Subunit interactions in bovine papillomavirus

1.16 Cryo-Electron Microscopy and Tomography of Virus Particles

Human infectious disease is classified into five etiologies: bacterial, viral, parasitic, fungal, and prion. Viral infections are unique in that they recruit human cellular machinery to replicate themselves and spread infection. The number of viruses causing human disease is vast, and viruses can be broadly categorized by their structures. Many viruses, such as influenza, appear to be amorphous particles, whereas others, such as herpes simplex virus, rhinovirus, dengue virus, and adenovirus, have roughly symmetric structural components. Icosahedral viruses have been a target of electron microscopists for years, and they were some of the first objects to be reconstructed three-dimensionally from electron micrographs. The ease with which highly purified and conformationally uniform virus samples can be produced makes them an ideal target structural studies. Apart from their biological significance, these virus samples have played a pivotal role in the development of new methodologies in the field of molecular biology as well as in cryo-electron microscopy and cryo-electron tomography.

Principles of virus structural organization

Viruses, the molecular nanomachines infecting hosts ranging from prokaryotes to eukaryotes, come in different sizes, shapes, and symmetries. Questions such as what principles govern their structural organization, what factors guide their assembly, how these viruses integrate multifarious functions into one unique structure have enamored researchers for years. In the last five decades, following Caspar and Klug's elegant conceptualization of how viruses are constructed, high-resolution structural studies using X-ray crystallography and more recently cryo-EM techniques have provided a wealth of information on structures of a variety of viruses. These studies have significantly -furthered our understanding of the principles that underlie structural organization in viruses. Such an understanding has practical impact in providing a rational basis for the design and development of antiviral strategies. In this chapter, we review principles underlying capsid formation in a variety of viruses, emphasizing the recent developments along with some historical perspective.

Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy

We report on initial results of using a new direct detection device (DDD) for single particle reconstruction of vitreous ice embedded specimens. Images were acquired on a Tecnai F20 at 200keV and a nominal magnification of 29,000×. This camera has a significantly improved signal to noise ratio and modulation transfer function (MTF) at 200keV compared to a standard CCD camera installed on the same microscope. Control of the DDD has been integrated into Leginon, an automated data collection system. Using GroEL as a test specimen, we obtained images of ∼30K particles with the CCD and the DDD from the same specimen sample using essentially identical imaging conditions. Comparison of the maps reconstructed from the CCD images and the DDD images demonstrates the improved performance of the DDD. We also obtained a 3D reconstruction from ∼70K GroEL particles acquired using the DDD; the quality of the density map demonstrates the potential of this new recording device for cryoEM data acquisition.

Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects

Although cryo-electron microscopy (cryo-EM) of biological macromolecules has made important advances in the past few years, the level of current technical performance is still well below what the physics of electron scattering would allow. It should be possible, for example, to use cryo-EM to solve protein structures at atomic resolution for particle sizes well below 80 kDa, but currently this has been achieved only for particles at least 10 times larger than that. In this review, we first examine some of the reasons for this large gap in performance. We then give an overview of work that is currently in progress to 1), improve the signal/noise ratio for area detectors; 2), improve the signal transfer between the scattered electrons and the corresponding images; and 3), reduce the extent to which beam-induced movement causes a steep fall-off of signal at high resolution. In each case, there is substantial reason to think that cryo-EM can indeed be made to approach the estimated physical limits.

Limiting factors in atomic resolution cryo electron microscopy: no simple tricks

To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors--in both cryoEM image acquisition and 3D reconstruction--that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. (b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. (c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved 'characteristic surfaces' in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. (d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction.

4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus

Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo-microscopy (cryo-EM), we determined the structure of an attenuated vaccine strain, TC-83, of VEEV to 4.4 Å resolution. Our density map clearly resolves regions (including E1, E2 transmembrane helices and cytoplasmic tails) that were missing in the crystal structures of domains of alphavirus subunits. These new features are implicated in the fusion, assembly and budding processes of alphaviruses. Furthermore, our map reveals the unexpected E3 protein, which is cleaved and generally thought to be absent in the mature VEEV. Our structural results suggest a mechanism for the initial stage of nucleocapsid core formation, and shed light on the virulence attenuation, host recognition and neutralizing activities of VEEV and other alphavirus pathogens.

