Mechanisms of viral capsid assembly around a polymer

Capsids of many viruses assemble around nucleic acids or other polymers. Understanding how the properties of the packaged polymer affect the assembly process could promote biomedical efforts to prevent viral assembly or nanomaterials applications that exploit assembly. To this end, we simulate on a lattice the dynamical assembly of closed, hollow shells composed of several hundred to 1000 subunits, around a flexible polymer. We find that assembly is most efficient at an optimum polymer length that scales with the surface area of the capsid; significantly longer than optimal polymers often lead to partial-capsids with unpackaged polymer `tails' or a competition between multiple partial-capsids attached to a single polymer. These predictions can be tested with bulk experiments in which capsid proteins assemble around homopolymeric RNA or synthetic polyelectrolytes. We also find that the polymer can increase the net rate of subunit accretion to a growing capsid both by stabilizing the addition of new subunits and by enhancing the incoming flux of subunits; the effects of these processes may be distinguishable with experiments that monitor the assembly of individual capsids.Comment: 7 figure

Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle

Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)–infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5'-triphosphate incorporation localized between inner and outer mitochondrial membranes inside ∼50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of ∼10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of ∼100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions

A model for the structure of satellite tobacco mosaic virus

Satellite tobacco mosaic virus (STMV) is an icosahedral T=1 single-stranded RNA virus with a genome containing 1058 nucleotides. X-ray crystallography revealed a structure containing 30 double-helical RNA segments, with each helix having nine base pairs and an unpaired nucleotide at the 3’ end of each strand. Based on this structure, Larson and McPherson proposed a model of 30 hairpin-loop elements occupying the edges of the icosahedron and connected by single-stranded regions. More recently, Schroeder et al. have combined the results of chemical probing with a novel helix searching algorithm to propose a specific secondary structure for the STMV genome, compatible with the Larson-McPherson model. Here we report an all-atom model of STMV, using the complete protein and RNA sequences and the Schroeder RNA secondary structure. As far as we know, this is the first all-atom model for the complete structure of any virus (100% of the atoms) using the natural genomic sequence

VARIABILITY IN LEVELS OF LOW-DENSITY LIPOPROTEINS CHOLESTEROL IN PATIENTS WITH FAMILIAL HYPERCHOLESTEROLEMIA DEPENDING ON AGE AND SEX AND ITS IMPORTANCE IN THE DIAGNOSIS OF THIS DISEASE

Aim. To study the ranges of low density lipoprotein (LDL) cholesterol depending on the age and gender of patients with familial hypercholesterolemia (FHC) by an example of a sample of patients living in the Republic of Karelia.Material and methods. Parameters of lipid spectrum of 219 patients (aged 52.5±1.7 years; males 38.3%) with heterozygous FHC were studied before the start of statin therapy. Definite FHC was diagnosed in 102 patients. Lipid profile was estimated by enzymatic calorimetric method. The diagnosis of FHC was established according to the criteria of The Dutch Lipid Clinic Network.  Genetic analysis was performed in 102 patients (46.6%); pathogenic mutation in the LDL receptor was identified in 21 patients. The control group consisted of 539 people with the excluded diagnosis of FHC (aged 46.8±0.8 years; males 53.8%).Results. We determined the level of LDL cholesterol (LDLC) associated with increased frequency of mutations of the LDL receptor in patients with definite FHC; mutation frequency was 3 times higher when LDLC level was more than 6.5 mmol/L. We revealed the following characteristic intervals of the LDLC levels in patients with a definite FHC: up to 20 years old – 4.8-6.2 mmol/l; in patients of 20-29 years old – 5.9-8.2 mmol/l; in the age range of 30-39 years the upper value of the LDLC levels reached 9.6 mmol/l; in individuals of 40-49 years old a stabilization, "plateau", was observed – LDLC level did not differ significantly compared to the previous decade, and was 5.4-9.0 mmol/l. In the age range  of 50-59 years the upper LDLC level was up to 11.4 mmol/l. Similar indicators were identified in patients aged 60-69 years. Patients older than 70 years with a definite FHC an upper level of LDLC was higher and reached 12.5 mmol/l. Tendency to increase in the characteristic values of LDLC with age was observed both in men and in women. Specific age-related trends  for men (an increase from a plateau by the age of 50 years, with some decrease after 60 years) and women (smooth increase of LDLC levels with age) were demonstrated.Conclusion. Characteristic values of LDLC levels for the Russian population of patients with FHС were shown; relationship between LDLC levels and detection of mutations of the LDL receptor was analyzed

Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction

Rice yellow mottle virus (RYMV) and southern bean mosaic virus, cowpea strain (SCPMV) are members of the Sobemovirus genus of RNA-containing viruses. We used electron cryo-microscopy (cryo-EM) and icosahedral image analysis to examine the native structures of these two viruses at 25 A resolution. Both viruses have a single tightly packed capsid layer with 180 subunits assembled on a T = 3 icosahedral lattice. Distinctive crown-like pentamers emanate from the 12 f-fold axes of symmetry. The exterior face of SCPMV displays deep valleys along the 2-fold axes and protrusions at the quasi-3-fold axes. While having a similar topography, the surface of RYMV is comparatively smooth. Two concentric shells of density reside beneath the capsid layer of RYMV and SCPMV, which we interpret as ordered regions of genomic RNA. In the absence of divalent cations, SCPMV particles swell and fracture, whereas the expanded form of RYMV is stable. We previously proposed that the cell-to-cell movement of RYMV in xylem involves chelation of Ca2+ from pit membranes of infected cells, thereby stabilizing the capsid shells and allowing a pathway for spread of RYMV through destabilized membranes. In the context of this model, we propose that the expanded form of RYMV is an intermediate in the in vivo assembly of virions. (Résumé d'auteur

Immature and Mature Human Astrovirus: Structure, Conformational Changes, and Similarities to Hepatitis E Virus

Human astroviruses (HAstVs) are a major cause of gastroenteritis. HAstV assembles from the structural protein VP90 and undergoes a cascade of proteolytic cleavages. Cleavage to VP70 is required for release of immature particles from cells, and subsequent cleavage by trypsin confers infectivity. We used electron cryomicroscopy and icosahedral image analysis to determine the first experimentally derived, three-dimensional structures of an immature VP70 virion and a fully proteolyzed, infectious virion. Both particles display T=3 icosahedral symmetry and nearly identical solid capsid shells with diameters of ~350Å. Globular spikes emanate from the capsid surface, yielding an overall diameter of ~440Å. While the immature particles display 90 dimeric spikes, the mature capsid only displays 30 spikes, located on the icosahedral 2-fold axes. Loss of the 60 peripentonal spikes likely plays an important role in viral infectivity. In addition, immature HAstV bears a striking resemblance to the structure of hepatitis E virus (HEV)-like particles, as previously predicted from structural similarity of the crystal structure of the astrovirus spike domain with the HEV P-domain [Dong, J., Dong, L., Méndez, E. & Tao, Y. (2011). Crystal structure of the human astrovirus capsid spike. Proc. Natl. Acad. Sci. USA108, 12681–12686]. Similarities between their capsid shells and dimeric spikes and between the sequences of their capsid proteins suggest that these viral families are phylogenetically related and may share common assembly and activation mechanisms. [Display omitted] ► Three‐dimensional electron cryomicroscopy density maps of immature and mature HAstV. ► Mature virions only display 30 of 90 spikes after proteolytic cleavage. ► Immature virions are remarkably similar to HEV