Fig. 5.

Views of Pf1 bacteriophage capsid structure models colored by Cβ side-chain order parameters. The views are of only a small section of the entire Pf1 virion. In the exploded views, the N termini of the subunits appear to be loose but they overlap either other major coat subunits along the filament contour or the minor coat proteins that initiate assembly at the end that emerges first from the cell. The two alternate structure models are displayed because a consensus structure has not been produced in the literature. The 1PFI model (11) and the 1PJF model (16) are for the low- and high-temperature forms, respectively, and they are based on different types of data. 1PJF was chosen because it was based primarily on NMR results, whereas 1PFI was chosen as the only model that includes DNA. Although the 1PJF model does not include DNA, the data on which it was based were for intact virions with DNA (17). The amino acid dynamics obtained in this study are for high-temperature conditions. We show here that the dynamics map onto the same regions of the subunit regardless of which structure model is considered. Both models show a mixture of dynamic (green and yellow) and static (blue) sites mapping to the outer surface of the virion exposed to solvent. The exploded views show progressively more static sites from the outside of the virion into the buried protein–protein interface between overlapping subunits. Of particular importance, the cutaway view of the 1PFI image shows that side chains near the DNA are dynamic (yellow), despite the dense packing in this region. In both images the capsid has been pulled apart and tilted to show other views of the unexpectedly dynamic side chains of the C termini in the core region (green, yellow, and orange). The remarkably dynamic side chains include the side chains of Arg-44 and Lys-45.