Falklöf Olle, Durbeej Bo
Division of Computational Physics, IFM, Linköping University, SE-581 83 Linköping, Sweden.
J Comput Chem. 2013 Jun 15;34(16):1363-74. doi: 10.1002/jcc.23265. Epub 2013 Mar 1.
Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.
植物色素是自然界中六个特征明确的光感蛋白家族之一。然而，从计算建模的角度来看，与大多数其他光感蛋白家族相比，对植物色素的研究要少得多，这可能是因为相关的高分辨率结构数据直到近年来才可得。在这项工作中，采用混合量子力学/分子力学（QM/MM）方法计算耐辐射球菌细菌光敏色素的紫外可见吸收光谱。我们研究了QM/MM方法的选择如何影响所得光谱，并证明QM/MM方法能够以约0.15电子伏特的精度重现Q带和索雷特带的实验吸收最大值。此外，我们评估了蛋白质环境如何影响胆色素发色团的固有吸收，特别关注植物色素初级光化学所依赖的Q带。
