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Figure 4
(a) The 2FoFc electron-density map (contoured at 1σ) of the portion of the N-terminal domain of the PPD1 subunit with the highest overall B factor, showing evidence for two main chains in this region of the structure. (b) Graphical depiction of all-atom normal-mode states of the PPD1 hexamer. The trajectories for the first six nontrivial low-frequency normal modes are shown superimposed as directional arrows. The largest structural fluctuations are centred on the N-terminal domains, which undergo rigid-body displacements relative to the PAP domain. Determination of the motional correlation between these domain fluctuations and their import with respect to potential allosteric properties would require the analysis of a larger number of nodes (Wynsberghe & Cui, 2006BB61); nevertheless, these low-frequency modes may have a functional significance in view of the proximity of the N-terminal domains to the active sites, shown here as pink (Mn) and purple (Fe) spheres.

Volume 1| Part 2| February 2014| Pages 101-109
ISSN: 2052-2525