Single-Cell Activation of the cAMP-Signaling Pathway in 3D Tissues with FRET-Assisted Two-Photon Activation of bPAC

Unveiling the Photoactivation Mechanism of BLUF Photoreceptor Protein through Hybrid Quantum Mechanics/Molecular Mechanics Free-Energy Calculation

OaPAC is a photoactivated enzyme that forms a homodimer. The two blue-light using flavin (BLUF) photoreceptor domains are connected to the catalytic domains with long coiled-coil C-terminal helices. Upon photoreception, reorganization of the hydrogen bonding network between Tyr6, Gln48, and the chromophore in the BLUF domain and keto-enol tautomerization of Gln48 are thought to occur. However, the quantitative energetics of the photoisomerization reaction and how the BLUF domain's structural change propagates toward the catalytic domain are still unknown. We evaluate the free-energy differences among the dark-state and two different light-state structures by the free-energy perturbation calculations combined with QM/MM free-energy optimizations. Furthermore, we performed long-time MD simulations for the free-energetically optimized dark- and light-state structures to clarify the differences in protein dynamics upon photoisomerization. The free-energy difference between the two optimized light-state structures was estimated at ∼4.7 kcal/mol. The free-energetically optimized light-state structure indicates that the chemically unstable enol tautomer of Gln48 in the light state is stabilized by forming a strong hydrogen bonding network with the chromophore and Tyr6. In addition, the components of free-energy difference between the dark- and light-state structures show that the energy upon photoreception is stored in the environment rather than the internal photoreceived region, suggesting a mechanism to keep the photoactivated signaling state with the chemically unstable enol tautomer of Gln48. In the light state, a fluctuation of Trp90 near the C-terminal helix becomes large, which causes subsequent structural changes in the BLUF core and the C-terminal helix. We also identified residue pairs with significant differences concerning residue-wise contact maps between the dark and light states.

Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling

Beyond natural stimuli such as growth factors and stresses, the ability to experimentally modulate at will the levels or activity of specific intracellular signaling molecule(s) in specified cells within a tissue can be a powerful tool for uncovering new regulation and tissue behaviors. Here we perturb the levels of cAMP within specific cells of an epithelial monolayer to probe the time-dynamic behavior of cell-cell communication protocols implemented by the cAMP/PKA pathway and its coupling to the ERK pathway. The time-dependent ERK responses we observe in the perturbed cells for spatially uniform cAMP perturbations (all cells) can be very different from those due to spatially localized perturbations (a few cells). Through a combination of pharmacological and genetic perturbations, signal analysis, and computational modeling, we infer how intracellular regulation and regulated cell-cell coupling each impact the intracellular ERK response in single cells. Our approach reveals how a dynamic gap junction state helps sculpt the intracellular ERK response over time in locally perturbed cells.