Biotechnology, Beijing Institute of Biotechnology, Beijing, 100071, China
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7
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Rencilin CF, Chatterjee A, Ansari MY, Deshpande S, Mukherjee S, Singh R, Jayatheertha SB, Reddy PM, Hingankar N, Varadarajan R, Bhattacharya J, Dutta S. Cryo-EM reveals conformational variability in the SARS-CoV-2 spike protein RBD induced by two broadly neutralizing monoclonal antibodies. RSC Adv 2025; 15:14385-14399. [PMID: 40330036 PMCID: PMC12053377 DOI: 10.1039/d5ra00373c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 03/21/2025] [Indexed: 05/08/2025] Open
Abstract
SARS-CoV-2 spike proteins play a critical role in infection by interacting with the ACE2 receptors. Their receptor-binding domains and N-terminal domains exhibit remarkable flexibility and can adopt various conformations that facilitate receptor engagement. Previous structural studies have reported the RBD of the spike protein in "up", "down", and various intermediate states, as well as its different conformational changes during ACE2 binding. This flexibility also influences its interactions with the neutralizing antibodies, yet its role in the antibody complexes remains understudied. In this study, we used cryo-electron microscopy to investigate the structural properties of two broadly neutralizing monoclonal antibodies, THSC20.HVTR04 and THSC20.HVTR26. These antibodies were isolated from an unvaccinated individual and demonstrated potent neutralization of multiple SARS-CoV-2 variants. Our analysis revealed distinct binding characteristics and conformational changes in the spike RBD upon binding with the monoclonal antibodies. The structural characterization of the spike protein-monoclonal antibody complexes provided valuable insights into the structural variability of the spike protein and the possible mechanisms for antibody-mediated neutralization.
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Affiliation(s)
| | - Arnab Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India
| | - Mohammad Yousuf Ansari
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Suprit Deshpande
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
- BRIC-Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Sohini Mukherjee
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
- IAVI Gurugram Haryana 122022 India
- IAVI New York NY 10004 USA
| | - Randhir Singh
- Mynvax Private Limited Vani Vilas Road, Basavanagudi Bengaluru 560004 India
| | | | - Poorvi M Reddy
- Mynvax Private Limited Vani Vilas Road, Basavanagudi Bengaluru 560004 India
| | - Nitin Hingankar
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India
- Mynvax Private Limited Vani Vilas Road, Basavanagudi Bengaluru 560004 India
| | - Jayanta Bhattacharya
- Antibody Translational Research Program, Translational Health Science & Technology Institute Faridabad Haryana 121001 India
- BRIC-Translational Health Science & Technology Institute Faridabad Haryana 121001 India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science Bengaluru 560012 India
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8
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Dillard KE, Zhang H, Dubbs LZ, Chou CW, Terrace C, Javanmardi K, Kim W, Forsberg KJ, Finkelstein IJ. Mechanism of Cas9 inhibition by AcrIIA11. Nucleic Acids Res 2025; 53:gkaf318. [PMID: 40277083 PMCID: PMC12022753 DOI: 10.1093/nar/gkaf318] [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: 02/23/2025] [Revised: 04/03/2025] [Accepted: 04/13/2025] [Indexed: 04/26/2025] Open
Abstract
Mobile genetic elements evade CRISPR-Cas adaptive immunity by encoding anti-CRISPR proteins (Acrs). Acrs inactivate CRISPR-Cas systems via diverse mechanisms but generally coevolve with a narrow subset of Cas effectors that share high sequence similarity. Here, we demonstrate that AcrIIA11 inhibits Streptococcus pyogenes (Sp), Staphylococcus aureus (Sa), and Francisella novicida (Fn) Cas9s in vitro and in human cells. Single-molecule imaging reveals that AcrIIA11 hinders SaCas9 target search by reducing its diffusion on nonspecific DNA. DNA cleavage is inhibited because the AcrIIA11:SaCas9 complex binds to protospacer adjacent motif (PAM)-rich off-target sites, preventing SaCas9 from reaching its target. AcrIIA11 also greatly slows down DNA cleavage after SaCas9 reaches its target site. A negative-stain electron microscopy reconstruction of an AcrIIA11:SaCas9 RNP complex reveals that the heterodimer assembles with a 1:1 stoichiometry. Physical AcrIIA11-Cas9 interactions across type IIA and IIB Cas9s correlate with nuclease inhibition and support its broad-spectrum activity. These results add a kinetic inhibition mechanism to the phage-CRISPR arms race.
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Affiliation(s)
- Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Hongshan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Lianne Z Dubbs
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Cynthia Terrace
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Wantae Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Kevin J Forsberg
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, United States
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9
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Sherry J, Pawar KI, Dolat L, Smith E, Chang IC, Pha K, Kaake R, Swaney DL, Herrera C, McMahon E, Bastidas RJ, Johnson JR, Valdivia RH, Krogan NJ, Elwell CA, Verba K, Engel JN. The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection. Cell Rep 2025; 44:115509. [PMID: 40186871 DOI: 10.1016/j.celrep.2025.115509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Revised: 01/09/2025] [Accepted: 03/12/2025] [Indexed: 04/07/2025] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis replicates in a specialized membrane-bound compartment where it repositions host organelles during infection to acquire nutrients and evade host surveillance. We describe a bacterial effector, Dre1, that binds specifically to dynactin associated with host microtubule organizing centers without globally impeding dynactin function. Dre1 is required to reposition the centrosome, mitotic spindle, Golgi apparatus, and primary cilia around the inclusion and contributes to pathogen fitness in cell-based and mouse models of infection. We utilized Dre1 to affinity purify the megadalton dynactin protein complex and determined the first cryoelectron microscopy (cryo-EM) structure of human dynactin. Our results suggest that Dre1 binds to the pointed end of dynactin and uncovers the first bacterial effector that modulates dynactin function. Our work highlights how a pathogen employs a single effector to evoke targeted, large-scale changes in host cell organization that facilitate pathogen growth without inhibiting host viability.
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Affiliation(s)
- Jessica Sherry
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Komal Ishwar Pawar
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lee Dolat
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Erin Smith
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - I-Chang Chang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Khavong Pha
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robyn Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Clara Herrera
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eleanor McMahon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cherilyn A Elwell
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Kliment Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Joanne N Engel
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
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10
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Mietzsch M, Hsi J, Nelson AR, Khandekar N, Huang AM, Smith NJ, Zachary J, Potts L, Farrar MA, Chipman P, Ghanem M, Alexander IE, Logan GJ, Huiskonen JT, McKenna R. Structural characterization of antibody-responses following Zolgensma treatment for AAV capsid engineering to expand patient cohorts. Nat Commun 2025; 16:3731. [PMID: 40253479 PMCID: PMC12009303 DOI: 10.1038/s41467-025-59088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 04/11/2025] [Indexed: 04/21/2025] Open
Abstract
Monoclonal antibodies are useful tools to dissect the neutralizing antibody response against the adeno-associated virus (AAV) capsids that are used as gene therapy delivery vectors. The presence of pre-existing neutralizing antibodies in large portions of the human population poses a significant challenge for AAV-mediated gene therapy, primarily targeting the capsid leading to vector inactivation and loss of treatment efficacy. This study structurally characterizes the interactions of 21 human-derived neutralizing antibodies from three patients treated with the AAV9 vector, Zolgensma®, utilizing high-resolution cryo-electron microscopy. The antibodies bound to the 2-fold depression or the 3-fold protrusions do not conform to the icosahedral symmetry of the capsid, thus requiring localized reconstructions. These complex structures provide unprecedented details of the mAbs binding interfaces, with many antibodies inducing structural perturbations of the capsid upon binding. Key surface capsid amino acid residues were identified facilitating the design of capsid variants with antibody escape phenotypes. These AAV9 capsid variants have the potential to expand the patient cohort to include those that were previously excluded due to their pre-existing neutralizing antibodies against the wtAAV9 capsid, and the possibly of further treatment to those requiring redosing.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Jane Hsi
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA
| | - Austin R Nelson
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA
| | - Neeta Khandekar
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Ann-Maree Huang
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Nicholas Jc Smith
- Discipline of Paediatrics, University of Adelaide, Women's and Children's Hospital, North Adelaide, SA, Australia
- Department of Neurology and Clinical Neurophysiology, Women's and Children's Health Network, North Adelaide, SA, Australia
| | - Jon Zachary
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA
| | - Lindsay Potts
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA
| | - Michelle A Farrar
- School of Clinical Medicine, UNSW Medicine and Health, UNSW Medicine, Sydney, NSW, Australia
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Paul Chipman
- Interdisciplinary Center of Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Mohammad Ghanem
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
- Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, Australia
| | - Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland
| | - Robert McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, McKnight Brain Institute. College of Medicine, University of Florida, Gainesville, FL, USA.
