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Zhang H, Li X, Liu J, Lan YQ, Han Y. Advancing Single-Particle Analysis in Synthetic Chemical Systems: A Forward-Looking Discussion. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2406914. [PMID: 39180273 DOI: 10.1002/adma.202406914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/30/2024] [Indexed: 08/26/2024]
Abstract
Single-particle analysis (SPA) is a fundamental method of cryo-electron microscopy developed to resolve the structures of biological macromolecules. This method has seen significant success in structural biology, yet its potential applications in synthetic chemical systems remain underexplored. In this perspective article, SPA and associated electron microscopy techniques are first briefly introduced. It is then proposed that SPA is well-suited for structural analysis of chemical systems where discrete, identical macromolecules can be readily obtained. Applicable systems include various clusters such as coinage metal clusters, metal-oxo/sulfur clusters, metal-organic clusters, and supramolecular compounds like coordination cages and metallo-supramolecular cages. When high-quality large single crystals are unattainable, SPA provides an alternative method for determining their structures. Beyond these end products, it is suggested that SPA can be instrumental in studying synthetic intermediates of materials with specific building units, such as metal-organic frameworks and zeolites. Given that various intermediates coexist in the reaction system, a purification step is necessary before conducting SPA, which can be facilitated by soft-landing electrospray ionization mass spectrometry.
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Affiliation(s)
- Hui Zhang
- Center for Electron Microscopy, South China University of Technology, Guangzhou, 510640, China
- School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Basic Research Center of Excellence for Energy & Information Polymer Materials, Guangzhou, 510640, China
| | - Xiaopeng Li
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518055, China
| | - Jiang Liu
- School of Chemistry, South China Normal University, Guangzhou, 510631, China
| | - Ya-Qian Lan
- School of Chemistry, South China Normal University, Guangzhou, 510631, China
| | - Yu Han
- Center for Electron Microscopy, South China University of Technology, Guangzhou, 510640, China
- School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Basic Research Center of Excellence for Energy & Information Polymer Materials, Guangzhou, 510640, China
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Duan J, He XH, Li SJ, Xu HE. Cryo-electron microscopy for GPCR research and drug discovery in endocrinology and metabolism. Nat Rev Endocrinol 2024; 20:349-365. [PMID: 38424377 DOI: 10.1038/s41574-024-00957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, with many GPCRs having crucial roles in endocrinology and metabolism. Cryogenic electron microscopy (cryo-EM) has revolutionized the field of structural biology, particularly regarding GPCRs, over the past decade. Since the first pair of GPCR structures resolved by cryo-EM were published in 2017, the number of GPCR structures resolved by cryo-EM has surpassed the number resolved by X-ray crystallography by 30%, reaching >650, and the number has doubled every ~0.63 years for the past 6 years. At this pace, it is predicted that the structure of 90% of all human GPCRs will be completed within the next 5-7 years. This Review highlights the general structural features and principles that guide GPCR ligand recognition, receptor activation, G protein coupling, arrestin recruitment and regulation by GPCR kinases. The Review also highlights the diversity of GPCR allosteric binding sites and how allosteric ligands could dictate biased signalling that is selective for a G protein pathway or an arrestin pathway. Finally, the authors use the examples of glycoprotein hormone receptors and glucagon-like peptide 1 receptor to illustrate the effect of cryo-EM on understanding GPCR biology in endocrinology and metabolism, as well as on GPCR-related endocrine diseases and drug discovery.
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Affiliation(s)
- Jia Duan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xin-Heng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shu-Jie Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Traditional Chinese Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Matinyan S, Filipcik P, van Genderen E, Abrahams JP. DiffraGAN: a conditional generative adversarial network for phasing single molecule diffraction data to atomic resolution. Front Mol Biosci 2024; 11:1386963. [PMID: 38841186 PMCID: PMC11150865 DOI: 10.3389/fmolb.2024.1386963] [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: 02/16/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction Proteins that adopt multiple conformations pose significant challenges in structural biology research and pharmaceutical development, as structure determination via single particle cryo-electron microscopy (cryo-EM) is often impeded by data heterogeneity. In this context, the enhanced signal-to-noise ratio of single molecule cryo-electron diffraction (simED) offers a promising alternative. However, a significant challenge in diffraction methods is the loss of phase information, which is crucial for accurate structure determination. Methods Here, we present DiffraGAN, a conditional generative adversarial network (cGAN) that estimates the missing phases at high resolution from a combination of single particle high-resolution diffraction data and low-resolution image data. Results For simulated datasets, DiffraGAN allows effectively determining protein structures at atomic resolution from diffraction patterns and noisy low-resolution images. Discussion Our findings suggest that combining single particle cryo-electron diffraction with advanced generative modeling, as in DiffraGAN, could revolutionize the way protein structures are determined, offering an alternative and complementary approach to existing methods.
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Affiliation(s)
- S. Matinyan
- Biozentrum, Basel University, Basel, Switzerland
| | - P. Filipcik
- Biozentrum, Basel University, Basel, Switzerland
| | | | - J. P. Abrahams
- Biozentrum, Basel University, Basel, Switzerland
- Paul Scherrer Institute, Villigen, Switzerland
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Corum MR, Venkannagari H, Hryc CF, Baker ML. Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure. Biophys J 2024; 123:435-450. [PMID: 38268190 PMCID: PMC10912932 DOI: 10.1016/j.bpj.2024.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
Over the last 15 years, structural biology has seen unprecedented development and improvement in two areas: electron cryo-microscopy (cryo-EM) and predictive modeling. Once relegated to low resolutions, single-particle cryo-EM is now capable of achieving near-atomic resolutions of a wide variety of macromolecular complexes. Ushered in by AlphaFold, machine learning has powered the current generation of predictive modeling tools, which can accurately and reliably predict models for proteins and some complexes directly from the sequence alone. Although they offer new opportunities individually, there is an inherent synergy between these techniques, allowing for the construction of large, complex macromolecular models. Here, we give a brief overview of these approaches in addition to illustrating works that combine these techniques for model building. These examples provide insight into model building, assessment, and limitations when integrating predictive modeling with cryo-EM density maps. Together, these approaches offer the potential to greatly accelerate the generation of macromolecular structural insights, particularly when coupled with experimental data.
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Affiliation(s)
- Michael R Corum
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas
| | - Harikanth Venkannagari
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas
| | - Corey F Hryc
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, Texas.
