BackgroundIn order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly).ResultsIn order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results.ConclusionsOur analysis shows for which molecular parameters hierarchical assembly schemes can outperform direct ones and suggests that viruses with high bond stability might prefer hierarchical assembly schemes. These insights increase our physical understanding of an essential biological process, with many interesting potential applications in medicine and materials science.

Alzheimer's Disease (AD) is a common neurodegenerative disease and the 6th leading cause of death in the US. One neurological marker of AD is the deposition of extracellular plaques composed of aggregates of the amyloid-b (Ab) protein. Ab aggregation follows a nucleation-dependent pathway, beginning with monomer forming nuclei that grow into soluble aggregates and proceed to form the insoluble fibrils deposited in AD brain. As such, many therapeutic treatments target the inhibition of Ab aggregation. It is hypothesized that compounds containing a phenol structure can interrupt aggregate b-sheet formation by disrupting p-p stacking at phenylalanine residues in the core of the protein. In this study, the phenlyethanoid oleuropein, along with metabolites hydroxytyrosol and tyrosol, were studied for their effect on Ab aggregation. Aggregation of SEC-purified Ab was initiated via agitation in the presence of a 5-fold excess of compound and monitored using thioflavin-T to detect aggregate b-sheet structure. To examine the earliest stages of aggregation, oligomerization was induced by combining DMSO-solubilized Ab with a 10-fold excess of inhibitor and diluting into PBS. Oligomer formation was monitored via SDS-PAGE and Western blotting to quantify oligomer size. Distinct correlations were observed between compound structure and the effect on oligomer size and the formation of larger aggregates. Hydroxytyrosol, a metabolite of oleuropein, exhibited the most effective inhibition among these compounds in aggregation and oligomerization. Thus, effectiveness of phenylthanoid compounds in Ab inhibition is influenced by the substitutions present on the ring. In contrast, the structure with only one hydroxyl group, tyrosol, has little effect. Further study will elucidate the effect that these changes in Ab aggregation have upon Ab neurotoxicity.