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11
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Woollard G, Zhou W, Thiede EH, Lin C, Grigorieff N, Cossio P, Dao Duc K, Hanson SM. InstaMap: instant-NGP for cryo-EM density maps. Acta Crystallogr D Struct Biol 2025; 81:147-169. [PMID: 40135651 PMCID: PMC11966239 DOI: 10.1107/s2059798325002025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 03/03/2025] [Indexed: 03/27/2025] Open
Abstract
Despite the parallels between problems in computer vision and cryo-electron microscopy (cryo-EM), many state-of-the-art approaches from computer vision have yet to be adapted for cryo-EM. Within the computer-vision research community, implicits such as neural radiance fields (NeRFs) have enabled the detailed reconstruction of 3D objects from few images at different camera-viewing angles. While other neural implicits, specifically density fields, have been used to map conformational heterogeneity from noisy cryo-EM projection images, most approaches represent volume with an implicit function in Fourier space, which has disadvantages compared with solving the problem in real space, complicating, for instance, masking, constraining physics or geometry, and assessing local resolution. In this work, we build on a recent development in neural implicits, a multi-resolution hash-encoding framework called instant-NGP, that we use to represent the scalar volume directly in real space and apply it to the cryo-EM density-map reconstruction problem (InstaMap). We demonstrate that for both synthetic and real data, InstaMap for homogeneous reconstruction achieves higher resolution at shorter training stages than five other real-spaced representations. We propose a solution to noise overfitting, demonstrate that InstaMap is both lightweight and fast to train, implement masking from a user-provided input mask and extend it to molecular-shape heterogeneity via bending space using a per-image vector field.
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Affiliation(s)
- Geoffrey Woollard
- Center for Computational Biology, Flatiron Institute, New York, NY10010, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010, USA
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenda Zhou
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010, USA
| | - Erik H. Thiede
- Center for Computational Biology, Flatiron Institute, New York, NY10010, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010, USA
- Cornell University, Ithaca, New York, USA
| | - Chen Lin
- Center for Computational Biology, Flatiron Institute, New York, NY10010, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010, USA
| | - Nikolaus Grigorieff
- University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Pilar Cossio
- Center for Computational Biology, Flatiron Institute, New York, NY10010, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010, USA
| | - Khanh Dao Duc
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sonya M. Hanson
- Center for Computational Biology, Flatiron Institute, New York, NY10010, USA
- Center for Computational Mathematics, Flatiron Institute, New York, NY10010, USA
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12
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von Rosen T, Zdanowicz R, El Hadeg Y, Afanasyev P, Boehringer D, Leitner A, Glockshuber R, Weber-Ban E. Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa. Nat Commun 2025; 16:3042. [PMID: 40155375 PMCID: PMC11953334 DOI: 10.1038/s41467-025-58073-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/12/2025] [Indexed: 04/01/2025] Open
Abstract
Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
- International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland
| | - Yasser El Hadeg
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, Zurich, Switzerland
| | | | - Alexander Leitner
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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13
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Ruma YN, Nannenga BL, Gonen T. Unraveling atomic complexity from frozen samples. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2025; 12:020901. [PMID: 40255534 PMCID: PMC12009148 DOI: 10.1063/4.0000303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Accepted: 03/26/2025] [Indexed: 04/22/2025]
Abstract
Cryo-electron microscopy (cryo-EM) is a significant driver of recent advances in structural biology. Cryo-EM is comprised of several distinct and complementary methods, which include single particle analysis, cryo-electron tomography, and microcrystal electron diffraction. In this Perspective, we will briefly discuss the different branches of cryo-EM in structural biology and the current challenges in these areas.
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Affiliation(s)
| | | | - Tamir Gonen
- Author to whom correspondence should be addressed:
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14
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Ojha AA, Blackwell R, Cruz-Chú ER, Dsouza R, Astore MA, Schwander P, Hanson SM. The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation. Acta Crystallogr D Struct Biol 2025; 81:89-104. [PMID: 40019002 DOI: 10.1107/s2059798325001469] [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: 11/25/2024] [Accepted: 02/17/2025] [Indexed: 03/01/2025] Open
Abstract
Resolving continuous conformational heterogeneity in single-particle cryo-electron microscopy (cryo-EM) is a field in which new methods are now emerging regularly. Methods range from traditional statistical techniques to state-of-the-art neural network approaches. Such ongoing efforts continue to enhance the ability to explore and understand the continuous conformational variations in cryo-EM data. One of the first methods was the manifold embedding approach or ManifoldEM. However, comparing it with more recent methods has been challenging due to software availability and usability issues. In this work, we introduce a modern Python implementation that is user-friendly, orders of magnitude faster than its previous versions and designed with a developer-ready environment. This implementation allows a more thorough evaluation of the strengths and limitations of methods addressing continuous conformational heterogeneity in cryo-EM, paving the way for further community-driven improvements.
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Affiliation(s)
- Anupam Anand Ojha
- Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA
| | - Robert Blackwell
- Scientific Computing Core, Flatiron Institute, New York, NY 10010, USA
| | - Eduardo R Cruz-Chú
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Raison Dsouza
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Miro A Astore
- Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Sonya M Hanson
- Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA
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15
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Zhang K, Cossio P, Rangan AV, Lucas BA, Grigorieff N. A new statistical metric for robust target detection in cryo-EM using 2D template matching. IUCRJ 2025; 12:155-176. [PMID: 39819740 PMCID: PMC11878444 DOI: 10.1107/s2052252524011771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 12/03/2024] [Indexed: 01/19/2025]
Abstract
2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects spherical targets such as large ribosomal subunits, challenges remain in detecting smaller and more aspherical targets in various environments. In this work, a novel 2DTM metric, referred to as the 2DTM p-value, is developed to extend the 2DTM framework to more complex applications. The 2DTM p-value combines information from two previously used 2DTM metrics, namely the 2DTM signal-to-noise ratio (SNR) and z-score, which are derived from the cross-correlation coefficient between the target and the template. The 2DTM p-value demonstrates robust detection accuracies under various imaging and sample conditions and outperforms the 2DTM SNR and z-score alone. Specifically, the 2DTM p-value improves the detection of aspherical targets such as a modified artificial tubulin patch particle (500 kDa) and a much smaller clathrin monomer (193 kDa) in simulated data. It also accurately recovers mature 60S ribosomes in yeast lamellae samples, even under conditions of increased Gaussian noise. The new metric will enable the detection of a wider variety of targets in both purified and cellular samples through 2DTM.
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Affiliation(s)
- Kexin Zhang
- RNA Therapeutics InstituteUniversity of Massachusetts Chan Medical SchoolWorcesterUSA
- Howard Hughes Medical InstituteUniversity of Massachusetts Chan Medical SchoolWorcesterUSA
| | - Pilar Cossio
- Center for Computational Mathematics, Flatiron Institute, New York, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Aaditya V. Rangan
- Center for Computational Mathematics, Flatiron Institute, New York, USA
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUSA
| | - Bronwyn A. Lucas
- RNA Therapeutics InstituteUniversity of Massachusetts Chan Medical SchoolWorcesterUSA
| | - Nikolaus Grigorieff
- RNA Therapeutics InstituteUniversity of Massachusetts Chan Medical SchoolWorcesterUSA
- Howard Hughes Medical InstituteUniversity of Massachusetts Chan Medical SchoolWorcesterUSA
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16
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Johnson A, Dodes Traian M, Walsh RM, Jenni S, Harrison SC. Octahedral small virus-like particles of dengue virus type 2. J Virol 2025; 99:e0180924. [PMID: 39745459 PMCID: PMC11853069 DOI: 10.1128/jvi.01809-24] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Accepted: 12/02/2024] [Indexed: 02/26/2025] Open
Abstract
Flavivirus envelope (E) and precursor M (prM) proteins, when ectopically expressed, assemble into empty, virus-like particles (VLPs). Cleavage of prM to M and loss of the pr fragment converts the VLPs from immature to mature particles, mimicking a similar maturation of authentic virions. Most of the VLPs obtained by prM-E expression are smaller than virions; early, low-resolution cryo-EM studies suggested a simple, 60-subunit, icosahedral organization. We describe here the cryo-EM structure of immature, small VLPs (smVLPs) from dengue virus type 2 and show that they have octahedral rather than icosahedral symmetry. The asymmetric unit of the octahedral particle is an asymmetric trimer of prM-E heterodimers, just as it is on icosahedral immature virions; the full, octahedrally symmetric particle thus has 24 such asymmetric trimers or 72 prM-E heterodimers in all. Cleavage of prM and release of pr generates ovoid, somewhat irregular, mature particles. Previous work has shown that mature smVLPs have fusion properties identical to those of virions, consistent with local, virion-like clustering of 36 E dimers on their surface. The cryo-EM structure and the properties of the smVLPs described here relate directly to ongoing efforts to use them as vaccine immunogens. IMPORTANCE Ectopic expression of flavivirus envelope (E) and precursor M (prM) proteins leads to the formation and secretion of empty, virus-like particles (VLPs). We show that a major class of VLPs, of smaller diameter than those of virion size ("small VLPs": smVLPs), are octahedrally symmetric particles. The known characteristics of immature virions (asymmetric trimers of prM-E heterodimers) allow us to understand the assembly of an octahedral (rather than icosahedral) surface lattice. Cleavage of prM and formation of mature, fusogenic smVLPs yield somewhat irregular, ovoid particles. These observations are directly relevant to proposals for using immunogenic but non-infectious VLPs as components of specific flavivirus vaccines.
