<p>We report
the first computational characterization of an optogenetic system composed of
two photosensing BLUF (<u>b</u>lue <u>l</u>ight sensor <u>u</u>sing <u>f</u>lavin
adenine dinucleotide) domains and two catalytic adenylyl cyclase (AC) domains. Conversion
of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) and
pyrophosphate (PPi) catalyzed by ACs coupled with excitation in photosensing
domains has emerged in the focus of modern optogenetic applications because of
the request in photoregulated
enzymes to modulate cellular concentrations of signaling messengers. The photoactivated adenylyl
cyclase from the soil
bacterium <i>Beggiatoa sp.</i> (bPAC) is an
important model showing considerable increase of 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 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 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. </p>
Modular 31
P wideband inversion transfer for integrative analysis of adenosine triphosphate metabolism, T1
relaxation and molecular dynamics in skeletal muscle at 7T