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Cuervo A, Losana P, Carrascosa JL. Observation of Bacteriophage Ultrastructure by Cryo-Electron Microscopy. Methods Mol Biol 2024; 2734:13-25. [PMID: 38066360 DOI: 10.1007/978-1-0716-3523-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Transmission electron microscopy (TEM) is an ideal method to observe and determine the structure of bacteriophages. From early studies by negative staining to the present atomic structure models derived from cryo-TEM, bacteriophage detection, classification, and structure determination have been mostly done by electron microscopy. Although embedding in metal salts has been a routine method for virus observation for many years, the preservation of bacteriophages in a thin layer of fast frozen buffer has proven to be the most convenient preparation method for obtaining images using cryo-electron microscopy (cryo-EM). In this technique, frozen samples are observed at liquid nitrogen temperature, and the images are acquired using different recording media. The incorporation of direct electron detectors has been a fundamental step in achieving atomic resolution images of a number of viruses. These projection images can be numerically combined using different approaches to render a three-dimensional model of the virus. For those viral components exhibiting any symmetry, averaging can nowadays achieve atomic structures in most cases. Image processing methods have also evolved to improve the resolution in asymmetric viral components or regions showing different types of symmetries (symmetry mismatch).
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Affiliation(s)
- Ana Cuervo
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
| | - Patricia Losana
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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6
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Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [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: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Asensio-Cob D, Rodríguez JM, Luque D. Rotavirus Particle Disassembly and Assembly In Vivo and In Vitro. Viruses 2023; 15:1750. [PMID: 37632092 PMCID: PMC10458742 DOI: 10.3390/v15081750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Rotaviruses (RVs) are non-enveloped multilayered dsRNA viruses that are major etiologic agents of diarrheal disease in humans and in the young in a large number of animal species. The viral particle is composed of three different protein layers that enclose the segmented dsRNA genome and the transcriptional complexes. Each layer defines a unique subparticle that is associated with a different phase of the replication cycle. Thus, while single- and double-layered particles are associated with the intracellular processes of selective packaging, genome replication, and transcription, the viral machinery necessary for entry is located in the third layer. This modular nature of its particle allows rotaviruses to control its replication cycle by the disassembly and assembly of its structural proteins. In this review, we examine the significant advances in structural, molecular, and cellular RV biology that have contributed during the last few years to illuminating the intricate details of the RV particle disassembly and assembly processes.
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Affiliation(s)
- Dunia Asensio-Cob
- Department of Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G0A4, Canada;
| | - Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Daniel Luque
- Electron Microscopy Unit UCCT/ISCIII, 28220 Majadahonda, Spain
- School of Biomedical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, NSW 2052, Australia
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Fernandez de la Mora J, Almazán F, Rodríguez JM. Spontaneous Interconversion between Different Narrowly Defined Shapes of Rotavirus Double-Layered Particles Studied in Real Time by High-Resolution Mobility Analysis. Anal Chem 2023; 95:11483-11490. [PMID: 37463035 DOI: 10.1021/acs.analchem.3c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Rotavirus double-layered particles (DLPs) are studied in the gas phase with a high-resolution differential mobility analyzer (DMA). DLPs were transferred to 10 mM aqueous ammonium acetate, electrosprayed into the gas phase, converted into primarily singly charged particles, and DMA-analyzed. Up to seven slightly different conformations were resolved, whose apparently random, fast (minutes), and reversible interconversions were followed in real time. They sometimes evolved into just two distinct structures, with periods of one dominating over the other and vice versa. Differences between the DLP structures in solution and in the gas phase are clearly revealed by the smaller DLP diameter found here (60 versus 70 nm). Nevertheless, we argue that the multiple gas-phase conformers observed originate in as many conformations pre-existing in solution. We further hypothesize that these conformers correspond to incomplete DLPs having lost some of the VP6 trimer quintets surrounding each of the 12 5-fold axes. Instances of this peculiar loss have been previously documented by cryoelectron microscopy for the rotavirus Wa strain, as well as via charge detection mass spectrometry for five other rotavirus strains included in the RotaTec vaccine. Evidence of this loss systematically found for all 7 rotavirus types so far studied in aqueous ammonium acetate may be a special feature of this electrolyte.
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Affiliation(s)
- Juan Fernandez de la Mora
- Department of Mechanical Engineering and Materials Science, Yale University, 9 Hillhouse Avenue, New Haven, Connecticut 06520-8286, United States
| | - Fernando Almazán
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
| | - Javier M Rodríguez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
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9
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Pei X, Zhou L, Huang C, Boyce M, Kim JS, Liberti E, Hu Y, Sasaki T, Nellist PD, Zhang P, Stuart DI, Kirkland AI, Wang P. Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer. Nat Commun 2023; 14:3027. [PMID: 37230988 PMCID: PMC10212999 DOI: 10.1038/s41467-023-38268-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 04/22/2023] [Indexed: 05/27/2023] Open
Abstract
Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.
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Affiliation(s)
- Xudong Pei
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Liqi Zhou
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
- Department of Physics, University of Warwick, Coventry, UK
| | - Chen Huang
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Mark Boyce
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Judy S Kim
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Department of Materials, University of Oxford, Oxford, UK
| | - Emanuela Liberti
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
| | - Yiming Hu
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | | | | | - Peijun Zhang
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - David I Stuart
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Angus I Kirkland
- The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK.
- Department of Materials, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
| | - Peng Wang
- National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
- Department of Physics, University of Warwick, Coventry, UK.
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Andrusenko I, Gemmi M. 3D
electron diffraction for structure determination of small‐molecule nanocrystals: A possible breakthrough for the pharmaceutical industry. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1810. [PMID: 35595285 PMCID: PMC9539612 DOI: 10.1002/wnan.1810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
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Rotavirus Spike Protein VP4 Mediates Viroplasm Assembly by Association to Actin Filaments. J Virol 2022; 96:e0107422. [PMID: 35938869 PMCID: PMC9472636 DOI: 10.1128/jvi.01074-22] [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] [Indexed: 11/30/2022] Open
Abstract
Rotavirus (RV) viroplasms are cytosolic inclusions where both virus genome replication and primary steps of virus progeny assembly take place. A stabilized microtubule cytoskeleton and lipid droplets are required for the viroplasm formation, which involves several virus proteins. The viral spike protein VP4 has not previously been shown to have a direct role in viroplasm formation. However, it is involved with virus-cell attachment, endocytic internalization, and virion morphogenesis. Moreover, VP4 interacts with actin cytoskeleton components, mainly in processes involving virus entrance and egress, and thereby may have an indirect role in viroplasm formation. In this study, we used reverse genetics to construct a recombinant RV, rRV/VP4-BAP, that contains a biotin acceptor peptide (BAP) in the K145-G150 loop of the VP4 lectin domain, permitting live monitoring. The recombinant virus was replication competent but showed a reduced fitness. We demonstrate that rRV/VP4-BAP infection, as opposed to rRV/wt infection, did not lead to a reorganized actin cytoskeleton as viroplasms formed were insensitive to drugs that depolymerize actin and inhibit myosin. Moreover, wild-type (wt) VP4, but not VP4-BAP, appeared to associate with actin filaments. Similarly, VP4 in coexpression with NSP5 and NSP2 induced a significant increase in the number of viroplasm-like structures. Interestingly, a small peptide mimicking loop K145-G150 rescued the phenotype of rRV/VP4-BAP by increasing its ability to form viroplasms and hence improve virus progeny formation. Collectively, these results provide a direct link between VP4 and the actin cytoskeleton to catalyze viroplasm assembly. IMPORTANCE The spike protein VP4 participates in diverse steps of the rotavirus (RV) life cycle, including virus-cell attachment, internalization, modulation of endocytosis, virion morphogenesis, and virus egress. Using reverse genetics, we constructed for the first time a recombinant RV, rRV/VP4-BAP, harboring a heterologous peptide in the lectin domain (loop K145-G150) of VP4. The rRV/VP4-BAP was replication competent but with reduced fitness due to a defect in the ability to reorganize the actin cytoskeleton, which affected the efficiency of viroplasm assembly. This defect was rescued by adding a permeable small-peptide mimicking the wild-type VP4 loop K145-G150. In addition to revealing a new role of VP4, our findings suggest that rRV harboring an engineered VP4 could be used as a new dual vaccination platform providing immunity against RV and additional heterologous antigens.
