The central role of Gln63 for the hydrogen bonding network and UV-visible spectrum of the AppA BLUF domain.
In blue-light sensing using flavin (BLUF) domains, the side-chain orientation of key residues close to the flavin chromophore is still under debate. We report quantum refinements of the wild-type AppA BLUF protein from Rhodobacter sphaeroides starting from two published X-ray structures (1YRX and 2IYG) with different arrangements of the residues around the chromophore. Quantum refinement uses the same experimental X-ray raw data as conventional refinement, but includes data from quantum mechanics/molecular mechanics (QM/MM) calculations as restraints, which is expected to be more reliable than the normally employed MM data. In addition to quantum refinement, pure QM/MM geometry optimizations are performed for the 1YRX and 2IYG structures and for five models derived therefrom. Vertical excitation energies are computed at the QM(DFT/MRCI)/MM level to assess the resulting structures. The experimental absorption maximum of the dark state of wild-type AppA is well reproduced for structures that contain the Gln63 residue in 1YRX-type orientation. The computed excitation energies are red-shifted for structures with a flipped Gln63 residue in 2IYG-type orientation. The calculated 1YRX- and 2IYG-type hydrogen-bonding networks are discussed in detail, particularly with regard to the orientation of the chromophore and the Gln63, Trp104, and Met106 residues.
Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany.
Ya-Wen
YW
Hsiao
Jan P
JP
Götze
Walter
W
Thiel
D018360:Crystallography, X-Ray; D015226:Dinucleoside Phosphates / Q000737:chemistry*; D005998:Glycine / Q000737:chemistry*; D006860:Hydrogen Bonding; D008027:Light; D015394:Molecular Structure; D018087:Plastids; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D014466:Ultraviolet Rays
D015226:Dinucleoside Phosphates; C012276:diadenosine pyrophosphate; D005998:Glycine