Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany.
J Phys Chem B. 2012 Jul 19;116(28):8064-73. doi: 10.1021/jp3028758. Epub 2012 Jul 3.
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.
在使用黄素 (BLUF) 结构域进行蓝光感应中，靠近黄素发色团的关键残基的侧链取向仍存在争议。我们报告了来自球形红杆菌的 AppA BLUF 蛋白的野生型的量子细化，该蛋白基于两个发表的 X 射线结构（1YRX 和 2IYG），其发色团周围的残基排列不同。量子细化使用与传统细化相同的实验 X 射线原始数据，但包括量子力学/分子力学 (QM/MM) 计算的数据作为约束，这预计比通常使用的 MM 数据更可靠。除了量子细化外，还对 1YRX 和 2IYG 结构以及由此衍生的五个模型进行了纯 QM/MM 几何优化。在 QM(DFT/MRCI)/MM 水平上计算垂直激发能，以评估所得结构。对于包含 1YRX 型取向的 Gln63 残基的结构，野生型 AppA 的暗态的实验吸收最大值得到了很好的重现。对于 Gln63 残基翻转的 2IYG 型取向的结构，计算出的激发能发生红移。详细讨论了计算出的 1YRX 和 2IYG 型氢键网络，特别是关于发色团和 Gln63、Trp104 和 Met106 残基的取向。