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Wu JG, Yan Y, Zhang DX, Liu BW, Zheng QB, Xie XL, Liu SQ, Ge SX, Hou ZG, Xia NS. Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022; 33:452-472. [PMID: 34932487 DOI: 10.1109/tnnls.2021.3131325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recently, single-particle cryo-electron microscopy (cryo-EM) has become an indispensable method for determining macromolecular structures at high resolution to deeply explore the relevant molecular mechanism. Its recent breakthrough is mainly because of the rapid advances in hardware and image processing algorithms, especially machine learning. As an essential support of single-particle cryo-EM, machine learning has powered many aspects of structure determination and greatly promoted its development. In this article, we provide a systematic review of the applications of machine learning in this field. Our review begins with a brief introduction of single-particle cryo-EM, followed by the specific tasks and challenges of its image processing. Then, focusing on the workflow of structure determination, we describe relevant machine learning algorithms and applications at different steps, including particle picking, 2-D clustering, 3-D reconstruction, and other steps. As different tasks exhibit distinct characteristics, we introduce the evaluation metrics for each task and summarize their dynamics of technology development. Finally, we discuss the open issues and potential trends in this promising field.
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Martinez-Seidel F, Hsieh YC, Walther D, Kopka J, Pereira Firmino AA. [Formula: see text]: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes. BMC Bioinformatics 2021; 22:605. [PMID: 34930116 PMCID: PMC8686616 DOI: 10.1186/s12859-021-04510-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: 05/01/2021] [Accepted: 12/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Upon environmental stimuli, ribosomes are surmised to undergo compositional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter ([Formula: see text]), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit abundance changes under specific conditions are spatially confined to particular regions within the large ribosomal complex. RESULTS [Formula: see text] translates experimentally determined structures into graphs, with nodes representing proteins and edges the spatial proximity between them. In its first implementation, [Formula: see text] considers rProteins and ignores rRNA and other objects. Spatial regions are defined using a random walk with restart methodology, followed by a procedure to obtain a minimum set of regions that cover all proteins in the complex. Structural coherence is achieved by applying weights to the edges reflecting the physical proximity between purportedly contacting proteins. The weighting probabilistically guides the random-walk path trajectory. Parameter tuning during region selection provides the option to tailor the method to specific biological questions by yielding regions of different sizes with minimum overlaps. In addition, other graph community detection algorithms may be used for the [Formula: see text] workflow, considering that they yield different sized, non-overlapping regions. All tested algorithms result in the same node kernels under equivalent regions. Based on the defined regions, available abundance change information of proteins is mapped onto the graph and subsequently tested for enrichment in any of the defined spatial regions. We applied [Formula: see text] to the cytosolic ribosome structures of Saccharomyces cerevisiae, Oryctolagus cuniculus, and Triticum aestivum using datasets with available quantitative protein abundance change information. We found that in yeast, substoichiometric rProteins depleted from translating polysomes are significantly constrained to a ribosomal region close to the tRNA entry and exit sites. CONCLUSIONS [Formula: see text] offers a computational method to partition multi-protein complexes into structural regions and a statistical approach to test for spatial enrichments of any given subsets of proteins. [Formula: see text] is applicable to any multi-protein complex given appropriate structural and abundance-change data. [Formula: see text] is publicly available as a GitHub repository https://github.com/MSeidelFed/COSNet_i and can be installed using the python installer pip.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- School of BioSciences, University of Melbourne, Parkville, VC 3010 Australia
| | - Yin-Chen Hsieh
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Institute for Arctic and Marine Biology, UiT Arctic University of Norway, 9037 Tromsø, Norway
| | - Dirk Walther
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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Niklasch M, Zimmermann P, Nassal M. The Hepatitis B Virus Nucleocapsid-Dynamic Compartment for Infectious Virus Production and New Antiviral Target. Biomedicines 2021; 9:1577. [PMID: 34829806 PMCID: PMC8615760 DOI: 10.3390/biomedicines9111577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a severe liver disease responsible for nearly a million deaths each year. Most of HBV's only seven primary gene products are multifunctional. Though less obvious than for the multi-domain polymerase, P protein, this is equally crucial for Cp with its multiple roles in the viral life-cycle. Cp provides a stable genome container during extracellular phases, allows for directed intracellular genome transport and timely release from the capsid, and subsequent assembly of new nucleocapsids around P protein and the pregenomic (pg) RNA, forming a distinct compartment for reverse transcription. These opposing features are enabled by dynamic post-transcriptional modifications of Cp which result in dynamic structural alterations. Their perturbation by capsid assembly modulators (CAMs) is a promising new antiviral concept. CAMs inappropriately accelerate assembly and/or distort the capsid shell. We summarize the functional, biochemical, and structural dynamics of Cp, and discuss the therapeutic potential of CAMs based on clinical data. Presently, CAMs appear as a valuable addition but not a substitute for existing therapies. However, as part of rational combination therapies CAMs may bring the ambitious goal of a cure for CHB closer to reality.
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Affiliation(s)
| | | | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany; (M.N.); (P.Z.)
