The Mechanism of Scaffolding-Assisted Assembly

The fact that truncated scaffolding protein molecules such as fragment 240—303 used for NMR can activate the coat protein for assembly yet only weakly dimerize suggests that scaffolding binding can activate the coat protein for assembly. However, the breakdown of fidelity observed suggests that the information required for form determination is not simply locally transmitted (Parker et al, 1998). Fidelity of assembly seems to be correlated with the dimerization affinity. On the basis of a series of N-terminal deletion mutants (wild type, Al-140, A1-237), which show decreased ability to dimerize, fidelity seems to correlate with dimerization potential. 

In this case, the role of scaffolding protein would be to transiently stabilize unstable coat subunit additions, allowing assembly to proceed. It is also possible that this stabilization servers to energetically steer the assembly pathway. For example, in the absence of scaffolding protein T=4 structures are built, and the pentameric and hexameric capsomers in these T=4 particles are virtually identical to those seen in the T=7 form (Thuman-Commike et aL, 1998). However, to form a T=4 capsid requires the c coat protein subunits (Fig. 5) to form a trimer cluster, which would require trimeric clustering of the scaffolding protein. It is possible that scaffolding protein functions to prevent the formation of the trimer cluster and thereby steer the assembly toward T=7 particles. 

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