Differentiation-dependent interpentameric disulfide bond stabilizes native human papillomavirus type 16

Genetic and biochemical analyses of human papillomavirus type 16 (HPV16) capsids have shown that certain conserved L1 cysteine residues are critical for capsid assembly, integrity, and maturation. Since previous studies utilized HPV capsids produced in monolayer culture-based protein expression systems, the ascribed roles for these cysteine residues were not placed in the temporal context of the natural host environment for HPV, stratifying and differentiating human tissue. Here we extend upon previous observation, that HPV16 capsids mature and become stabilized over time (10-day to 20-day) in a naturally occurring tissue-spanning redox gradient, by identifying temporal roles for individual L1 cysteine residues. Specifically, the C175S substitution severely undermined wild-type titers of the virus within both 10 and 20-day tissue, while C428S, C185S, and C175,185S substitutions severely undermined wild-type titers only within 20-day tissue. All mutations led to 20-day virions that were less stable than wild-type and failed to form L1 multimers via nonreducing SDS-PAGE. Furthermore, Optiprep-fractionated 20-day C428S, C175S, and C175,185S capsids appeared permeable to endonucleases in comparison to wild-type and C185S capsids. Exposure to an oxidizing environment failed to enhance infectious titers of any of the cysteine mutants over time as with wild-type. Introduction of these cys mutants results in failure of the virus to mature.

Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly

The number of viral particles in the biosphere is enormous. Virus classification helps to comprehend the virosphere and to understand the relationship between different virus groups. However, the evolutionary reach of the currently employed sequence-based approaches in virus taxonomy is rather limited, producing a fragmented view of the virosphere. As a result, viruses are currently classified into 87 different families. However, studies on virion architectures have unexpectedly revealed that their structural diversity is far more limited. Here we describe structures of the major capsid proteins of double-stranded DNA viruses infecting hosts residing in different domains of life. We note that viruses belonging to 20 different families fall into only five distinct structural groups, suggesting that optimal virus classification approach should equally rely on both sequence and structural information.

Real time monitoring of antigenicity development of HBsAg virus-like particles (VLPs) during heat- and redox-treatment

The Hepatitis B virus major surface antigen (HBsAg) is a cysteine-rich, membrane-bound protein which self-assembles into 22-nm spherical virus-like particles (VLPs). While this VLP based human vaccine has been demonstrated to be safe and efficacious since 1986, the structural and exact molecular basis for its antigenic determinants has not been elucidated. Maturation of the yeast-derived purified VLPs was characterized for the changes in 37 their biophysical properties. Using rapid and label-free surface plasmon resonance technique with a neutralizing monoclonal antibody - A1.2, the epitope evolution kinetics of purified VLPs was monitored in real time. Evidence supporting the mechanism that the correct disulfide bond pairing is the molecular basis for shaping up the native virion-like epitopes was obtained. At least 10-fold enhancement in antigenicity probed by A1.2 of the VLPs was achieved by heat-treatment (t(1/2) ∼ 6-10 h), and another 2- to 3-fold enhancement was obtained when they were treated with redox buffer. This antigenicity development, presumably via disulfide formation/isomerization, was shown to be inhibited by a free radical scavenger and facilitated in the presence of light. Relative antigenicity determination with surface plasmon resonance was shown to be a valuable tool for process characterization in the kinetic monitoring mode or for final VLP product assessment in the end point antigenicity testing mode.

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map

Structural models of macromolecular assemblies are instrumental for gaining a mechanistic understanding of cellular processes. Determining these structures is a major challenge for experimental techniques, such as X-ray crystallography, NMR spectroscopy and electron microscopy (EM). Thus, computational modeling techniques, including molecular docking, are required. The development of most molecular docking methods has so far been focused on modeling of binary complexes. We have recently introduced the MultiFit method for modeling the structure of a multisubunit complex by simultaneously optimizing the fit of the model into an EM density map of the entire complex and the shape complementarity between interacting subunits. Here, we report algorithmic advances of the MultiFit method that result in an efficient and accurate assembly of the input subunits into their density map. The successful predictions and the increasing number of complexes being characterized by EM suggests that the CAPRI challenge could be extended to include docking-based modeling of macromolecular assemblies guided by EM.

Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy

Nine different near-atomic resolution structures of icosahedral viruses, determined by electron cryo-microscopy and published between early 2008 and late 2010, fulfil predictions made 15 years ago that single-particle cryo-EM techniques could visualize molecular detail at 3-4Å resolution. This review summarizes technical developments, both in instrumentation and in computation, that have led to the new structures, which advance our understanding of virus assembly and cell entry.