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15
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Zielinski M, Röder C, Schröder GF. Challenges in sample preparation and structure determination of amyloids by cryo-EM. J Biol Chem 2021; 297:100938. [PMID: 34224730 PMCID: PMC8335658 DOI: 10.1016/j.jbc.2021.100938] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023] Open
Abstract
Amyloids share a common architecture but play disparate biological roles in processes ranging from bacterial defense mechanisms to protein misfolding diseases. Their structures are highly polymorphic, which makes them difficult to study by X-ray diffraction or NMR spectroscopy. Our understanding of amyloid structures is due in large part to recent advances in the field of cryo-EM, which allows for determining the polymorphs separately. In this review, we highlight the main stepping stones leading to the substantial number of high-resolution amyloid fibril structures known today as well as recent developments regarding automation and software in cryo-EM. We discuss that sample preparation should move closer to physiological conditions to understand how amyloid aggregation and disease are linked. We further highlight new approaches to address heterogeneity and polymorphism of amyloid fibrils in EM image processing and give an outlook to the upcoming challenges in researching the structural biology of amyloids.
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Affiliation(s)
- Mara Zielinski
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Christine Röder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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16
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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17
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Uprety T, Sreenivasan CC, Hause BM, Li G, Odemuyiwa SO, Locke S, Morgan J, Zeng L, Gilsenan WF, Slovis N, Metcalfe L, Carter CN, Timoney P, Horohov D, Wang D, Erol E, Adam E, Li F. Identification of a Ruminant Origin Group B Rotavirus Associated with Diarrhea Outbreaks in Foals. Viruses 2021; 13:1330. [PMID: 34372536 PMCID: PMC8310321 DOI: 10.3390/v13071330] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022] Open
Abstract
Equine rotavirus group A (ERVA) is one of the most common causes of foal diarrhea. Starting in February 2021, there was an increase in the frequency of severe watery to hemorrhagic diarrhea cases in neonatal foals in Central Kentucky. Diagnostic investigation of fecal samples failed to detect evidence of diarrhea-causing pathogens including ERVA. Based on Illumina-based metagenomic sequencing, we identified a novel equine rotavirus group B (ERVB) in fecal specimens from the affected foals in the absence of any other known enteric pathogens. Interestingly, the protein sequence of all 11 segments had greater than 96% identity with group B rotaviruses previously found in ruminants. Furthermore, phylogenetic analysis demonstrated clustering of the ERVB with group B rotaviruses of caprine and bovine strains from the USA. Subsequent analysis of 33 foal diarrheic samples by RT-qPCR identified 23 rotavirus B-positive cases (69.69%). These observations suggest that the ERVB originated from ruminants and was associated with outbreaks of neonatal foal diarrhea in the 2021 foaling season in Kentucky. Emergence of the ruminant-like group B rotavirus in foals clearly warrants further investigation due to the significant impact of the disease in neonatal foals and its economic impact on the equine industry.
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Affiliation(s)
- Tirth Uprety
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Chithra C. Sreenivasan
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Ben M. Hause
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA;
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Solomon O. Odemuyiwa
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO 65212, USA;
| | - Stephan Locke
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Jocelynn Morgan
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Li Zeng
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | | | - Nathan Slovis
- Hagyard Equine Medical Institute, Lexington, KY 40511, USA;
| | - Laurie Metcalfe
- Rood and Riddle Equine Hospital, Lexington, KY 40511, USA; (W.F.G.); (L.M.)
| | - Craig N. Carter
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Peter Timoney
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - David Horohov
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Erdal Erol
- Veterinary Diagnostic Laboratory, University of Kentucky, Lexington, KY 40512, USA; (S.L.); (J.M.); (L.Z.); (C.N.C.)
| | - Emma Adam
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (T.U.); (C.C.S.); (P.T.); (D.H.); (D.W.)
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18
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Wu H, Su H, Joosten RRM, Keizer ADA, van Hazendonk LS, Wirix MJM, Patterson JP, Laven J, de With G, Friedrich H. Mapping and Controlling Liquid Layer Thickness in Liquid-Phase (Scanning) Transmission Electron Microscopy. SMALL METHODS 2021; 5:e2001287. [PMID: 34927906 DOI: 10.1002/smtd.202001287] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/18/2021] [Indexed: 06/14/2023]
Abstract
Liquid-Phase (Scanning) Transmission Electron Microscopy (LP-(S)TEM) has become an essential technique to monitor nanoscale materials processes in liquids in real-time. Due to the pressure difference between the liquid and the microscope vacuum, bending of the silicon nitride (SiNx ) membrane windows generally occurs. This causes a spatially varying liquid layer thickness that makes interpretation of LP-(S)TEM results difficult due to a locally varying achievable resolution and diffusion limitations. To mediate these difficulties, it is shown: 1) how to quantitatively map liquid layer thickness for any liquid at less than 0.01 e- Å-2 total dose; 2) how to dynamically modulate the liquid thickness by tuning the internal pressure in the liquid cell, co-determined by the Laplace pressure and the external pressure. It is demonstrated that reproducible inward bulging of the window membranes can be realized, leading to an ultra-thin liquid layer in the central window area for high-resolution imaging. Furthermore, it is shown that the liquid thickness can be dynamically altered in a programmed way, thereby potentially overcoming the diffusion limitations towards achieving bulk solution conditions. The presented approaches provide essential ways to measure and dynamically adjust liquid thickness in LP-(S)TEM experiments, enabling new experiment designs and better control of solution chemistry.
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Affiliation(s)
- Hanglong Wu
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Hao Su
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Rick R M Joosten
- Center for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Arthur D A Keizer
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Laura S van Hazendonk
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Maarten J M Wirix
- Materials & Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, Eindhoven, 5651 GG, The Netherlands
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Jozua Laven
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Gijsbertus de With
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
| | - Heiner Friedrich
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
- Center for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO box 513, Eindhoven, MB, 5600, The Netherlands
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19
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Abstract
Group A rotaviruses (RVAs) are the major cause of severe acute gastroenteritis (AGE) in children under 5 years of age, annually resulting in nearly 130,000 deaths worldwide. Social conditions in developing countries that contribute to decreased oral rehydration and vaccine efficacy and the lack of approved antiviral drugs position RVA as a global health concern. In this minireview, we present an update in the field of antiviral compounds, mainly in relation to the latest findings in RVA virion structure and the viral replication cycle. In turn, we attempt to provide a perspective on the possible treatments for RVA-associated AGE, with special focus on novel approaches, such as those representing broad-spectrum therapeutic options. In this context, the modulation of host factors, lipid droplets, and the viral polymerase, which is highly conserved among AGE-causing viruses, are analyzed as possible drug targets.
