Spectral Signal-to-Noise Ratio and Resolution Assessment of 3D Reconstructions

Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone

Viral nanomotors for packaging of dsDNA and dsRNA

While capsid proteins are assembled around single-stranded genomic DNA or RNA in rod-shaped viruses, the lengthy double-stranded genome of other viruses is packaged forcefully within a preformed protein shell. This entropically unfavourable DNA or RNA packaging is accomplished by an ATP-driven viral nanomotor, which is mainly composed of two components, the oligomerized channel and the packaging enzymes. This intriguing DNA or RNA packaging process has provoked interest among virologists, bacteriologists, biochemists, biophysicists, chemists, structural biologists and computational scientists alike, especially those interested in nanotechnology, nanomedicine, AAA+ family proteins, energy conversion, cell membrane transport, DNA or RNA replication and antiviral therapy. This review mainly focuses on the motors of double-stranded DNA viruses, but double-stranded RNA viral motors are also discussed due to interesting similarities. The novel and ingenious configuration of these nanomotors has inspired the development of biomimetics for nanodevices. Advances in structural and functional studies have increased our understanding of the molecular basis of biological movement to the point where we can begin thinking about possible applications of the viral DNA packaging motor in nanotechnology and medical applications

The capsid architecture of channel catfish virus, an evolutionarily distant herpesvirus, is largely conserved in the absence of discernible sequence homology with herpes simplex virus

Although herpesviruses have a wide host range and their genomes vary substantially in size, the nucleocapsid appears to be a conservative element of viral design. The capsid shell is icosahedrally symmetric (T = 16), and 125 nm in diameter and 15nm thick in the case of herpes simplex virus 1 (HSV-1). Channel catfish virus (CCV) has the gross morphology of a herpesvirus, although no relationship to other herpesviruses is evident from the sequences of its proteins. To examine CCV capsid architecture more closely, we have determined its structure by cryoelectron microscopy and three-dimensional image reconstruction. The CCV capsid is smaller than that of HSV-1, but its 12% smaller genome is packed to essentially the same average density; its icosahedral facets are flatter, and its shell is about 20% thinner, consistent with the smaller size of its major capsid protein. Otherwise, their major features are remarkably similar: CCV has the same triangulation number; its hexons and pentons also have chimney-like protrusions with an axial channel through each capsomer; and there are "triplexes" on the outer surface at the sites of local threefold symmetry. The basic herpesvirus capsid architecture is, therefore, remarkably well conserved in CCV and implies a utilitarian basis to this design. The protein composition of CCV mirrors that of HSV-1, except for the absence of the 12-kDa protein, VP26, which is dispensable for assembly in the HSV-1 system and, apparently, wholly dispensable for CCV

Assembly of VP26 in herpes simplex virus-1 inferred from structures of wild-type and recombinant capsids

The 1250 A diameter herpes simplex virus-1 (HSV-1) capsid shell consists of four major structural proteins, of which VP26 (approximately 12,000 M(r)) is the smallest. Using 400 kV electron cryomicroscopy and computer reconstruction, we have determined the three-dimensional structures of the wild-type capsid and a recombinant baculovirus-generated HSV-1 capsid which lacks VP26. Their difference map demonstrates the presence of VP26 hexamers attached to all the hexons in the wild-type capsid, and reveals that the VP26 molecule consists of a large and a small domain. Although both hexons and pentons are predominantly composed of VP5, VP26 is not present on the penton. Based on the interactions involving VP26 and the hexon subunits, we propose a mechanism for VP26 assembly which would account for its distribution. Possible roles of VP26 in capsid stability and DNA packaging are discussed