Papillomavirus capsid proteins mutually impact structure

We studied a panel of mutant viruses containing wild-type and chimeric capsid HPV16 and HPV18 proteins. The mutant capsid protein expression, genome amplification, and episomal maintenance were comparable with the wild-type virus. However, the chimeric viruses varied in their titers from wild-type. We show that the intertypical mutant chimeric capsid viruses, that L2 affects the structure of L1 and that L1 affects the structure of L2 in the virion. These effects were measured using a panel of conformation-dependent neutralizing L1 MAbs and an L2 capsid surface peptide derived neutralizing antibody. These data suggest that variation of one capsid gene not only affects its own structure and antigenicity, but also affects the structure and antigenicity of the other capsid protein. Implications of our data suggest that for the continued effectiveness of a vaccine, variation in both capsid proteins need to be considered and not just the protein the vaccine is directed against.

Modeling protein structure at near atomic resolutions with Gorgon

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.

Three-dimensional asymmetric reconstruction of tailed bacteriophage

A universal goal in studying the structures of macromolecules and macromolecular complexes by means of electron cryo-microscopy (cryo-TEM) and three-dimensional (3D) image reconstruction is the derivation of a reliable atomic or pseudoatomic model. Such a model provides the foundation for exploring in detail the mechanisms by which biomolecules function. Though a variety of highly ordered, symmetric specimens such as 2D crystals, helices, and icosahedral virus capsids have been studied by these methods at near-atomic resolution, until recently, numerous challenges have made it difficult to achieve sub-nanometer resolution with large (≥~500Å), asymmetric molecules such as the tailed bacteriophages. After briefly reviewing some of the history behind the development of asymmetric virus reconstructions, we use recent structural studies of the prolate phage ϕ29 as an example to illustrate the step-by-step procedures used to compute an asymmetric reconstruction at sub-nanometer resolution. In contrast to methods that have been employed to study other asymmetric complexes, we demonstrate how symmetries in the head and tail components of the phage can be exploited to obtain the structure of the entire phage in an expedited, stepwise process. Prospects for future enhancements to the procedures currently employed are noted in the concluding section.

The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4

Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.

Functional and structural studies of TRP channels heterologously expressed in budding yeast

The transient receptor potential (TRP) superfamily is one of the largest families of cation channels. The metazoan TRP family has been subdivided into major branches: TRPC, TRPA, TRPM, TRPP, TRPV, TRPML, and TRPN, while the TRPY family is found in fungi. They are involved in many physiological processes and in the pathogenesis of various disorders. An efficient high-yield expression system for TRP channels is a necessary step towards biophysical and biochemical characterization and structural analysis of these proteins, and the budding yeast, Saccharomyces cerevisiae has proven to be very useful for this purpose. In addition, genetic screens in this organism can be carried out rapidly to identify amino acid residues important for function and to generate useful mutants. Here we present an overview of current developments towards understanding TRP channel function and structure using Saccharomyces cerevisiae as an expression system. In addition, we will summarize recent progress in understanding gating mechanisms of TRP channels using endogenously expressing TRPY channels in S. cerevisiae, and insights gained from genetic screens for mutants in mammalian channels. The discussion will focus particular attention of the use of cryo-electron microscopy (cryo-EM) to determine TRP channel structure, and outlines a "divide and concur" methodology for combining high resolution structures of TRP channel domains determined by X-ray crystallography with lower resolution techniques including cryo-EM and spectroscopy.

Atomic resolution cryo electron microscopy of macromolecular complexes

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their "native," noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines.

Precise beam-tilt alignment and collimation are required to minimize the phase error associated with coma in high-resolution cryo-EM

Electron microscopy at a resolution of 0.4nm or better requires more careful adjustment of the illumination than is the case at a resolution of 0.8nm. The use of current-axis alignment is not always sufficient, for example, to avoid the introduction of large phase errors, at higher resolution, due to axial coma. In addition, one must also ensure that off-axis coma does not corrupt the data quality at the higher resolution. We particularly emphasize that the standard CTF correction does not account for the phase error associated with coma. We explain the cause of both axial coma and the typically most troublesome component of off-axis coma in terms of the well-known shift of the electron diffraction pattern relative to the optical axis that occurs when the illumination is not parallel to the axis. We review the experimental conditions under which coma causes unacceptably large phase errors, and we discuss steps that can be taken when setting up the conditions of illumination, so as to ensure that neither axial nor off-axis coma is a problem.