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20
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Chiu W, Schmid MF, Pintilie GD, Lawson CL. Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. J Biol Chem 2021; 296:100560. [PMID: 33744287 PMCID: PMC8050867 DOI: 10.1016/j.jbc.2021.100560] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) methods began to be used in the mid-1970s to study thin and periodic arrays of proteins. Following a half-century of development in cryo-specimen preparation, instrumentation, data collection, data processing, and modeling software, cryo-EM has become a routine method for solving structures from large biological assemblies to small biomolecules at near to true atomic resolution. This review explores the critical roles played by the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in partnership with the community to develop the necessary infrastructure to archive cryo-EM maps and associated models. Public access to cryo-EM structure data has in turn facilitated better understanding of structure–function relationships and advancement of image processing and modeling tool development. The partnership between the global cryo-EM community and PDB and EMDB leadership has synergistically shaped the standards for metadata, one-stop deposition of maps and models, and validation metrics to assess the quality of cryo-EM structures. The advent of cryo-electron tomography (cryo-ET) for in situ molecular cell structures at a broad resolution range and their correlations with other imaging data introduce new data archival challenges in terms of data size and complexity in the years to come.
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Affiliation(s)
- Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, California, USA; Division of CryoEM and Bioimaging, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA.
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Grigore D Pintilie
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Catherine L Lawson
- Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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21
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Abstract
Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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22
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Ahmed I, Akram Z, Sahar MSU, Iqbal HMN, Landsberg MJ, Munn AL. WITHDRAWN: Structural studies of vitrified biological proteins and macromolecules - A review on the microimaging aspects of cryo-electron microscopy. Int J Biol Macromol 2020:S0141-8130(20)33915-5. [PMID: 32710963 DOI: 10.1016/j.ijbiomac.2020.07.156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/03/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Ishtiaq Ahmed
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia.
| | - Zain Akram
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia
| | - M Sana Ullah Sahar
- School of Engineering, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alan L Munn
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Gold Coast campus, Parklands Drive, Southport, QLD 4222, Australia
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23
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Sun C, Gonzalez B, Vago FS, Jiang W. High resolution single particle Cryo-EM refinement using JSPR. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:37-42. [PMID: 32622834 DOI: 10.1016/j.pbiomolbio.2020.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 11/30/2022]
Abstract
JSPR is a single particle cryo-EM image processing and 3D reconstruction software developed in the Jiang laboratory at Purdue University. It began as a few refinement scripts for symmetric and asymmetric reconstructions of icosahedral viruses, but has grown into a comprehensive suite of tools for building ab initio reconstructions, high resolution refinements of viruses, protein complexes of arbitrary symmetries including helical tubes/filaments, and image file handling utilities. In this review, we will present examples achieved using JSPR and demonstrate recently implemented features of JSPR such as multi-aberration "alignments" and automatic optimization of masking for the assessment of map resolution using "true" FSC.
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Affiliation(s)
- Chen Sun
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Brenda Gonzalez
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA.
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24
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Conserved Rotavirus NSP5 and VP2 Domains Interact and Affect Viroplasm. J Virol 2020; 94:JVI.01965-19. [PMID: 31915278 DOI: 10.1128/jvi.01965-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/21/2019] [Indexed: 01/15/2023] Open
Abstract
One step of the life cycle common to all rotaviruses (RV) studied so far is the formation of viroplasms, membrane-less cytosolic inclusions providing a microenvironment for early morphogenesis and RNA replication. Viroplasm-like structures (VLS) are simplified viroplasm models consisting of complexes of nonstructural protein 5 (NSP5) with the RV core shell VP2 or NSP2. We identified and characterized the domains required for NSP5-VP2 interaction and VLS formation. VP2 mutations L124A, V865A, and I878A impaired both NSP5 hyperphosphorylation and NSP5/VP2 VLS formation. Moreover, NSP5-VP2 interaction does not depend on NSP5 hyperphosphorylation. The NSP5 tail region is required for VP2 interaction. Notably, VP2 L124A expression acts as a dominant-negative element by disrupting the formation of either VLS or viroplasms and blocking RNA synthesis. In silico analyses revealed that VP2 L124, V865, and I878 are conserved among RV species A to H. Detailed knowledge of the protein interaction interface required for viroplasm formation may facilitate the design of broad-spectrum antivirals to block RV replication.IMPORTANCE Alternative treatments to combat rotavirus infection are a requirement for susceptible communities where vaccines cannot be applied. This demand is urgent for newborn infants, immunocompromised patients, adults traveling to high-risk regions, and even for the livestock industry. Aside from structural and physiological divergences among RV species studied before now, all replicate within cytosolic inclusions termed viroplasms. These inclusions are composed of viral and cellular proteins and viral RNA. Viroplasm-like structures (VLS), composed of RV protein NSP5 with either NSP2 or VP2, are models for investigating viroplasms. In this study, we identified a conserved amino acid in the VP2 protein, L124, necessary for its interaction with NSP5 and the formation of both VLSs and viroplasms. As RV vaccines cover a narrow range of viral strains, the identification of VP2 L124 residue lays the foundations for the design of drugs that specifically block NSP5-VP2 interaction as a broad-spectrum RV antiviral.
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25
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Kyrilis FL, Meister A, Kastritis PL. Integrative biology of native cell extracts: a new era for structural characterization of life processes. Biol Chem 2020; 400:831-846. [PMID: 31091193 DOI: 10.1515/hsz-2018-0445] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/29/2019] [Indexed: 01/04/2023]
Abstract
Advances in electron microscopy have provided unprecedented access to the structural characterization of large, flexible and heterogeneous complexes. Until recently, cryo-electron microscopy (cryo-EM) has been applied to understand molecular organization in either highly purified, isolated biomolecules or in situ. An emerging field is developing, bridging the gap between the two approaches, and focuses on studying molecular organization in native cell extracts. This field has demonstrated its potential by resolving the structure of fungal fatty acid synthase (FAS) at 4.7 Å [Fourier shell correlation (FSC) = 0.143]; FAS was not only less than 50% enriched, but also retained higher-order binders, previously unknown. Although controversial in the sense that the lysis step might introduce artifacts, cell extracts preserve aspects of cellular function. In addition, cell extracts are accessible, besides cryo-EM, to modern proteomic methods, chemical cross-linking, network biology and biophysical modeling. We expect that automation in imaging cell extracts, along with the integration of molecular/cell biology approaches, will provide remarkable achievements in the study of closer-to-life biomolecular states of pronounced biotechnological and medical importance. Such steps will, eventually, bring us a step closer to the biophysical description of cellular processes in an integrative, holistic approach.