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Affiliation(s)
- Adam Johnson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Martín Dodes Traian
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard M. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen C. Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
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17
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Howard MK, Hoppe N, Huang XP, Mitrovic D, Billesbølle CB, Macdonald CB, Mehrotra E, Rockefeller Grimes P, Trinidad DD, Delemotte L, English JG, Coyote-Maestas W, Manglik A. Molecular basis of proton sensing by G protein-coupled receptors. Cell 2025; 188:671-687.e20. [PMID: 39753132 PMCID: PMC11849372 DOI: 10.1016/j.cell.2024.11.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 09/23/2024] [Accepted: 11/21/2024] [Indexed: 02/09/2025]
Abstract
Three proton-sensing G protein-coupled receptors (GPCRs)-GPR4, GPR65, and GPR68-respond to extracellular pH to regulate diverse physiology. How protons activate these receptors is poorly understood. We determined cryogenic-electron microscopy (cryo-EM) structures of each receptor to understand the spatial arrangement of proton-sensing residues. Using deep mutational scanning (DMS), we determined the functional importance of every residue in GPR68 activation by generating ∼9,500 mutants and measuring their effects on signaling and surface expression. Constant-pH molecular dynamics simulations provided insights into the conformational landscape and protonation patterns of key residues. This unbiased approach revealed that, unlike other proton-sensitive channels and receptors, no single site is critical for proton recognition. Instead, a network of titratable residues extends from the extracellular surface to the transmembrane region, converging on canonical motifs to activate proton-sensing GPCRs. Our approach integrating structure, simulations, and unbiased functional interrogation provides a framework for understanding GPCR signaling complexity.
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Affiliation(s)
- Matthew K Howard
- Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Biophysics graduate program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xi-Ping Huang
- Department of Pharmacology and the National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Darko Mitrovic
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden
| | - Christian B Billesbølle
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christian B Macdonald
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eshan Mehrotra
- Tetrad graduate program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Rockefeller Grimes
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donovan D Trinidad
- Department of Medicine, Division of Infectious Disease, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, 12121 Solna, Stockholm, Stockholm County 114 28, Sweden
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Willow Coyote-Maestas
- Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94148, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94115, USA.
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18
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Farheen F, Terashi G, Zhu H, Kihara D. AI-based methods for biomolecular structure modeling for Cryo-EM. Curr Opin Struct Biol 2025; 90:102989. [PMID: 39864242 PMCID: PMC11793015 DOI: 10.1016/j.sbi.2025.102989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 12/29/2024] [Accepted: 01/04/2025] [Indexed: 01/28/2025]
Abstract
Cryo-electron microscopy (Cryo-EM) has revolutionized structural biology by enabling the determination of macromolecular structures that were challenging to study with conventional methods. Processing cryo-EM data involves several computational steps to derive three-dimensional structures from raw projections. Recent advancements in artificial intelligence (AI) including deep learning have significantly improved the performance of these processes. In this review, we discuss state-of-the-art AI-based techniques used in key steps of cryo-EM data processing, including macromolecular structure modeling and heterogeneity analysis.
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Affiliation(s)
- Farhanaz Farheen
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Han Zhu
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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19
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Burton-Smith RN, Yagi-Utsumi M, Yanaka S, Song C, Murata K, Kato K. Elucidating the Unique J-Shaped Protomer Structure of Amyloid-β(1-40) Fibril with Cryo-Electron Microscopy. Int J Mol Sci 2025; 26:1179. [PMID: 39940945 PMCID: PMC11817843 DOI: 10.3390/ijms26031179] [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: 12/26/2024] [Revised: 01/13/2025] [Accepted: 01/22/2025] [Indexed: 02/16/2025] Open
Abstract
Although the structural diversity of amyloid-β (Aβ) fibrils plays a critical role in the pathology of Alzheimer's disease (AD), the mechanisms underlying this diversity remain poorly understood. In this study, we report the discovery of a novel J-shaped protomer structure of Aβ40 fibrils, resolved at 3.3 Å resolution using cryo-electron microscopy. Under controlled conditions (20 mM sodium phosphate buffer, pH 8.0) designed to emphasize intra-protomer interactions and slow fibril elongation, the J-shaped structure revealed distinct salt bridges (e.g., D1-K28, R5-E22) that stabilize the fibril core. These findings expand our understanding of the free energy landscape of fibril formation, shedding light on how specific environmental factors, such as pH and ionic strength, may influence fibril polymorphism. Importantly, the unique features of the J-shaped protomer provide insights into the structural basis of amyloid plaque diversity in AD and suggest potential therapeutic strategies targeting intra-protomer interactions. This study underscores the importance of fibril polymorphism in AD pathology and offers a foundation for future research into fibril-targeted therapies.
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Affiliation(s)
- Raymond N. Burton-Smith
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan (M.Y.-U.); (S.Y.); (C.S.)
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Kanagawa 240-0193, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan (M.Y.-U.); (S.Y.); (C.S.)
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan (M.Y.-U.); (S.Y.); (C.S.)
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan (M.Y.-U.); (S.Y.); (C.S.)
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan (M.Y.-U.); (S.Y.); (C.S.)
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Kanagawa 240-0193, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan (M.Y.-U.); (S.Y.); (C.S.)
- Graduate Institute for Advanced Studies, SOKENDAI, Kanagawa 240-0193, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
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20
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Bi M, Wang X, Wang J, Xu J, Sun W, Adediwura VA, Miao Y, Cheng Y, Ye L. Structure and function of a near fully-activated intermediate GPCR-Gαβγ complex. Nat Commun 2025; 16:1100. [PMID: 39875358 PMCID: PMC11775185 DOI: 10.1038/s41467-025-56434-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 01/20/2025] [Indexed: 01/30/2025] Open
Abstract
Unraveling the signaling roles of intermediate complexes is pivotal for G protein-coupled receptor (GPCR) drug development. Despite hundreds of GPCR-Gαβγ structures, these snapshots primarily capture the fully activated complex. Consequently, the functions of intermediate GPCR-G protein complexes remain elusive. Guided by a conformational landscape visualized via 19F quantitative NMR and molecular dynamics (MD) simulations, we determined the structure of an intermediate GPCR-mini-Gαsβγ complex at 2.6 Å using cryo-EM, by blocking its transition to the fully activated complex. Furthermore, we present direct evidence that the complex at this intermediate state initiates a rate-limited nucleotide exchange before transitioning to the fully activated complex. In this state, BODIPY-GDP/GTP based nucleotide exchange assays further indicated the α-helical domain of the Gα is partially open, allowing it to grasp a nucleotide at a non-canonical binding site, distinct from the canonical nucleotide-binding site. These advances bridge a significant gap in our understanding of the complexity of GPCR signaling.
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Affiliation(s)
- Maxine Bi
- Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, CA, 94143, USA
| | - Xudong Wang
- Department of Molecular Biosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - Jinan Wang
- Pharmacology & Computational Medicine Program, University of North Carolina at Chapel Hill, 116 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenkai Sun
- Department of Molecular Biosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA
| | - Victor Ayo Adediwura
- Pharmacology & Computational Medicine Program, University of North Carolina at Chapel Hill, 116 Manning Drive, Chapel Hill, NC, 27599, USA
| | - Yinglong Miao
- Pharmacology & Computational Medicine Program, University of North Carolina at Chapel Hill, 116 Manning Drive, Chapel Hill, NC, 27599, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, CA, 94143, USA.
- Howard Hughes Medical Institute, University of California, 600 16th Street, San Francisco, CA, 94143, USA.
| | - Libin Ye
- Department of Molecular Biosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA.
- H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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21
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Qian C, Chen J, Yang Y, Lu Y, Ren T, Jiang Y, Huang Y, Chi X, Zhang S, Zhang C, Li K, Shen J, Zhang S, Wang D, Zhou L, Li T, Zheng Q, Yu H, Gu Y, Xia N, Li S. Rational design of a triple-type HPV53/56/66 vaccine with one preferable base particle incorporating two identified immunodominant sites. J Nanobiotechnology 2025; 23:28. [PMID: 39828682 PMCID: PMC11744962 DOI: 10.1186/s12951-024-03080-5] [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: 06/24/2024] [Accepted: 12/20/2024] [Indexed: 01/22/2025] Open
Abstract
The numerous high-risk carcinogenic types of human papillomavirus (HR-HPV) that lack vaccine protection underscore the urgent need to develop broader-spectrum HPV vaccines. This study addresses this need by focusing on HR-HPV types 53, 56, and 66, which are not currently targeted by existing vaccines. It introduces an effective method for their soluble expression, as well as that of their mutants, within an Escherichia coli expression system. Through strategic homologous loop swapping among HPV53, HPV56, and HPV66, we designed twenty double-type chimeric molecules. Comprehensive evaluations identified unique dominant immunogenic loops for each type: the FG loop for HPV53, the HI loop for HPV56, and the DE loop for HPV66, with HPV66 emerging as the optimal chimeric backbone virus-like particle (VLP). By incorporating two identified immunodominant sites into the preferable base particle, the study constructed a triple-type chimera H66-56HI-53FG, which could efficiently self-assemble into VLPs in vitro that closely resembled the wild-type HPV66 VLP and, induced balanced triple-type neutralization titers (~ 3 log unites), as contrast to none observable HPV53 neutralization titer and lower HPV56 titer elicited by the immunization of the wild-type HPV66 alone. This research outlines an amenable way to simultaneously identify immunodominant sites and their preferable particle base context for cross-type vaccine design, thereby offering a paradigm as extending antigenic variety in single particle to broaden vaccine protection coverage.
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Affiliation(s)
- Ciying Qian
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Jie Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Yurou Yang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Yihan Lu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Tianyu Ren
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Yanan Jiang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Yang Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Xin Chi
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Shuyue Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Chengzong Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Kewei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Jingjia Shen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Sibo Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Daning Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Lizhi Zhou
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Tingting Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Qingbing Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Hai Yu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China.
