Early stages of the HIV-1 capsid protein lattice formation

Theoretical frameworks for multiscale modeling and simulation

Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.

Coarse-grain modelling of protein-protein interactions

Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are separately described, but we note the parallel development that is present in both research fields with three important themes: firstly, combining CG modelling with knowledge-based approaches to predict and refine protein-protein complexes; secondly, using physics-based CG models for de novo prediction of protein-protein complexes; and thirdly modelling of large scale protein aggregates.

Impact of the topology of viral RNAs on their encapsulation by virus coat proteins

Single-stranded RNAs of simple viruses seem to be topologically more compact than other types of single-stranded RNA. It has been suggested that this has an evolutionary purpose: more compact structures are more easily encapsulated in the limited space that the cavity of the virus capsid offers. We employ a simple Flory theory to calculate the optimal amount of polymers confined in a viral shell. We find that the free energy gain or more specifically the efficiency of RNA encapsidation increases substantially with topological compactness. We also find that the optimal length of RNA encapsidated in a capsid increases with the degree of branching of the genome even though this effect is very weak. Further, we show that if the structure of the branching of the polymer is allowed to anneal, the optimal loading increases substantially.