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Affiliation(s)
- Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, D-06120 Halle/Saale, Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle/Saale, Germany.,Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, D-06120 Halle/Saale, Germany
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26
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Shigematsu H. Electron cryo-microscopy for elucidating the dynamic nature of live-protein complexes. Biochim Biophys Acta Gen Subj 2020; 1864:129436. [DOI: 10.1016/j.bbagen.2019.129436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022]
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27
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Smith JW, Chen Q. Liquid-phase electron microscopy imaging of cellular and biomolecular systems. J Mater Chem B 2020; 8:8490-8506. [DOI: 10.1039/d0tb01300e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid-phase electron microscopy, a new method for real-time nanoscopic imaging in liquid, makes it possible to study cells or biomolecules with a singular combination of spatial and temporal resolution. We review the state of the art in biological research in this growing and promising field.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
- Department of Chemistry
- University of Illinois at Urbana–Champaign
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28
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Ohashi M, Maeda SI, Sato C. Bayesian inference for three-dimensional helical reconstruction using a soft-body model. Phys Rev E 2019; 100:042411. [PMID: 31770999 DOI: 10.1103/physreve.100.042411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 11/07/2022]
Abstract
Estimation of the three-dimensional (3D) structure of a protein using cryo transmission electron microscopy (cryo-TEM) is an inverse problem, which aims to estimate the parameters of a specific physical process from observations. In general, we need to model the observation process to estimate a structure. However, the inconsistency between the model and a real observation process decreases the estimation accuracy. In cryo-TEM, the flexibility of a soft protein, including the bending of a helix, can lead to inconsistencies between the observations because of the assumption that there is a consistent 3D structure behind each observed image. In this paper, we propose a 3D reconstruction algorithm for helical structures using a parametric soft-body model that can represent continuous deformation. We performed an approximate Bayesian inference for unobservable (hidden) variables, such as the deformation parameters, projection angle, and two-dimensional origin offset (shift) of each protein in the 3D structure estimation problem. Our principled approach is not only beneficial to deal with the uncertainties in the estimation, but also beneficial to make the optimization algorithm convergent and efficient. Reconstructions with artificial molecules validated the advantage of the proposed method, particularly, when deformed helices were imaged under a low signal-to-noise ratio condition. Moreover, we confirmed that the proposed method successfully reconstructed a 3D structure from cryo-TEM images of the tobacco mosaic virus.
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Affiliation(s)
- Masataka Ohashi
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki Prefecture 305-8574, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki Prefecture 305-8566, Japan.,BioNet Ltd., 2-3-28 Nishikityo, Tachikawa, Tokyo 190-0022, Japan
| | - Shin-Ichi Maeda
- Preferred Networks, Inc., 1-6-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Chikara Sato
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki Prefecture 305-8574, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki Prefecture 305-8566, Japan
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29
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Harastani M, Sorzano COS, Jonić S. Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Protein Sci 2019; 29:223-236. [PMID: 31693263 DOI: 10.1002/pro.3772] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) method was introduced in 2014. HEMNMA computes normal modes of a reference model (an atomic structure or an electron microscopy map) of a molecular complex and uses this model and its normal modes to analyze single-particle images of the complex to obtain information on its continuous conformational changes, by determining the full distribution of conformational variability from the images. An advantage of HEMNMA is a simultaneous determination of all parameters of each image (particle conformation, orientation, and shift) through their iterative optimization, which allows applications of HEMNMA even when the effects of conformational changes dominate those of orientational changes. HEMNMA was first implemented in Xmipp and was using MATLAB for statistical analysis of obtained conformational distributions and for fitting of underlying trajectories of conformational changes. A HEMNMA implementation independent of MATLAB is now available as part of a plugin of Scipion V2.0 (http://scipion.i2pc.es). This plugin, named ContinuousFlex, can be installed by following the instructions at https://pypi.org/project/scipion-em-continuousflex. In this article, we present this new HEMNMA software, which is user-friendly, totally free, and open-source. STATEMENT FOR A BROADER AUDIENCE: This article presents Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) software that allows analyzing single-particle images of a complex to obtain information on continuous conformational changes of the complex, by determining the full distribution of conformational variability from the images. The HEMNMA software is user-friendly, totally free, open-source, and available as part of ContinuousFlex plugin (https://pypi.org/project/scipion-em-continuousflex) of Scipion V2.0 (http://scipion.i2pc.es).
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Affiliation(s)
- Mohamad Harastani
- Sorbonne Université, UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | | | - Slavica Jonić
- Sorbonne Université, UMR CNRS 7590, Muséum National d'Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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30
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Khatib F, Desfosses A, Koepnick B, Flatten J, Popović Z, Baker D, Cooper S, Gutsche I, Horowitz S. Building de novo cryo-electron microscopy structures collaboratively with citizen scientists. PLoS Biol 2019; 17:e3000472. [PMID: 31714936 PMCID: PMC6850521 DOI: 10.1371/journal.pbio.3000472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
With the rapid improvement of cryo-electron microscopy (cryo-EM) resolution, new computational tools are needed to assist and improve upon atomic model building and refinement options. This communication demonstrates that microscopists can now collaborate with the players of the computer game Foldit to generate high-quality de novo structural models. This development could greatly speed the generation of excellent cryo-EM structures when used in addition to current methods.
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Affiliation(s)
- Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, United States of America
- * E-mail: (FB); (SH)
| | - Ambroise Desfosses
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jeff Flatten
- Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Zoran Popović
- Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Seth Cooper
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Irina Gutsche
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Scott Horowitz
- Department of Chemistry and Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado, United States of America
- * E-mail: (FB); (SH)
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31
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Valente AP, Moraes AH. Zika virus proteins at an atomic scale: how does structural biology help us to understand and develop vaccines and drugs against Zika virus infection? J Venom Anim Toxins Incl Trop Dis 2019; 25:e20190013. [PMID: 31523227 PMCID: PMC6727858 DOI: 10.1590/1678-9199-jvatitd-2019-0013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In Brazil and in other tropical areas Zika virus infection was directly associated with clinical complications as microcephaly in newborn children whose mothers were infected during pregnancy and the Guillain-Barré syndrome in adults. Recently, research has been focused on developing new vaccines and drug candidates against Zika virus infection since none of those are available. In order to contribute to vaccine and drug development efforts, it becomes important the understanding of the molecular basis of the Zika virus recognition, infection and blockade. To this purpose, it is essential the structural determination of the Zika virus proteins. The genome sequencing of the Zika virus identified ten proteins, being three structural (protein E, protein C and protein prM) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). Together, these proteins are the main targets for drugs and antibody recognition. Here we examine new discoveries on high-resolution structural biology of Zika virus, observing the interactions and functions of its proteins identified via state-of-art structural methodologies as X-ray crystallography, nuclear magnetic resonance spectroscopy and cryogenic electronic microscopy. The aim of the present study is to contribute to the understanding of the structural basis of Zika virus infection at an atomic level and to point out similarities and differences to others flaviviruses.
