Seeing the Portal in Herpes Simplex Virus Type 1 B Capsids

Structural Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, Texas 77030, USA.
Journal of Virology (Impact Factor: 4.44). 02/2011; 85(4):1871-4. DOI: 10.1128/JVI.01663-10
Source: PubMed


Resolving the nonicosahedral components in large icosahedral viruses remains a technical challenge in structural virology.
We have used the emerging technique of Zernike phase-contrast electron cryomicroscopy to enhance the image contrast of ice-embedded
herpes simplex virus type 1 capsids. Image reconstruction enabled us to retrieve the structure of the unique portal vertex
in the context of the icosahedral capsid and, for the first time, show the subunit organization of a portal in a virus infecting
eukaryotes. Our map unequivocally resolves the 12-subunit portal situated beneath one of the pentameric vertices, thus removing
uncertainty over the location and stoichiometry of the herpesvirus portal.

Download full-text


Available from: Frazer Rixon
  • Source
    • "When portal proteins of phages or herpesviruses are expressed at high levels, polymorphisms are commonly encountered in the number of subunits in the ring. However, it appears that, in both cases, only 12-mers are assembled into capsids (Lurz et al. 2001; Rochat et al. 2011). Crystal structures of several phage portals, of varying size, have been determined (Simpson et al. 2001; Lebedev et al. 2007; Olia et al. 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Herpesviruses, a family of animal viruses with large (125-250 kbp) linear DNA genomes, are highly diversified in terms of host range; nevertheless, their virions conform to a common architecture. The genome is confined at high density within a thick-walled icosahedral capsid with the uncommon (among viruses, generally) but unvarying triangulation number T = 16. The envelope is a membrane in which some 11 different viral glycoproteins are implanted. Between the capsid and the envelope is a capacious compartment called the tegument that accommodates ∼20-40 different viral proteins (depending on which virus) destined for delivery into a host cell. A strong body of evidence supports the hypothesis that herpesvirus capsids and those of tailed bacteriophages stem from a distant common ancestor, whereas their radically different infection apparatuses - envelope on one hand and tail on the other - reflect subsequent coevolution with divergent hosts. Here we review the molecular components of herpesvirus capsids and the mechanisms that regulate their assembly, with particular reference to the archetypal alphaherpesvirus, herpes simplex virus type 1; assess their duality with the capsids of tailed bacteriophages; and discuss the mechanism whereby, once DNA packaging has been completed, herpesvirus nucleocapsids exit from the nucleus to embark on later stages of the replication cycle.
    Full-text · Article · Jan 2012 · Advances in Experimental Medicine and Biology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The use of a Zernike-type phase plate in biologic cryo-electron microscopy allows the imaging, without using defocus, of what are predominantly phase objects. It is thought that such phase-plate implementations might result in higher quality images, free from the problems of CTF correction that occur when images must be recorded at extremely high values of defocus. In single-particle cryo-electron microscopy it is hoped that these improvements in image quality will facilitate work on structures that have proved difficult to study, either because of their relatively small size or because the structures are not completely homogeneous. There is still a need, however, to quantitate how much improvement can be gained by using a phase plate for single-particle cryo-electron microscopy. We present a method for quantitatively modeling the images recorded with 200keV electrons, for single particles embedded in vitreous ice. We then investigate what difference the use of a phase-plate device could have on the processing of single-particle data. We confirm that using a phase plate results in single-particle datasets in which smaller molecules can be detected, particles can be more accurately aligned and problems of heterogeneity can be more easily addressed.
    Preview · Article · Apr 2011 · Journal of Structural Biology
  • [Show abstract] [Hide abstract]
    ABSTRACT: Images acquired with a phase plate often exhibit fringing and/or contrast reversal artifacts. The two basic parameters controlling the performance of the phase plate are phase shift and cut-on periodicity. We investigate theoretically and numerically the effect of these parameters on the image quality. The analysis covers not just the typical negative phase shift phase plates but also positive phase shift ones. The theoretical study derives formulas for calculating the optimal phase plate phase shift and for the maximum achievable contrast with a given specimen. Two figures of merit - fidelity and contrast - were defined and used to quantify the numerical results. Larger cut-on periodicities provide better performance with higher contrast and less artifacts in the images. Both, the theoretical results and the simulations indicate that positive phase shift phase plates generate higher contrast with better linearity and are free from contrast reversal artifacts. However, with such phase plates the amplitude and the phase contrast components are opposed to each other and the simulations show stronger fringing outside of objects. Based on these results it is difficult to predict if and to what extent the positive phase shift phase plates will be advantageous in practice. Two methods for reduction of fringing artifacts were compared-tapered phase plate and low-frequency amplification software filter. Overall the software solution produced better results and is much easier to implement than modifying the hardware of the phase plate to realize the taper.
    No preview · Article · Jul 2011 · Ultramicroscopy
Show more