Chemically Controlled Spatiotemporal Oscillations of Colloidal Assemblies.

We report an autonomous oscillatory micromotor system in which active colloidal particles form clusters, the size of which changes periodically. The system consists of an aqueous suspension of silver orthophosphate microparticles under UV illumination, in the presence of varying concentrations of hydrogen peroxide. The colloid particles first attract each other to form clusters. After a short delay, these clusters abruptly disperse and oscillation begins, alternating between clustering and dispersion of particles. After a cluster oscillation initiates, the oscillatory wave propagates to nearby clusters and eventually all the clusters oscillate in phase-shifted synchrony. The oscillatory behavior is governed by an electrolytic self-diffusiophoretic mechanism which involves alternating electric fields generated by the competing reduction and oxidation of silver. The oscillation frequency is tuned by changing the concentration of hydrogen peroxide. The addition of inert silica particles to the system results in hierarchical sorting and packing of clusters. Densely packed Ag3 PO4 particles form a non-oscillating core with an oscillating shell composed largely of silica microparticles.

Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.

RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity.