The Central Role of Gln63 for the Hydrogen Bonding Network and UV鈥揤isible Spectrum of the AppA BLUF Domain

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• 作者：Ya-Wen Hsiao ; Jan P. G枚tze ; Walter Thiel
• 刊名：The Journal of Physical Chemistry B
• 出版年：2012
• 出版时间：July 19, 2012
• 年：2012
• 卷：116
• 期：28
• 页码：8064-8073
• 全文大小：363K
• 年卷期：v.116,no.28(July 19, 2012)
• ISSN：1520-5207

文摘

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.