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China.
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Discipline of Intelligent Instrument and Equipment, Department of Experimental Medicine, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, China.
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22
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Huang Y, Song F, Zeng Y, Sun H, Sheng R, Wang X, Liu L, Luo G, Jiang Y, Chen Y, Zhang M, Zhang S, Gu Y, Yu H, Li S, Li T, Zheng Q, Ge S, Zhang J, Xia N. A single residue switch mediates the broad neutralization of Rotaviruses. Nat Commun 2025; 16:838. [PMID: 39833145 PMCID: PMC11746992 DOI: 10.1038/s41467-025-56114-3] [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: 06/28/2024] [Accepted: 01/08/2025] [Indexed: 01/22/2025] Open
Abstract
Broadly neutralizing antibodies (bNAbs) could offer escape-tolerant and lasting protection against viral infections and therefore guide development of broad-spectrum vaccines. The increasing challenge posed by viral evolution and immune evasion intensifies the importance of the discovery of bNAbs and their underlying neutralization mechanism. Here, focusing on the pivotal viral protein VP4 of rotavirus (RV), we identify a potent bNAb, 7H13, exhibiting broad-spectrum neutralization across diverse RV genotypes and demonstrating strong prevention of virus infection in female mice. A combination of time-resolved cryo-electron microscopy (cryo-EM) and in situ cryo-electron tomography (cryo-ET) analysis reveals a counterintuitive dynamic process of virus inactivation, in which 7H13 asymmetrically binds to a conserved epitope in the capsid-proximal aspect of VP4, triggers a conformational switch in a critical residue-F418-thereby disrupts the meta-stable conformation of VP4 essential for normal viral infection. Structure-guided mutagenesis corroborates the essential role of the 7H13 heavy chain I54 in activating F418 switch and destabilizing VP4. These findings define an atypical NAbs' neutralization mechanism and reveal a potential type of virus vulnerable site for universal vaccine and therapeutics design.
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Affiliation(s)
- Yang Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Feibo Song
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Yuanjun Zeng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
- Collaborative Innovation Center for Translation Medical Testing and Application Technology, Department of Medical Technology, Zhangzhou Health Vocational College, Zhangzhou, PR China
| | - Hui Sun
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Roufang Sheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Xuechun Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Liqin Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Guoxing Luo
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
- Novel Product R&D Department, Xiamen Innovax Biotech Co., Ltd., Xiamen, PR China
| | - Yanan Jiang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Yaling Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Mengxuan Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Shiyin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Ying Gu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Hai Yu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
| | - Tingdong Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
| | - Qingbing Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, PR China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, PR China.
- Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, Fujian, PR China.
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23
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Hassan A, Pinkas M, Yaeshima C, Ishino S, Uchiumi T, Ito K, Demo G. Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization. Nucleic Acids Res 2025; 53:gkae1324. [PMID: 39797736 PMCID: PMC11724365 DOI: 10.1093/nar/gkae1324] [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: 08/21/2024] [Revised: 12/17/2024] [Accepted: 12/30/2024] [Indexed: 01/13/2025] Open
Abstract
Protein synthesis (translation) consumes a substantial proportion of cellular resources, prompting specialized mechanisms to reduce translation under adverse conditions. Ribosome inactivation often involves ribosome-interacting proteins. In both bacteria and eukaryotes, various ribosome-interacting proteins facilitate ribosome dimerization or hibernation, and/or prevent ribosomal subunits from associating, enabling the organisms to adapt to stress. Despite extensive studies on bacteria and eukaryotes, understanding factor-mediated ribosome dimerization or anti-association in archaea remains elusive. Here, we present cryo-electron microscopy structures of an archaeal 30S dimer complexed with an archaeal ribosome dimerization factor (designated aRDF), from Pyrococcus furiosus, resolved at a resolution of 3.2 Å. The complex features two 30S subunits stabilized by aRDF homodimers in a unique head-to-body architecture, which differs from the disome architecture observed during hibernation in bacteria and eukaryotes. aRDF interacts directly with eS32 ribosomal protein, which is essential for subunit association. The binding mode of aRDF elucidates its anti-association properties, which prevent the assembly of archaeal 70S ribosomes.
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Affiliation(s)
- Ahmed H Hassan
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Matyas Pinkas
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Chiaki Yaeshima
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Niigata 950-2181, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Niigata 950-2181, Japan
| | - Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Niigata 950-2181, Japan
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
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24
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Liu YT, Fan H, Hu JJ, Zhou ZH. Overcoming the preferred-orientation problem in cryo-EM with self-supervised deep learning. Nat Methods 2025; 22:113-123. [PMID: 39558095 DOI: 10.1038/s41592-024-02505-1] [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: 04/18/2024] [Accepted: 10/10/2024] [Indexed: 11/20/2024]
Abstract
While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the '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 map anisotropy and particle misalignment caused by 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 ability to generate 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
- 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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25
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Elferich J, Kong L, Zottig X, Grigorieff N. CTFFIND5 provides improved insight into quality, tilt, and thickness of TEM samples. eLife 2024; 13:RP97227. [PMID: 39704651 DOI: 10.7554/elife.97227] [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: 12/21/2024] Open
Abstract
Images taken by transmission electron microscopes are usually affected by lens aberrations and image defocus, among other factors. These distortions can be modeled in reciprocal space using the contrast transfer function (CTF). Accurate estimation and correction of the CTF is essential for restoring the high-resolution signal in cryogenic electron microscopy (cryoEM). Previously, we described the implementation of algorithms for this task in the cisTEM software package (Grant et al., 2018). Here we show that taking sample characteristics, such as thickness and tilt, into account can improve CTF estimation. This is particularly important when imaging cellular samples, where measurement of sample thickness and geometry derived from accurate modeling of the Thon ring pattern helps judging the quality of the sample. This improved CTF estimation has been implemented in CTFFIND5, a new version of the cisTEM program CTFFIND. We evaluated the accuracy of these estimates using images of tilted aquaporin crystals and eukaryotic cells thinned by focused ion beam milling. We estimate that with micrographs of sufficient quality CTFFIND5 can measure sample tilt with an accuracy of 3° and sample thickness with an accuracy of 5 nm.
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Affiliation(s)
- Johannes Elferich
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, United States
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, United States
| | - Lingli Kong
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, United States
| | - Ximena Zottig
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, United States
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, United States
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, United States
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, United States
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26
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Rickgauer JP, Choi H, Moore AS, Denk W, Lippincott-Schwartz J. Structural dynamics of human ribosomes in situ reconstructed by exhaustive high-resolution template matching. Mol Cell 2024; 84:4912-4928.e7. [PMID: 39626661 DOI: 10.1016/j.molcel.2024.11.003] [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: 10/13/2023] [Revised: 07/29/2024] [Accepted: 11/06/2024] [Indexed: 12/13/2024]
Abstract
Protein synthesis is central to life and requires the ribosome, which catalyzes the stepwise addition of amino acids to a polypeptide chain by undergoing a sequence of structural transformations. Here, we employed high-resolution template matching (HRTM) on cryoelectron microscopy (cryo-EM) images of directly cryofixed living cells to obtain a set of ribosomal configurations covering the entire elongation cycle, with each configuration occurring at its native abundance. HRTM's position and orientation precision and ability to detect small targets (∼300 kDa) made it possible to order these configurations along the reaction coordinate and to reconstruct molecular features of any configuration along the elongation cycle. Visualizing the cycle's structural dynamics by combining a sequence of >40 reconstructions into a 3D movie readily revealed component and ligand movements, some of them surprising, such as spring-like intramolecular motion, providing clues about the molecular mechanisms involved in some still mysterious steps during chain elongation.
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Affiliation(s)
- J Peter Rickgauer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - Heejun Choi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew S Moore
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Winfried Denk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Max Planck Institute for Biological Intelligence, Martinsried, Germany
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27
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Dagotto G, Fisher JL, Li D, Li Z, Jenni S, Li Z, Tartaglia LJ, Abbink P, Barouch DH. Identification of a novel neutralization epitope in rhesus AAVs. Mol Ther Methods Clin Dev 2024; 32:101350. [PMID: 39469420 PMCID: PMC11513466 DOI: 10.1016/j.omtm.2024.101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 09/30/2024] [Indexed: 10/30/2024]
Abstract
Adeno-associated viruses (AAVs) are popular gene therapy delivery vectors, but their application can be limited by anti-vector immunity. Both preexisting neutralizing antibodies (NAbs) and post-administration NAbs can limit transgene expression and reduce the clinical utility of AAVs. The development of novel AAVs will advance our understanding of AAV immunity and may also have practical applications. In this study, we identified five novel AAV capsids from rhesus macaques. RhAAV4282 exhibited 91.4% capsid sequence similarity with AAV7 and showed similar tissue tropism with slightly diminished overall signal. Despite this sequence homology, RhAAV4282 and AAV7 showed limited cross-neutralization. We determined a cryo-EM structure of the RhAAV4282 capsid at 2.57 Å resolution and identified a small segment within the hypervariable region IV, involving seven amino acids that formed a shortened external loop in RhAAV4282 compared with AAV7. We generated RhAAV4282 and AAV7 mutants that involved swaps of this region and showed that this region partially determined neutralization phenotype. We termed this region the hypervariable region IV neutralizing epitope (HRNE). Our data suggests that modification of the HRNE can lead to AAVs with altered neutralization profiles.
