SummaryDouble-stranded DNA viruses use ATP-powered molecular motors to package their genomes. To do so, these motors must efficiently transition between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes dimerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination.
A double conformationally restricted kinetically labile supramolecular catalytic system, the third generation, was designed and synthesized. We investigated the substrate selectivity of this system by performing competitive pairwise epoxidations of pyridyl‐ and phenyl‐appended olefins. We compared the obtained substrate selectivities to previous less preorganized generations of this system. Five different substrate pairs were investigated, and the present double conformationally restricted system showed higher normalized substrate selectivities (pyridyl versus phenyl) for two of the substrate pairs than the previous less conformationally restricted generations. As for the preorganization of the components of the system, the catalyst, and the receptor part, it was shown that for each substrate pair there was one generation that was better than the other to generate substrate‐selective catalysis.
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