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.