On the structure of the scaffolding core of bacteriophage T4

The scaffolding core in bacteriophages is a temporary structure that plays a major role in determining the shape of the protein shell that encapsulates the viral DNA. In the currently accepted structure for the scaffolding core in bacteriophage T4, there is a symmetry mismatch between the protein shell, which has fivefold symmetry, and the scaffolding core, which is believed to consist of six helical chains. The analysis of T4 giant prohead data that was used to determine this structure made an implicit assumption about the manner in which giant proheads flatten during preparation for electron microscopy. Namely, it was assumed that techniques for analysis of Fourier transforms of flattened single-layer cylinders could be applied independently to the shell and the core. This analysis makes the implicit assumption that connections between the core and the shell do not affect the flattening process, and thus are stretched or broken during the flattening process. Reexamination of the experimental data shows that this assumption is likely to be incorrect. A reanalysis shows that the data could be consistent with six, eight, or 10 helical chains, and is a better match for eight or 10 helical chains. Ten helical chains would match the fivefold symmetry of the shell. The 10-helix core model is particularly attractive because it suggests a Vernier mechanism, which is able to explain the process of length determination in giant head mutants of T4. It is possible that the same assumption has been made for structural analysis of other biological systems. If this is the case, any results obtained should also be reexamined.