Viral nanoparticles and virus-like particles: platforms for contemporary vaccine design

Current vaccines that provide protection against infectious diseases have primarily relied on attenuated or inactivated pathogens. Virus‐like particles (VLPs), comprised of capsid proteins that can initiate an immune response but do not include the genetic material required for replication, promote immunogenicity and have been developed and approved as vaccines in some cases. In addition, many of these VLPs can be used as molecular platforms for genetic fusion or chemical attachment of heterologous antigenic epitopes. This approach has been shown to provide protective immunity against the foreign epitopes in many cases. A variety of VLPs and virus‐based nanoparticles are being developed for use as vaccines and epitope platforms. These particles have the potential to increase efficacy of current vaccines as well as treat diseases for which no effective vaccines are available. WIREs Nanomed Nanobiotechnol 2011 3 174–196 DOI: 10.1002/wnan.119

This article is categorized under: 1

Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease

GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors

Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we modified the computer program, FREALIGN, to execute the computationally most intensive procedures on Graphics Processing Units (GPUs). Using the modified program, the execution speed increased between 10 and 240-fold depending on the task performed by FREALIGN. Here we report the steps necessary to parallelize critical FREALIGN subroutines and evaluate its performance on computers with multiple GPUs.

Primed for Discovery: Atomic-Resolution Cryo-EM Structure of a Reovirus Entry Intermediate

A recently solved structure of the aquareovirus virion (Zhang, X; Jin, L.; Fang, Q; Hui, W.H.; Zhou Z.H. 3.3 Å Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry. Cell2010, 141, 472-482 [1]) provides new insights into the order of entry events, as well as confirming and refining several aspects of the entry mechanism, for aquareovirus and the related orthoreovirus. In particular, the structure provides evidence of a defined order for the progressive proteolytic cleavages of myristoylated penetration protein VP5 that prime the virion for membrane penetration. These observations reinforce the concept that, much like enveloped viruses, nonenveloped virions often undergo priming events that lead to a meta-stable state, preparing the virus for membrane penetration under the appropriate circumstances. In addition, this and other recent studies highlight the increasing power of electron cryomicroscopy to analyze large, geometrically regular structures, such as icosahedral viruses, at atomic resolution.

GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM

Here, we review the GraFix (Gradient Fixation) method to purify and stabilize macromolecular complexes for single particle cryo-electron microscopy (cryo-EM). During GraFix, macromolecules undergo a weak, intramolecular chemical cross-linking while being purified by density gradient ultracentrifugation. GraFix-stabilized particles can be used directly for negative-stain cryo-EM or, after a brief buffer-exchange step, for unstained cryo-EM. This highly reproducible method has proved to dramatically reduce problems in heterogeneity due to particle dissociation during EM grid preparation. Additionally, there is often an appreciable increase in particles binding to the carbon support film. This and the fact that binding times can be drastically increased, with no apparent disruption of the native structures of the macromolecules, makes GraFix a method of choice when preparing low-abundance complexes for cryo-EM. The higher sample quality following GraFix purification is evident when examining raw images, which usually present a low background of fragmented particles, good particle dispersion, and high-contrast, well-defined particles. Setting up the GraFix method is straightforward, and the resulting improvement in sample homogeneity has been beneficial in successfully obtaining the 3D structures of numerous macromolecular complexes by cryo-EM in the past few years.

Single particle analysis at high resolution

Electron cryomicroscopy (cryo-EM) and single particle analysis is emerging as a powerful technique for determining the 3D structure of large biomolecules and biomolecular assemblies in close to their native solution environment. Over the last decade, this technology has improved, first to sub-nanometer resolution, and more recently beyond 0.5 nm resolution. Achieving sub-nanometer resolution is now readily approachable on mid-range microscopes with straightforward data processing, so long as the target specimen meets some basic requirements. Achieving resolutions beyond 0.5 nm currently requires a high-end microscope and careful data acquisition and processing, with much more stringent specimen requirements. This chapter will review and discuss the methodologies for determining high-resolution cryo-EM structures of nonvirus particles to sub-nanometer resolution and beyond, with a particular focus on the reconstruction strategy implemented in the EMAN software suite.