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Affiliation(s)
- Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jana L. Fisher
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zhenyu Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Zongli Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | | | - Peter Abbink
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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28
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Mietzsch M, Kamat M, Basso K, Chipman P, Huiskonen JT, McKenna R. Structural characterization and epitope mapping of the AAVX affinity purification ligand. Mol Ther Methods Clin Dev 2024; 32:101377. [PMID: 39677563 PMCID: PMC11638594 DOI: 10.1016/j.omtm.2024.101377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 11/08/2024] [Indexed: 12/17/2024]
Abstract
The application of adeno-associated virus (AAV) vectors in human gene therapies requires reproducible and homogeneous preparations for clinical efficacy and safety. For the AAV production process, often scalable affinity chromatography columns are utilized, such as the POROS CaptureSelect AAVX affinity resin, during downstream processing to ensure highly purified AAV vectors. The AAVX ligand is based on a camelid single-domain antibody capturing a wide range of recombinant AAV capsids. Described here is the identification of the AAV8 capsid epitope to AAVX at 2.3 Å resolution using cryo-electron microscopy. The ligand binds near the 5-fold axis of the capsid in a similar manner to the previously characterized AVB affinity ligand but does not conform to the capsid's icosahedral symmetry. The cross-reactivity of AAVX to other AAV capsids is achieved by primarily interacting with the peptide backbone of the AAV capsid's structurally conserved DE and HI loops. These observations will guide AAV capsid engineering efforts to retain the ability of future recombinant capsid designs to be purified using antibody-based affinity ligands.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Manasi Kamat
- Department of Chemistry, Mass Spectrometry Research and Education Center, University of Florida, Gainesville, FL 32610, USA
| | - Kari Basso
- Department of Chemistry, Mass Spectrometry Research and Education Center, University of Florida, Gainesville, FL 32610, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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29
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Sholi E, Loveland AB, Korostelev AA. Assay for ribosome stimulation of angiogenin nuclease activity. Methods Enzymol 2024; 711:381-404. [PMID: 39952716 PMCID: PMC11839171 DOI: 10.1016/bs.mie.2024.11.007] [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: 02/17/2025]
Abstract
Angiogenin (RNase 5) is an unusual member of the RNase A family with very weak RNase activity and a preference for tRNA. The tRNAs cleaved by angiogenin are thought to have a variety of roles in cellular processes including translation reprogramming, apoptosis, angiogenesis, and neuroprotection. We recently demonstrated that angiogenin is potently activated by the cytoplasmic 80S ribosome. Angiogenin's binding to the ribosome rearranges the C-terminus of the protein, opening the active site for the cleavage of tRNA delivered to the ribosomal A site which angiogenin occupies. Here, we describe the biochemical procedure to test angiogenin's activation by the ribosome using the assay termed the Ribosome Stimulated Angiogenin Nuclease Assay (RiSANA). RiSANA can be used to test the activity of wild-type or mutant angiogenin, or other RNases, against different tRNAs and with different ribosome complexes. For example, given that angiogenin has been implicated in anti-microbial activity, we tested the ability of bacterial 70S ribosomes to stimulate angiogenin activity and found that the E. coli ribosome does not stimulate angiogenin. We also assayed whether angiogenin's closest homolog, RNase 4, could be stimulated by the ribosome, but unlike angiogenin this enzyme was not further activated by the ribosome. The RiSANA assay promises to reveal new aspects of angiogenin mechanism and may aid in the development of new diagnostic tools and therapeutics.
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Affiliation(s)
- Emily Sholi
- RNA Therapeutics Institute, UMass Chan Medical School, Plantation Street, Worcester, MA, United States
| | - Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, Plantation Street, Worcester, MA, United States.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, Plantation Street, Worcester, MA, United States.
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30
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Ochner H, Böhning J, Wang Z, Tarafder AK, Caspy I, Bharat TAM. Structure of the Pseudomonas aeruginosa PAO1 Type IV pilus. PLoS Pathog 2024; 20:e1012773. [PMID: 39666767 DOI: 10.1371/journal.ppat.1012773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 12/26/2024] [Accepted: 11/25/2024] [Indexed: 12/14/2024] Open
Abstract
Type IV pili (T4Ps) are abundant in many bacterial and archaeal species, where they play important roles in both surface sensing and twitching motility, with implications for adhesion, biofilm formation and pathogenicity. While Type IV pilus (T4P) structures from other organisms have been previously solved, a high-resolution structure of the native, fully assembled T4P of Pseudomonas aeruginosa, a major human pathogen, would be valuable in a drug discovery context. Here, we report a 3.2 Å-resolution structure of the P. aeruginosa PAO1 T4P determined by electron cryomicroscopy (cryo-EM). PilA subunits constituting the T4P exhibit a classical pilin fold featuring an extended N-terminal α-helix linked to a C-terminal globular β-sheet-containing domain, which are packed tightly along the pilus, in line with models derived from previous cryo-EM data of the P. aeruginosa PAK strain. The N-terminal helices constitute the pilus core where they stabilise the tubular assembly via hydrophobic interactions. The α-helical core of the pilus is surrounded by the C-terminal globular domain of PilA that coats the outer surface of the pilus, mediating interactions with the surrounding environment. Comparison of the P. aeruginosa PAO1 T4P with T4P structures from other organisms, both at the level of the pilin subunits and the fully assembled pili, confirms previously described common architectural principles whilst highlighting key differences between members of this abundant class of prokaryotic filaments. This study provides a structural framework for understanding the molecular and cell biology of these important cellular appendages mediating interaction of prokaryotes to surfaces.
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Affiliation(s)
- Hannah Ochner
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Zhexin Wang
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Abul K Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Ido Caspy
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, United Kingdom
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31
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Li Y, Zhou Y, Yuan J, Ye F, Gu Q. CryoSTAR: leveraging structural priors and constraints for cryo-EM heterogeneous reconstruction. Nat Methods 2024; 21:2318-2326. [PMID: 39472738 DOI: 10.1038/s41592-024-02486-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 09/25/2024] [Indexed: 12/07/2024]
Abstract
Resolving conformational heterogeneity in cryogenic electron microscopy datasets remains an important challenge in structural biology. Previous methods have often been restricted to working exclusively on volumetric densities, neglecting the potential of incorporating any preexisting structural knowledge as prior or constraints. Here we present cryoSTAR, which harnesses atomic model information as structural regularization to elucidate such heterogeneity. Our method uniquely outputs both coarse-grained models and density maps, showcasing the molecular conformational changes at different levels. Validated against four diverse experimental datasets, spanning large complexes, a membrane protein and a small single-chain protein, our results consistently demonstrate an efficient and effective solution to conformational heterogeneity with minimal human bias. By integrating atomic model insights with cryogenic electron microscopy data, cryoSTAR represents a meaningful step forward, paving the way for a deeper understanding of dynamic biological processes.
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Affiliation(s)
- Yilai Li
- ByteDance Research, San Jose, CA, USA
| | - Yi Zhou
- ByteDance Research, Shanghai, China
| | | | - Fei Ye
- ByteDance Research, Shanghai, China
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32
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Bennett A, Hull JA, Mietzsch M, Bhattacharya N, Chipman P, McKenna R. Maize Streak Virus: Single and Gemini Capsid Architecture. Viruses 2024; 16:1861. [PMID: 39772173 PMCID: PMC11680415 DOI: 10.3390/v16121861] [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: 10/02/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 01/11/2025] Open
Abstract
Geminiviridae are ssDNA plant viruses whose control has both economical and agricultural importance. Their capsids assemble into two distinct architectural forms: (i) a T = 1 icosahedral and (ii) a unique twinned quasi-isometric capsid. Described here are the high-resolution structures of both forms of the maize streak virus using cryo-EM. A comparison of these two forms provides details of the coat protein (CP) and CP-CP and CP-genome interactions that govern the assembly of the architecture of the capsids. Comparative analysis of other representative members of Geminiviridae reveals structural conservation of 60-95% compared to a sequence similarity of 21-30%. This study provides a structural atlas of these plant pathogens and suggests possible antiviral-targetable regions of these capsids.
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Affiliation(s)
- Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA; (M.M.); (J.A.H.); (P.C.)
| | - Joshua A. Hull
- Department of Biochemistry and Molecular Biology, College of Medicine Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA; (M.M.); (J.A.H.); (P.C.)
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA; (M.M.); (J.A.H.); (P.C.)
| | - Nilakshee Bhattacharya
- Biological Science Imaging Facility (BSIR), Department of Biology, Florida State University, 89 Chieftain Way, Tallahassee, FL 32306-4370, USA;
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA; (M.M.); (J.A.H.); (P.C.)
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610-0245, USA; (M.M.); (J.A.H.); (P.C.)
