We
report the first computational characterization of an optogenetic
system composed of two photosensing BLUF (blue light sensor using
flavin adenine dinucleotide) domains and two catalytic adenylyl cyclase
(AC) domains. Conversion of adenosine triphosphate (ATP) to the reaction
products, cyclic adenosine monophosphate (cAMP) and pyrophosphate
(PPi), catalyzed by ACs initiated by excitation in photosensing domains
has emerged in the focus of modern optogenetic applications because
of the request in photoregulated enzymes that modulate cellular concentrations
of signaling messengers. The photoactivated AC from the soil bacterium Beggiatoa sp. (bPAC) is an important model showing
a considerable increase in the ATP to cAMP conversion rate in the
catalytic domain after the illumination of the BLUF domain. The 1
μs classical molecular dynamics simulations reveal that the
activation of the BLUF domain leading to tautomerization of Gln49
in the chromophore-binding pocket results in switching of the position
of the side chain of Arg278 in the active site of AC. Allosteric signal
transmission pathways between Gln49 from BLUF and Arg278 from AC were
revealed by the dynamical network analysis. The Gibbs energy profiles
of the ATP → cAMP + PPi reaction computed using QM(DFT(ωB97X-D3/6-31G**))/MM(CHARMM)
molecular dynamics simulations for both Arg278 conformations in AC
clarify the reaction mechanism. In the light-activated system, the
corresponding arginine conformation stabilizes the pentacoordinated
phosphorus of the α-phosphate group in the transition state,
thus lowering the activation energy. Simulations of the bPAC system
with the Tyr7Phe replacement in the BLUF demonstrate occurrence of
both arginine conformations in an equal ratio, explaining the experimentally
observed intermediate catalytic activity of the bPAC-Y7F variant as
compared with the dark and light states of the wild-type bPAC.