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Affiliation(s)
- Ana Paula Valente
- National Center of Magnetic Resonance, Leopoldo de Meis Institute of Medical Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Adolfo Henrique Moraes
- Department of Chemistry, Institute of Exact Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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32
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Abstract
Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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33
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Song X, Smith JW, Kim J, Zaluzec NJ, Chen W, An H, Dennison JM, Cahill DG, Kulzick MA, Chen Q. Unraveling the Morphology-Function Relationships of Polyamide Membranes Using Quantitative Electron Tomography. ACS APPLIED MATERIALS & INTERFACES 2019; 11:8517-8526. [PMID: 30676014 DOI: 10.1021/acsami.8b20826] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
An understanding of how complex nanoscale morphologies emerge from synthesis would offer powerful strategies to construct soft materials with designed structures and functions. However, these kinds of morphologies have proven difficult to characterize, and therefore manipulate, because they are three-dimensional (3D), nanoscopic, and often highly irregular. Here, we studied polyamide (PA) membranes used in wastewater reclamation as a prime example of this challenge. Using electron tomography and quantitative morphometry, we reconstructed the nanoscale morphology of 3D crumples and voids in PA membranes for the first time. Various parameters governing film transport properties, such as surface-to-volume ratio and mass-per-area, were measured directly from the reconstructed membrane structure. In addition, we extracted information inaccessible by other means. For example, 3D reconstruction shows that membrane nanostructures are formed from PA layers 15-20 nm thick folding into 3D crumples which envelope up to 30% void by volume. Mapping local curvature and thickness in 3D quantitatively groups these crumples into three classes, "domes", "dimples", and "clusters", each being a distinct type of microenvironment. Elemental mapping of metal ion adsorption across the film demonstrates that these previously missed parameters are relevant to membrane performance. This imaging-morphometry platform can be applicable to other nanoscale soft materials and potentially suggests engineering strategies based directly on synthesis-morphology-function relationships.
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Affiliation(s)
| | | | | | - Nestor J Zaluzec
- Photon Sciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | | | | | | | | | - Matthew A Kulzick
- BP Corporate Research Center , Naperville , Illinois 60563 , United States
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34
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Kondylis P, Schlicksup CJ, Zlotnick A, Jacobson SC. Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids. Anal Chem 2019; 91:622-636. [PMID: 30383361 PMCID: PMC6472978 DOI: 10.1021/acs.analchem.8b04824] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Panagiotis Kondylis
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Christopher J. Schlicksup
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
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35
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Beckers M, Jakobi AJ, Sachse C. Thresholding of cryo-EM density maps by false discovery rate control. IUCRJ 2019; 6:18-33. [PMID: 30713700 PMCID: PMC6327189 DOI: 10.1107/s2052252518014434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/12/2018] [Indexed: 05/31/2023]
Abstract
Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.
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Affiliation(s)
- Maximilian Beckers
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Faculty of Biosciences, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Arjen J. Jakobi
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Hamburg Unit c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
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36
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Rodríguez JM, Luque D. Structural Insights into Rotavirus Entry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:45-68. [DOI: 10.1007/978-3-030-14741-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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37
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Nakamichi Y, Miyazaki N, Tsutsumi K, Higashiura A, Narita H, Murata K, Nakagawa A. An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism. Structure 2018; 27:439-448.e3. [PMID: 30581044 DOI: 10.1016/j.str.2018.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 08/29/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
Abstract
Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.
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Affiliation(s)
- Yusuke Nakamichi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; National Institute for Physiological Sciences, Okazaki, Aichi 444-8787 Japan
| | - Kenta Tsutsumi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8551 Japan
| | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8787 Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan.
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38
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Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E, Scheres SH. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 2018; 7:42166. [PMID: 30412051 PMCID: PMC6250425 DOI: 10.7554/elife.42166] [Citation(s) in RCA: 3137] [Impact Index Per Article: 522.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/06/2018] [Indexed: 12/28/2022] Open
Abstract
Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2–0.7 Å compared to previous RELION versions.
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Affiliation(s)
- Jasenko Zivanov
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Takanori Nakane
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Björn O Forsberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Dari Kimanius
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Wim Jh Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cryo-Electron Microscopy Service Platform, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
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39
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Jiménez-Zaragoza M, Yubero MP, Martín-Forero E, Castón JR, Reguera D, Luque D, de Pablo PJ, Rodríguez JM. Biophysical properties of single rotavirus particles account for the functions of protein shells in a multilayered virus. eLife 2018; 7:37295. [PMID: 30201094 PMCID: PMC6133545 DOI: 10.7554/elife.37295] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
The functions performed by the concentric shells of multilayered dsRNA viruses require specific protein interactions that can be directly explored through their mechanical properties. We studied the stiffness, breaking force, critical strain and mechanical fatigue of individual Triple, Double and Single layered rotavirus (RV) particles. Our results, in combination with Finite Element simulations, demonstrate that the mechanics of the external layer provides the resistance needed to counteract the stringent conditions of extracellular media. Our experiments, in combination with electrostatic analyses, reveal a strong interaction between the two outer layers and how it is suppressed by the removal of calcium ions, a key step for transcription initiation. The intermediate layer presents weak hydrophobic interactions with the inner layer that allow the assembly and favor the conformational dynamics needed for transcription. Our work shows how the biophysical properties of the three shells are finely tuned to produce an infective RV virion.
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Affiliation(s)
- Manuel Jiménez-Zaragoza
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Pl Yubero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Jose R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - David Reguera
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain
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40
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A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps. J Struct Biol 2018; 204:344-350. [PMID: 30036578 DOI: 10.1016/j.jsb.2018.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 12/24/2022]
Abstract
This article presents a methodology to assess a set of density maps, as used in the Blind Assessment Phase of the 2015/2016 Map Challenge (EMDataBank Validation Challenges). The synthetic and experimental cryo-electron microscopy (cryo-EM) density maps obtained by different single particle analysis protocols and by different participants, submitted in the Challenge Phase for assessment, were analyzed with this methodology and the obtained results are presented and discussed here. The goal of using such a methodology was to blindly identify the density maps with globally similar structural information, meaning the maps with the structural information mostly "reproduced" by different protocols. To this end, the density maps are "coarsened" using Gaussian-based approximations, with the same input approximation parameters for all maps of the target biological complex. The approximated maps are then represented in a common reduced-dimension (here, 3D) space of their correlation-coefficient-based distances, in which close maps mean similar maps. The distance analysis allows identifying maps with the most "reproduced" structural information by different protocols. The obtained results are also discussed taking into account the detailed information about the protocols that has been released after the end of the Blind Assessment Phase.