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33
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Dang T, EswarKumar N, Tripathi SK, Yan C, Wang CH, Cao M, Paul TK, Agboluaje EO, Xiong MP, Ivanov I, Ho MC, Zheng YG. Oligomerization of protein arginine methyltransferase 1 and its functional impact on substrate arginine methylation. J Biol Chem 2024; 300:107947. [PMID: 39491649 DOI: 10.1016/j.jbc.2024.107947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 10/20/2024] [Accepted: 10/23/2024] [Indexed: 11/05/2024] Open
Abstract
Protein arginine methyltransferases (PRMTs) are important posttranslational modifying enzymes in eukaryotic proteins and regulate diverse pathways from gene transcription, RNA splicing, and signal transduction to metabolism. Increasing evidence supports that PRMTs exhibit the capacity to form higher-order oligomeric structures, but the structural basis of PRMT oligomerization and its functional consequence are elusive. Herein, we revealed for the first time different oligomeric structural forms of the predominant arginine methyltransferase PRMT1 using cryo-EM, which included tetramer (dimer of dimers), hexamer (trimer of dimers), octamer (tetramer of dimers), decamer (pentamer of dimers), and also helical filaments. Through a host of biochemical assays, we showed that PRMT1 methyltransferase activity was substantially enhanced as a result of the high-ordered oligomerization. High-ordered oligomerization increased the catalytic turnover and the multimethylation processivity of PRMT1. Presence of a catalytically dead PRMT1 mutant also enhanced the activity of WT PRMT1, pointing out a noncatalytic role of oligomerization. Structural modeling demonstrates that oligomerization enhances substrate retention at the PRMT1 surface through electrostatic force. Our studies offered key insights into PRMT1 oligomerization and established that oligomerization constitutes a novel molecular mechanism that positively regulates the enzymatic activity of PRMTs in biology.
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Affiliation(s)
- Tran Dang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States
| | | | - Sunil Kumar Tripathi
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Mengtong Cao
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States
| | - Tanmoy Kumar Paul
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Elizabeth Oladoyin Agboluaje
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States
| | - May P Xiong
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei, Taiwan.
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States.
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34
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Garg P, Satheesh T, Ganji M, Dutta S. Cryo-EM Reveals the Mechanism of DNA Compaction by Mycobacterium smegmatis Dps2. J Mol Biol 2024; 436:168806. [PMID: 39349276 DOI: 10.1016/j.jmb.2024.168806] [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: 04/09/2024] [Revised: 09/25/2024] [Accepted: 09/25/2024] [Indexed: 10/02/2024]
Abstract
DNA binding protein from starved cells (Dps) is a miniature ferritin complex, which plays a vital role in protecting bacterial DNA during starvation to maintain the integrity of bacteria under hostile conditions. Several approaches, including cryo-electron tomography, have been previously implemented by other research groups to decipher the structure of the Dps protein bound to DNA. However, none of the structures of the Dps-DNA complex was resolved to high resolution to identify the DNA binding residues. Like other bacteria, Mycobacterium smegmatis also expresses Dps2 (called MsDps2), which binds DNA to protect it under oxidative stress conditions. In this study, we implemented various biochemical and biophysical studies to characterize the DNA protein interactions of Dps2 protein from Mycobacterium smegmatis. We employed single-particle cryo-EM-based structural analysis of MsDps2-DNA complexes and identified that the region close to the N-terminus confers the DNA binding property. Based on cryo-EM data, we also pinpointed several arginine residues, proximal to the DNA binding region, responsible for DNA binding. We also performed mutations of these residues, which dramatically reduced the MsDps2-DNA interaction. In addition, we proposed a model that elucidates the mechanism of DNA compaction, which adapts a lattice-like structure. We performed single-molecule imaging of MsDps2-DNA interactions that corroborate well with our structural studies. Taken together, our results delineate the specific MsDps2 residues that play an important role in DNA binding and compaction, providing new insights into Mycobacterial DNA compaction mechanisms under stress conditions.
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Affiliation(s)
- Priyanka Garg
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Thejas Satheesh
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India.
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35
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Sarkar D, Khan AH, Polepalli S, Sarkar R, Das PK, Dutta S, Sahoo N, Bhunia A. Multiscale Materials Engineering via Self-Assembly of Pentapeptide Derivatives from SARS CoV E Protein. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2404373. [PMID: 39011730 DOI: 10.1002/smll.202404373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/26/2024] [Indexed: 07/17/2024]
Abstract
Short peptide-based supramolecular hydrogels hold enormous potential for a wide range of applications. However, the gelation of these systems is very challenging to control. Minor changes in the peptide sequence can significantly influence the self-assembly mechanism and thereby the gelation propensity. The involvement of SARS CoV E protein in the assembly and release of the virus suggests that it may have inherent self-assembling properties that can contribute to the development of hydrogels. Here, three pentapeptide sequences derived from C-terminal of SARS CoV E protein are explored with same amino acid residues but different sequence distributions and discovered a drastic difference in the gelation propensity. By combining spectroscopic and microscopic techniques, the relationship between peptide sequence arrangement and molecular assembly structure are demonstrated, and how these influence the mechanical properties of the hydrogel. The present study expands the variety of secondary structures for generating supramolecular hydrogels by introducing the 310-helix as the primary building block for gelation, facilitated by a water-mediated structural transition into β-sheet conformation. Moreover, these Fmoc-modified pentapeptide hydrogels/supramolecular assemblies with tunable morphology and mechanical properties are suitable for tissue engineering, injectable delivery, and 3D bio-printing applications.
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Affiliation(s)
- Dibakar Sarkar
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Kolkata, 700 091, India
| | - Aftab Hossain Khan
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2A&B Raja S C Mullick Road, Kolkata, 700 032, India
| | - Sainath Polepalli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| | | | - Prasanta Kumar Das
- School of Biological Sciences, Indian Association for the Cultivation of Science, 2A&B Raja S C Mullick Road, Kolkata, 700 032, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| | - Nirakar Sahoo
- School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Anirban Bhunia
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake, EN 80, Kolkata, 700 091, India
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36
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Cameron CJF, Seager SJH, Sigworth FJ, Tagare HD, Gerstein MB. REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers. Commun Biol 2024; 7:1421. [PMID: 39482410 PMCID: PMC11528043 DOI: 10.1038/s42003-024-07045-0] [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: 04/11/2024] [Accepted: 10/10/2024] [Indexed: 11/03/2024] Open
Abstract
Cryo-EM particle identification from micrographs ("picking") is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computational algorithms ("pickers") identify different particle sets, complicating the selection of the best-suited picker for a protein of interest. Here, we present REliable PIcking by Consensus (REPIC), a computational approach to identifying particles common to the output of multiple pickers. We frame consensus particle picking as a graph problem, which REPIC solves using integer linear programming. REPIC picks high-quality particles even when the best picker is not known a priori or a protein is difficult-to-pick (e.g., NOMPC ion channel). Reconstructions using consensus particles without particle filtering achieve resolutions comparable to those from particles picked by experts. Our results show that REPIC requires minimal (often no) manual intervention, and considerably reduces the burden on cryo-EM users for picker selection and particle picking. Availability: https://github.com/ccameron/REPIC .
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Affiliation(s)
- Christopher J F Cameron
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA.
| | - Sebastian J H Seager
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fred J Sigworth
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Hemant D Tagare
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA.
- Department of Computer Science, Yale University, New Haven, CT, USA.
- Department of Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA.
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37
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Comas-Garcia M. How structural biology has changed our understanding of icosahedral viruses. J Virol 2024; 98:e0111123. [PMID: 39291975 PMCID: PMC11495149 DOI: 10.1128/jvi.01111-23] [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: 09/19/2024] Open
Abstract
Cryo-electron microscopy and tomography have allowed us to unveil the remarkable structure of icosahedral viruses. However, in the past few years, the idea that these viruses must have perfectly symmetric virions, but in some cases, it might not be true. This has opened the door to challenging paradigms in structural virology and raised new questions about the biological implications of "unusual" or "defective" symmetries and structures. Also, the continual improvement of these technologies, coupled with more rigorous sample purification protocols, improvements in data processing, and the use of artificial intelligence, has allowed solving the structure of sub-viral particles in highly heterogeneous samples and finding novel symmetries or structural defects. In this review, I initially analyzed the case of the symmetry and composition of hepatitis B virus-produced spherical sub-viral particles. Then, I focused on Alphaviruses as an example of "imperfect" icosahedrons and analyzed how structural biology has changed our understanding of the Alphavirus assembly and some biological implications arising from these discoveries.
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Affiliation(s)
- Mauricio Comas-Garcia
- Science Department, Autonomous University of San Luis Potosi, San Luis Potosí, Mexico
- High-Resolution Microscopy Section, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosi, San Luis Potosi, Mexico
- Translational and Molecular Medicine Section, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosi, San Luis Potosí, Mexico
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38
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Sun D, Storek KM, Tegunov D, Yang Y, Arthur CP, Johnson M, Quinn JG, Liu W, Han G, Girgis HS, Alexander MK, Murchison AK, Shriver S, Tam C, Ijiri H, Inaba H, Sano T, Yanagida H, Nishikawa J, Heise CE, Fairbrother WJ, Tan MW, Skelton N, Sandoval W, Sellers BD, Ciferri C, Smith PA, Reid PC, Cunningham CN, Rutherford ST, Payandeh J. The discovery and structural basis of two distinct state-dependent inhibitors of BamA. Nat Commun 2024; 15:8718. [PMID: 39379361 PMCID: PMC11461620 DOI: 10.1038/s41467-024-52512-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/09/2024] [Indexed: 10/10/2024] Open
Abstract
BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
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Affiliation(s)
- Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Dimitry Tegunov
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Ying Yang
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Christopher P Arthur
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Matthew Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - John G Quinn
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Weijing Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
- PTM Bio, Alameda, CA, USA
| | - Hany S Girgis
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Mary Kate Alexander
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Austin K Murchison
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Stephanie Shriver
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Christine Tam
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | - Christopher E Heise
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
- Septerna, South San Francisco, CA, USA
| | - Wayne J Fairbrother
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Vilya, South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Peter A Smith
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
- Revagenix, San Mateo, CA, USA
| | | | - Christian N Cunningham
- Department of Peptide Therapeutics, Genentech Inc., South San Francisco, CA, USA.
