Integrated Computational Study of the Light-Activated Structure of the AppA BLUF Domain and Its Spectral Signatures

We apply an integrated approach combining microsecond
MD simulations
and (polarizable) QM/MM calculations of NMR, FTIR, and UV–vis
spectra to validate the structure of the light-activated form of the
AppA photoreceptor, an example of blue light using flavin (BLUF) protein
domain. The latter photoactivate through a proton-coupled electron
transfer (PCET) that results in a tautomerization of a conserved glutamine
residue in the active site, but this mechanism has never been spectroscopically
proven for AppA, which has been always considered as an exception.
Our simulations instead confirm that the spectral features observed
upon AppA photoactivation are indeed directly connected to the tautomer
form of glutamine as predicted by the PCET mechanism. In addition,
we observe small but significant changes in the AppA structure, which
are transmitted from the flavin binding pocket to the surface of the
protein.