Preassembly analysis

The purpose of the analysis phase is to perceive the properties of the structure and create the drawing strategy that will be used in the assembly phase. The assembly phase will then be a relatively mechanical execution of these instructions. This division simplifies the logical solution of the problem, as modular reductions will do. More importantly, as discussed earlier, it is necessary to design ring systems before they are incorporated into the rest of the structure so that their angular demand may be assessed. 

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Bridged rings. It is not obvious how to compute coordinates for the bridged rings in Figure 6, and even wholly fused systems offer problems. Three different approaches exist and are taken up in a later section (see Preassembly Analysis). The number of rings is easily obtained with Frerejacque s formula. ... 

Desired chain angle (see later section on Chains in Preassembly Analysis), defaulting to 120°. 

The technique for placing the seed atom s neighbors depends on the nature of the seed atom. Most programs differentate between cyclic and acyclic cases. ChemDraw additionally distinguishes chain atoms from ordinary acyclic atoms (see the above section on Chains, Preassembly Analysis), and we present this more detailed version. 

During preassembly analysis, the direction of each bond is noted as explained earlier (see section on Recording Incoming Orientations). 

Further analysis of the cross-linked intermediate showed that lysine at position 250 of one capsid subunit was covalently linked to the identical amino acid on a second subunit. In a model of the nucleocapsid derived from both cryoelectron microscopy (cryo-EM) analysis and X-ray analysis of the nucleocapsid protein, the covalent bond connects a pentamer of coat proteins with a hexamer of coat proteins, that is, it is an intercapsomer contact rather than an intracapsomer contact. This finding was unexpected because a possible assembly model proposed preassembly of pentameric and hexameric units that would recruit RNA for assembly into the final structure. In light of the new data, however, this scenario is unlikely. Instead, the initial assembly intermediate appears to be a coat protein dimer bound to RNA and the dimer spans the intercapsomere space. 

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