- PeptiDream, Kawasaki, Japan.
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
- Exelixis, Alameda, CA, USA.
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39
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Penzes JJ, Holm M, Yost SA, Kaelber JT. Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles. Cell 2024; 187:5604-5619.e14. [PMID: 39208798 PMCID: PMC11781814 DOI: 10.1016/j.cell.2024.07.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect-rearing facilities have experienced a distinctive larval pathology and colony collapse of farmed Zophobas morio (superworm). By means of cryo-EM, we discovered the causative agent: a densovirus that we named Zophobas morio black wasting virus (ZmBWV). We confirmed the etiology of disease by fulfilling Koch's postulates and characterizing strains from across the United States. ZmBWV is a member of the family Parvoviridae with a 5,542 nt genome, and we describe intersubunit interactions explaining its expanded internal volume relative to human parvoviruses. Cryo-EM structures at resolutions up to 2.1 Å revealed single-strand DNA (ssDNA) ordering at the capsid inner surface pinned by base-binding pockets in the capsid inner surface. Also, we demonstrated the prophylactic potential of non-pathogenic strains to provide cross-protection in vivo.
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Affiliation(s)
- Judit J Penzes
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Martin Holm
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Samantha A Yost
- Research and Early Development, REGENXBIO Inc., Rockville, MD, USA
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
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40
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Vargas J, Modrego A, Canabal H, Martin-Benito J. Semantic segmentation-based detection algorithm for challenging cryo-electron microscopy RNP samples. Front Mol Biosci 2024; 11:1473609. [PMID: 39411403 PMCID: PMC11473350 DOI: 10.3389/fmolb.2024.1473609] [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: 07/31/2024] [Accepted: 09/17/2024] [Indexed: 10/19/2024] Open
Abstract
In this study, we present a novel and robust methodology for the automatic detection of influenza A virus ribonucleoproteins (RNPs) in single-particle cryo-electron microscopy (cryo-EM) images. Utilizing a U-net architecture-a type of convolutional neural network renowned for its efficiency in biomedical image segmentation-our approach is based on a pretraining phase with a dataset annotated through visual inspection. This dataset facilitates the precise identification of filamentous RNPs, including the localization of the filaments and their terminal coordinates. A key feature of our method is the application of semantic segmentation techniques, enabling the automated categorization of micrograph pixels into distinct classifications of particle and background. This deep learning strategy allows to robustly detect these intricate particles, a crucial step in achieving high-resolution reconstructions in cryo-EM studies. To encourage collaborative advancements in the field, we have made our routines, the pretrained U-net model, and the training dataset publicly accessible. The reproducibility and accessibility of these resources aim to facilitate further research and validation in the realm of cryo-EM image analysis.
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Affiliation(s)
- J. Vargas
- Departamento de Óptica, Universidad Complutense de Madrid, Madrid, Spain
| | - A. Modrego
- Department of Macromolecular Structure, National Centre for Biotechnology, Madrid, Spain
| | - H. Canabal
- Departamento de Óptica, Universidad Complutense de Madrid, Madrid, Spain
| | - J. Martin-Benito
- Department of Macromolecular Structure, National Centre for Biotechnology, Madrid, Spain
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41
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Lometto S, Sparvoli D, Malengo G, Heimerl T, Hochberg GKA. The mitochondrial citrate synthase from Tetrahymena thermophila does not form an intermediate filament. Eur J Protistol 2024; 96:126121. [PMID: 39432950 DOI: 10.1016/j.ejop.2024.126121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 10/06/2024] [Accepted: 10/07/2024] [Indexed: 10/23/2024]
Abstract
The mitochondrial citrate synthase (mCS) purified from the ciliate Tetrahymena thermophila has been reported to form intermediate-filament-like structures during conjugation and to self-assemble into fibers when recombinantly expressed. This would represent a rare example of a tractable and recent origin of a novel cytoskeletal element. In an attempt to investigate the evolutionary emergence of this behavior, we re-investigated the ability of Tetrahymena's mCS to form filaments in vivo. Using strep-tagged mCS in Tetrahymena and monoclonal antibodies, we found no evidence of filamentous structures during conjugation or starvation. Extensive biochemical characterization of mCS revealed that the self-assembly of recombinant protein is triggered by a specific chemical moiety shared by MES and HEPES buffers used in previous studies. The absence of indicative phenotypes in fiber-deficient GFP-tagged mutants indicates that Tetrahymena mCS did not evolve a structural role in sexual reproduction or metabolic regulation.
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Affiliation(s)
- Stefano Lometto
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniela Sparvoli
- Laboratory of Pathogen Host Interactions, UMR5294, Université de Montpellier, INSERM, CNRS, Montpellier, Pl E. Bataillon Bat. 24 2et, CC107, Montpellier 34095, France
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany; Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35043 Marburg, Germany.
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42
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Shen H, Lynch EM, Watson JL, Wu K, Bai H, Sheffler W, Derivery E, Kollman J, Baker D. Nucleation limited assembly and polarized growth of a de novo-designed allosterically modulatable protein filament. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.20.613980. [PMID: 39345553 PMCID: PMC11429946 DOI: 10.1101/2024.09.20.613980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The design of inducibly assembling protein nanomaterials is an outstanding challenge. Here, we describe the computational design of a protein filament formed from a monomeric subunit which binds a peptide ligand. The cryoEM structure of the micron scale fibers is very close to the computational design model. The ligand acts as a tunable allosteric modulator: while not part of the fiber subunit-subunit interfaces, the assembly of the filament is dependent on ligand addition, with longer peptides having more extensive interaction surfaces with the monomer promoting more rapid growth. Seeded growth and capping experiments reveal that the filaments grow primarily from one end. Oligomers containing 12 copies of the peptide ligand nucleate fiber assembly from monomeric subunit and peptide mixtures at concentrations where assembly occurs very slowly, likely by generating critical local concentrations of monomer in the assembly competent conformation. Following filament assembly, the peptide ligand can be exchanged with free peptide in solution, and it can be readily fused to any functional protein of interest, opening the door to a wide variety of tunable engineered materials.
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Affiliation(s)
- Hao Shen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Eric M. Lynch
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joseph L. Watson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hua Bai
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Justin Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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43
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Fan C, Cowgill J, Howard RJ, Lindahl E. Divergent mechanisms of steroid inhibition in the human ρ1 GABA A receptor. Nat Commun 2024; 15:7795. [PMID: 39242530 PMCID: PMC11379708 DOI: 10.1038/s41467-024-51904-7] [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: 04/12/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024] Open
Abstract
ρ-type γ-aminobutyric acid-A (GABAA) receptors are widely distributed in the retina and brain, and are potential drug targets for the treatment of visual, sleep and cognitive disorders. Endogenous neuroactive steroids including β-estradiol and pregnenolone sulfate negatively modulate the function of ρ1 GABAA receptors, but their inhibitory mechanisms are not clear. By combining five cryo-EM structures with electrophysiology and molecular dynamics simulations, we characterize binding sites and negative modulation mechanisms of β-estradiol and pregnenolone sulfate at the human ρ1 GABAA receptor. β-estradiol binds in a pocket at the interface between extracellular and transmembrane domains, apparently specific to the ρ subfamily, and disturbs allosteric conformational transitions linking GABA binding to pore opening. In contrast, pregnenolone sulfate binds inside the pore to block ion permeation, with a preference for activated structures. These results illuminate contrasting mechanisms of ρ1 inhibition by two different neuroactive steroids, with potential implications for subtype-specific gating and pharmacological design.
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Affiliation(s)
- Chen Fan
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - John Cowgill
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Erik Lindahl
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
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44
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Abe KM, Li G, He Q, Grant T, Lim CJ. Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing. Nat Commun 2024; 15:7705. [PMID: 39231985 PMCID: PMC11375022 DOI: 10.1038/s41467-024-52091-1] [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: 02/17/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Embryogenesis Abundant (LEA) proteins to withstand desiccation stress. Here we show that these LEA proteins, when used as additives during plunge freezing, effectively mitigate AWI damage to fragile multi-subunit molecular samples. The resulting high-resolution cryo-EM maps are comparable to or better than those obtained using existing AWI damage mitigation methods. Cryogenic electron tomography reveals that particles are localized at specific interfaces, suggesting LEA proteins form a barrier at the AWI. This interaction may explain the observed sample-dependent preferred orientation of particles. LEA proteins offer a simple, cost-effective, and adaptable approach for cryo-EM structural biologists to overcome AWI-related sample damage, potentially revitalizing challenging projects and advancing the field of structural biology.
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Affiliation(s)
- Kaitlyn M Abe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gan Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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45
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Liou SH, Boggavarapu R, Cohen NR, Zhang Y, Sharma I, Zeheb L, Mukund Acharekar N, Rodgers HD, Islam S, Pitts J, Arze C, Swaminathan H, Yozwiak N, Ong T, Hajjar RJ, Chang Y, Swanson KA, Delagrave S. Structure of anellovirus-like particles reveal a mechanism for immune evasion. Nat Commun 2024; 15:7219. [PMID: 39174507 PMCID: PMC11341859 DOI: 10.1038/s41467-024-51064-8] [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: 12/18/2023] [Accepted: 07/26/2024] [Indexed: 08/24/2024] Open
Abstract
Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic features of the virus, such as the identity of its capsid protein and the structure of the viral particle, have been unclear until now. Here, we use cryogenic electron microscopy to describe the first structure of an ANV-like particle. The particle, formed by 60 jelly roll domain-containing ANV capsid proteins, forms an icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axis to form crown-like features. The base of the spike domain, the P1 subdomain, shares some sequence conservation between ANV strains while a hypervariable region, forming the P2 subdomain, is at the spike domain apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved domains while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.
