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Abstract
Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.
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Affiliation(s)
- Scott
M. Stagg
- Department
of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States
- Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department
of Biomedical Engineering, Oregon Health
& Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S. Chapman
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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2
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Stuart DI, Abrescia NGA. From lows to highs: using low-resolution models to phase X-ray data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2257-65. [PMID: 24189238 PMCID: PMC3817700 DOI: 10.1107/s0907444913022336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/08/2013] [Indexed: 11/11/2022]
Abstract
The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ~13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.
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Affiliation(s)
- David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, England
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Bld 800, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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3
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Abstract
Structural descriptions of viral particles are key to our understanding of their assembly mechanisms and properties. We will describe the application of X-ray crystallography and electron cryomicroscopy to the structural determination of the bluetongue virus core and the herpesvirus capsid. These represent the highest resolution structural studies carried out by these techniques on such complex and large icosahedral virus particles. The bluetongue virus core consists of two layers of distinct proteins with different protein packing symmetries, while the herpes virus capsid is made up of four types of proteins with 3.3 MDa per asymmetric unit. The structural results reveal that each of these proteins has distinct folds and they are packed uniquely to form stable particles.
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Affiliation(s)
- Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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4
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Baker TS, Olson NH, Fuller SD. Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev 1999; 63:862-922, table of contents. [PMID: 10585969 PMCID: PMC98980 DOI: 10.1128/mmbr.63.4.862-922.1999] [Citation(s) in RCA: 367] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-A) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical.
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Affiliation(s)
- T S Baker
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
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5
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Abstract
Enveloped viruses mature by budding at cellular membranes. It has been generally thought that this process is driven by interactions between the viral transmembrane proteins and the internal virion components (core, capsid, or nucleocapsid). This model was particularly applicable to alphaviruses, which require both spike proteins and a nucleocapsid for budding. However, genetic studies have clearly shown that the retrovirus core protein, i.e., the Gag protein, is able to form enveloped particles by itself. Also, budding of negative-strand RNA viruses (rhabdoviruses, orthomyxoviruses, and paramyxoviruses) seems to be accomplished mainly by internal components, most probably the matrix protein, since the spike proteins are not absolutely required for budding of these viruses either. In contrast, budding of coronavirus particles can occur in the absence of the nucleocapsid and appears to require two membrane proteins only. Biochemical and structural data suggest that the proteins, which play a key role in budding, drive this process by forming a three-dimensional (cage-like) protein lattice at the surface of or within the membrane. Similarly, recent electron microscopic studies revealed that the alphavirus spike proteins are also engaged in extensive lateral interactions, forming a dense protein shell at the outer surface of the viral envelope. On the basis of these data, we propose that the budding of enveloped viruses in general is governed by lateral interactions between peripheral or integral membrane proteins. This new concept also provides answers to the question of how viral and cellular membrane proteins are sorted during budding. In addition, it has implications for the mechanism by which the virion is uncoated during virus entry.
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Affiliation(s)
- H Garoff
- Department of Biosciences at Novum, S-141 57 Huddinge, Sweden.
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6
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Walz T, Grigorieff N. Electron Crystallography of Two-Dimensional Crystals of Membrane Proteins. J Struct Biol 1998; 121:142-61. [PMID: 9618341 DOI: 10.1006/jsbi.1998.3945] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electron microscopy has become a powerful technique, along with X-ray crystallography and nuclear magnetic resonance spectroscopy, to study the three-dimensional structure of biological molecules. It has evolved into a number of methods dealing with a wide range of biological samples, with electron crystallography of two-dimensional crystals being so far the only method allowing data collection at near-atomic resolution. In this paper, we review the methodology of electron crystallography and its application to membrane proteins, starting with the pioneering work on bacteriorhodopsin, which led to the first visualization of the secondary structure of a membrane protein in 1975. Since then, improvements in instrumentation, sample preparation, and data analysis have led to atomic models for bacteriorhodopsin and light-harvesting complex II from higher plants. The structures of many more membrane proteins have been studied by electron crystallography and in this review examples are included where a resolution of better than 10 Å has been achieved. Indeed, in some of the given examples an atomic model can be expected in the near future. Finally, a brief outlook is given on current and future developments of electron crystallographic methods. Copyright 1998 Academic Press.
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Affiliation(s)
- T Walz
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
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Zhou ZH, Chiu W, Haskell K, Spears H, Jakana J, Rixon FJ, Scott LR. Refinement of herpesvirus B-capsid structure on parallel supercomputers. Biophys J 1998; 74:576-88. [PMID: 9449358 PMCID: PMC1299410 DOI: 10.1016/s0006-3495(98)77816-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Electron cryomicroscopy and icosahedral reconstruction are used to obtain the three-dimensional structure of the 1250-A-diameter herpesvirus B-capsid. The centers and orientations of particles in focal pairs of 400-kV, spot-scan micrographs are determined and iteratively refined by common-lines-based local and global refinement procedures. We describe the rationale behind choosing shared-memory multiprocessor computers for executing the global refinement, which is the most computationally intensive step in the reconstruction procedure. This refinement has been implemented on three different shared-memory supercomputers. The speedup and efficiency are evaluated by using test data sets with different numbers of particles and processors. Using this parallel refinement program, we refine the herpesvirus B-capsid from 355-particle images to 13-A resolution. The map shows new structural features and interactions of the protein subunits in the three distinct morphological units: penton, hexon, and triplex of this T = 16 icosahedral particle.
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Affiliation(s)
- Z H Zhou
- Texas Center for Advanced Molecular Computation, University of Houston, 77204-3476, USA
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Baker TS, Johnson JE. Low resolution meets high: towards a resolution continuum from cells to atoms. Curr Opin Struct Biol 1996; 6:585-94. [PMID: 8913679 DOI: 10.1016/s0959-440x(96)80023-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- T S Baker
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.
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Serysheva II, Orlova EV, Chiu W, Sherman MB, Hamilton SL, van Heel M. Electron cryomicroscopy and angular reconstitution used to visualize the skeletal muscle calcium release channel. NATURE STRUCTURAL BIOLOGY 1995; 2:18-24. [PMID: 7719847 DOI: 10.1038/nsb0195-18] [Citation(s) in RCA: 164] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We exploit the random orientations of ice-embedded molecules imaged in an electron cryomicroscope to determine the three-dimensional structure of the Ca(2+)-release channel from the sarcoplasmic reticulum (SR) in its closed state, without tilting the specimen holder. Our new reconstruction approach includes an exhaustive search of all different characteristic projection images in the micrographs and the assignment of Euler angle orientations to these views. The 30 A map implied reveals a structure in which the transmembrane region exhibits no apparent opening on the SR lumen side. The extended cytoplasmic region has a hollow appearance and consists, in each monomer, of a clamp-shaped and a handle-shaped domain.
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Affiliation(s)
- I I Serysheva
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030
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