RESUMO
Fluorescent emitters are quenched near the surfaces of metals via rapid energy transfer to the metal, via surface plasmons, waveguide modes, and absorption. Commonly, this quenching is reduced by introducing a polymeric or dielectric spacer but requires large distances, at least a fraction of the wavelength, between the metal and chromophore. Using the classical theory for a dipole above a metal/dielectric substrate, we investigate the fluorescent yield for emitters above a wide range of metals and spacers. For metals with low loss and low plasma frequencies, a high index spacer is shown to be advantageous for obtaining higher fluorescent yield in an "island of emission" at finely tuned spacer thickness just 20-30 nm from the metal surface. For such metal-dielectric combinations, fluorophores can be placed surprisingly close to the metal surface while remaining significantly emissive.
RESUMO
Many enzymes undergo major conformational changes to function in cells, particularly when they bind to more than one substrate. We quantify the large-amplitude hinge-bending landscape of human phosphoglycerate kinase (PGK) in a human cytoplasm. Approximately 70 µs of all-atom simulations, upon coarse graining, reveal three metastable states of PGK with different hinge angle distributions and additional substates. The "open" state was more populated than the "semi-open" or "closed" states. In addition to free energies and barriers within the landscape, we characterized the average transition state passage time of ≈0.3 µs and reversible substrate and product binding. Human PGK in a dilute solution simulation shows a transition directly from the open to closed states, in agreement with previous SAXS experiments, suggesting that the cell-like model environment promotes stability of the human PGK semi-open state. Yeast PGK also sampled three metastable states within the cytoplasm model, with the closed state favored in our simulation.