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Affiliation(s)
- Shu-Hao Liou
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Carbon Biosciences, Waltham, MA, 02451, USA
| | | | - Noah R Cohen
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- AbbVie Bioresearch Center, Worcester, MA, 01605, USA
| | - Yue Zhang
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Ishwari Sharma
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Lynn Zeheb
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | | | - Hillary D Rodgers
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Saadman Islam
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- GSK, Cambridge, MA, 02139, USA
| | - Jared Pitts
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Cesar Arze
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Harish Swaminathan
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- DaCapo Brainscience, Cambridge, MA, 02139, USA
| | - Nathan Yozwiak
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, 02139, USA
| | - Tuyen Ong
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Roger J Hajjar
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, 02139, USA
| | - Yong Chang
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Kurt A Swanson
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA.
| | - Simon Delagrave
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Delagrave Life Sciences, LLC, Sudbury, MA, 01776, USA
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46
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Nandi P, DeVore K, Wang F, Li S, Walker JD, Truong TT, LaPorte MG, Wipf P, Schlager H, McCleerey J, Paquette W, Columbres RCA, Gan T, Poh YP, Fromme P, Flint AJ, Wolf M, Huryn DM, Chou TF, Chiu PL. Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors. Commun Chem 2024; 7:177. [PMID: 39122922 PMCID: PMC11316111 DOI: 10.1038/s42004-024-01267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Human p97 ATPase is crucial in various cellular processes, making it a target for inhibitors to treat cancers, neurological, and infectious diseases. Triazole allosteric p97 inhibitors have been demonstrated to match the efficacy of CB-5083, an ATP-competitive inhibitor, in cellular models. However, the mechanism is not well understood. This study systematically investigates the structures of new triazole inhibitors bound to both wild-type and disease mutant forms of p97 and measures their effects on function. These inhibitors bind at the interface of the D1 and D2 domains of each p97 subunit, shifting surrounding helices and altering the loop structures near the C-terminal α2 G helix to modulate domain-domain communications. A key structural moiety of the inhibitor affects the rotameric conformations of interacting side chains, indirectly modulating the N-terminal domain conformation in p97 R155H mutant. The differential effects of inhibitor binding to wild-type and mutant p97 provide insights into drug design with enhanced specificity, particularly for oncology applications.
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Affiliation(s)
- Purbasha Nandi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kira DeVore
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Joel D Walker
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thanh Tung Truong
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
- Faculty of Pharmacy, Phenikaa University, Hanoi, Vietnam
| | - Matthew G LaPorte
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John McCleerey
- Curia Global, Albany, NY, USA
- Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
| | | | - Rod Carlo A Columbres
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Taiping Gan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yu-Ping Poh
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Mechanism of Evolution, Arizona State University, Tempe, AZ, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
| | - Andrew J Flint
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Donna M Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA.
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA.
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47
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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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48
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Ukleja M, Kricks L, Torrens G, Peschiera I, Rodrigues-Lopes I, Krupka M, García-Fernández J, Melero R, Del Campo R, Eulalio A, Mateus A, López-Bravo M, Rico AI, Cava F, Lopez D. Flotillin-mediated stabilization of unfolded proteins in bacterial membrane microdomains. Nat Commun 2024; 15:5583. [PMID: 38961085 PMCID: PMC11222466 DOI: 10.1038/s41467-024-49951-1] [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: 02/21/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
The function of many bacterial processes depends on the formation of functional membrane microdomains (FMMs), which resemble the lipid rafts of eukaryotic cells. However, the mechanism and the biological function of these membrane microdomains remain unclear. Here, we show that FMMs in the pathogen methicillin-resistant Staphylococcus aureus (MRSA) are dedicated to confining and stabilizing proteins unfolded due to cellular stress. The FMM scaffold protein flotillin forms a clamp-shaped oligomer that holds unfolded proteins, stabilizing them and favoring their correct folding. This process does not impose a direct energy cost on the cell and is crucial to survival of ATP-depleted bacteria, and thus to pathogenesis. Consequently, FMM disassembling causes the accumulation of unfolded proteins, which compromise MRSA viability during infection and cause penicillin re-sensitization due to PBP2a unfolding. Thus, our results indicate that FMMs mediate ATP-independent stabilization of unfolded proteins, which is essential for bacterial viability during infection.
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Affiliation(s)
- Marta Ukleja
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Lara Kricks
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Gabriel Torrens
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
| | - Ilaria Peschiera
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Ines Rodrigues-Lopes
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
| | - Marcin Krupka
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Julia García-Fernández
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Roberto Melero
- Department of Structural Biology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Rosa Del Campo
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ramón y Cajal Hospital, 28034, Madrid, Spain
| | - Ana Eulalio
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504, Coimbra, Portugal
- Department of Life Sciences, Center for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, United Kingdom
| | - André Mateus
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
- Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden
| | - María López-Bravo
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Ana I Rico
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS). Umeå Center for Microbial Research (UCMR). Science for Life Laboratory (SciLifeLab), Umeå, SE-901 87, Sweden
| | - Daniel Lopez
- Department of Microbiology, National Centre for Biotechnology, Spanish National Research Council (CNB-CSIC), Madrid, 28049, Spain.
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49
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Benoit MPMH, Rao L, Asenjo AB, Gennerich A, Sosa H. Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L. Nat Commun 2024; 15:5530. [PMID: 38956021 PMCID: PMC11219953 DOI: 10.1038/s41467-024-48720-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/10/2024] [Indexed: 07/04/2024] Open
Abstract
Mutations in the microtubule-associated motor protein KIF1A lead to severe neurological conditions known as KIF1A-associated neurological disorders (KAND). Despite insights into its molecular mechanism, high-resolution structures of KIF1A-microtubule complexes remain undefined. Here, we present 2.7-3.5 Å resolution structures of dimeric microtubule-bound KIF1A, including the pathogenic P305L mutant, across various nucleotide states. Our structures reveal that KIF1A binds microtubules in one- and two-heads-bound configurations, with both heads exhibiting distinct conformations with tight inter-head connection. Notably, KIF1A's class-specific loop 12 (K-loop) forms electrostatic interactions with the C-terminal tails of both α- and β-tubulin. The P305L mutation does not disrupt these interactions but alters loop-12's conformation, impairing strong microtubule-binding. Structure-function analysis reveals the K-loop and head-head coordination as major determinants of KIF1A's superprocessive motility. Our findings advance the understanding of KIF1A's molecular mechanism and provide a basis for developing structure-guided therapeutics against KAND.
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Affiliation(s)
- Matthieu P M H Benoit
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Lu Rao
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ana B Asenjo
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Arne Gennerich
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Hernando Sosa
- Department of Biochemistry and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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50
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Bi M, Wang X, Wang J, Xu J, Sun W, Adediwura VA, Miao Y, Cheng Y, Ye L. Structure and function of a ligand-free GPCR-Gαβγ intermediate complex. RESEARCH SQUARE 2024:rs.3.rs-4566652. [PMID: 38978591 PMCID: PMC11230506 DOI: 10.21203/rs.3.rs-4566652/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Unraveling the signaling roles of intermediate complexes is pivotal for G protein-coupled receptor (GPCR) drug development. Despite hundreds of GPCR-Gαβγ structures, these snapshots primarily capture the fully activated complex. Consequently, the functions of intermediate GPCR-G protein complexes remain elusive. Guided by a conformational landscape visualized via 19F quantitative NMR and molecular dynamics (MD) simulation, we determined the structure of an intermediate GPCR-mini-Gαsβγ complex at 2.8 Å using cryo-EM, by blocking its transition to the fully activated complex. Furthermore, we presented direct evidence that the intermediate complex initiates a rate-limited nucleotide exchange without progressing to the fully activated complex, in which the α-helical domain (AHD) of the Gα is partially open engaged by a second nucleotide. Our MD simulation supported the pose of the AHD domain. These advances bridge a significant gap in our understanding the complexity of GPCR signaling.
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Affiliation(s)
- Maxine Bi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | - Xudong Wang
- Department of Molecular Biosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL USA 33620
| | - Jinan Wang
- Department of Pharmacology & Computational Medicinal Program, University of North Carolina at Chapel Hill, 116 Manning Drive, 11004C Mary Ellen Jones Building, Chapel Hill, NC 27599
| | - Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wenkai Sun
- Department of Molecular Biosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL USA 33620
| | - Victor Ayo Adediwura
- Department of Pharmacology & Computational Medicinal Program, University of North Carolina at Chapel Hill, 116 Manning Drive, 11004C Mary Ellen Jones Building, Chapel Hill, NC 27599
| | - Yinglong Miao
- Department of Pharmacology & Computational Medicinal Program, University of North Carolina at Chapel Hill, 116 Manning Drive, 11004C Mary Ellen Jones Building, Chapel Hill, NC 27599
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - Libin Ye
- Department of Molecular Biosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL USA 33620
- H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL, USA 33612
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