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

We apply an integrated approach combining microsecondMD simulationsand (polarizable) QM/MM calculations of NMR, FTIR, and UV-visspectra to validate the structure of the light-activated form of theAppA photoreceptor, an example of blue light using flavin (BLUF) proteindomain. The latter photoactivate through a proton-coupled electrontransfer (PCET) that results in a tautomerization of a conserved glutamineresidue in the active site, but this mechanism has never been spectroscopicallyproven for AppA, which has been always considered as an exception.Our simulations instead confirm that the spectral features observedupon AppA photoactivation are indeed directly connected to the tautomerform of glutamine as predicted by the PCET mechanism. In addition,we observe small but significant changes in the AppA structure, whichare transmitted from the flavin binding pocket to the surface of theprotein.

Automated summary

We use a combination of microsecond MD simulations and (polarizable) QM/MM calculations of NMR, FTIR, and UV-vis spectra to confirm the structure of the light-activated form of AppA photoreceptor. Our simulations demonstrate that the observed spectral features are directly linked to the tautomer form of glutamine, supporting the PCET mechanism. Furthermore, we observe small but significant structural changes in AppA, which propagate from the flavin binding pocket to the protein surface.