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41
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42
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Kleywegt GJ, Velankar S, Patwardhan A. Structural biology data archiving - where we are and what lies ahead. FEBS Lett 2018; 592:2153-2167. [PMID: 29749603 PMCID: PMC6019198 DOI: 10.1002/1873-3468.13086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/31/2022]
Abstract
For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists.
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Affiliation(s)
- Gerard J. Kleywegt
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Sameer Velankar
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
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43
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Taylor LF, Yuan Y. Structure of Herpesvirus Capsid Sheds Light on Drug Discovery. Trends Microbiol 2018; 26:391-392. [PMID: 29602619 DOI: 10.1016/j.tim.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022]
Abstract
The atomic resolution structure of Kaposi's sarcoma-associated herpesvirus (KSHV) capsid reveals that protein-protein interfaces (PPIs) are essential for its structural stability. This structural information guided a mutagenesis study that identified novel drug targets interrupting PPIs essential for capsid assembly.
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Affiliation(s)
- Louis F Taylor
- Department of Microbiology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA 19104, USA
| | - Yan Yuan
- Department of Microbiology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA 19104, USA.
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Lau C, Hunter MJ, Stewart A, Perozo E, Vandenberg JI. Never at rest: insights into the conformational dynamics of ion channels from cryo-electron microscopy. J Physiol 2018; 596:1107-1119. [PMID: 29377132 PMCID: PMC5878226 DOI: 10.1113/jp274888] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 12/27/2017] [Indexed: 01/04/2023] Open
Abstract
The tightly regulated opening and closure of ion channels underlies the electrical signals that are vital for a wide range of physiological processes. Two decades ago the first atomic level view of ion channel structures led to a detailed understanding of ion selectivity and conduction. In recent years, spectacular developments in the field of cryo-electron microscopy have resulted in cryo-EM superseding crystallography as the technique of choice for determining near-atomic resolution structures of ion channels. Here, we will review the recent developments in cryo-EM and its specific application to the study of ion channel gating. We will highlight the advantages and disadvantages of the current technology and where the field is likely to head in the next few years.
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Affiliation(s)
- Carus Lau
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
- St Vincent's Clinical SchoolUniversity of NSWDarlinghurstNSW2010Australia
| | - Mark J. Hunter
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
| | - Alastair Stewart
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
- St Vincent's Clinical SchoolUniversity of NSWDarlinghurstNSW2010Australia
| | - Eduardo Perozo
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIL60637USA
| | - Jamie I. Vandenberg
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
- St Vincent's Clinical SchoolUniversity of NSWDarlinghurstNSW2010Australia
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Xu H, Lebrette H, Yang T, Srinivas V, Hovmöller S, Högbom M, Zou X. A Rare Lysozyme Crystal Form Solved Using Highly Redundant Multiple Electron Diffraction Datasets from Micron-Sized Crystals. Structure 2018; 26:667-675.e3. [DOI: 10.1016/j.str.2018.02.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 12/17/2017] [Accepted: 02/12/2018] [Indexed: 11/17/2022]
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Mak J, de Marco A. Recent advances in retroviruses via cryo-electron microscopy. Retrovirology 2018; 15:23. [PMID: 29471854 PMCID: PMC5824478 DOI: 10.1186/s12977-018-0405-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy.
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Affiliation(s)
- Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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Abstract
Transmission Electron Microscopy (TEM) is an ideal method to observe and determine the structure of bacteriophages. From early studies by negative staining to the present atomic structure models derived from cryo-TEM, bacteriophage detection, classification, and structure determination has been mostly done by electron microscopy. Although embedding in metal salts has been a routine method for virus observation for many years, preservation of bacteriophages in a thin layer of fast frozen buffer has proven to be a most convenient preparation method for obtaining images using cryo-electron microscopy (cryo-EM). In this technique, frozen samples are observed at liquid nitrogen temperature and the images are acquired using different recording media. The incorporation of direct electron detectors has been a fundamental step to achieve atomic resolution images of a number of viruses. These projection images can be numerically combined using different approaches to render a three-dimensional model of the virus. For those viral components exhibiting any symmetry, averaging procedures help to render near-atomic resolution structures.
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Affiliation(s)
- Ana Cuervo
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049, Madrid, Spain
| | - José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049, Madrid, Spain.
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Erdemci-Tandogan G, Orland H, Zandi R. RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses. PHYSICAL REVIEW LETTERS 2017; 119:188102. [PMID: 29219580 DOI: 10.1103/physrevlett.119.188102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Indexed: 05/21/2023]
Abstract
Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it remain poorly understood. We study the impact of base pairing on the conformations of RNA and find that it undergoes a swollen coil to globule continuous transition as a function of the strength of the pairing interaction. We also observe a first order transition and kink profile as a function of RNA length. All these transitions could explain the different RNA profiles observed inside viral shells.
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Affiliation(s)
- Gonca Erdemci-Tandogan
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA-Saclay, CEA, F-91191 Gif-sur-Yvette, France
- Beijing Computational Science Research Center, No. 10 East Xibeiwang Road, Haidan District, Beijing 100193, China
| | - Roya Zandi
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
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Jiang W, Tang L. Atomic cryo-EM structures of viruses. Curr Opin Struct Biol 2017; 46:122-129. [PMID: 28787658 PMCID: PMC5683926 DOI: 10.1016/j.sbi.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 01/30/2023]
Abstract
During the development of single particle cryo-EM in past five decades, icosahedral viruses have led the resolution progress owing to their large mass and high symmetry. Many technical advances in cryo-EM were first established with viruses. Since reaching ∼4Å resolution in 2008, it has become a relatively routine task to solve the atomic structure of isolated viruses. The future of structural virology will be increasingly focused on remaining challenges including solving structures of jumbo viruses, intermediate functional states during assembly, maturation, and infection, and in situ structures. Recent demonstrations of near-atomic resolution structure with electron tomography and sub-tomogram averaging opens a new direction for high resolution studies of pleomorphic viruses and the pleomorphic states of icosahedral viruses that have defied past efforts using the single particle cryo-EM approach.
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Affiliation(s)
- Wen Jiang
- Department of Biological Sciences, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Department of Chemistry, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Markey Center for Structural Biology, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA.
| | - Liang Tang
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.
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Chiu W, Downing KH. Editorial overview: Cryo Electron Microscopy: Exciting advances in CryoEM Herald a new era in structural biology. Curr Opin Struct Biol 2017; 46:iv-viii. [PMID: 28801059 DOI: 10.1016/j.sbi.2017.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wah Chiu
- Departments of Bioengineering and Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA; SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
| | - Kenneth H Downing
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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