Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy.
Phys Chem Chem Phys. 2020 Apr 29;22(16):8585-8594. doi: 10.1039/d0cp00372g.
We present the first comprehensive multiscale computational investigation of Resonance Raman, absorption and Circular Dichroism spectra of the resting state of the Deinococcus radiodurans phytochrome. The spectra are simulated in all their components, namely the energy position and the lineshapes of both the far-red and the blue bands. To achieve such a goal, we have combined a 4.5 μs MD simulation of the solvated dimeric phytochrome with a hybrid quantum mechanics/molecular mechanics (QM/MM) model, which accounts for both electrostatic and mutual polarization effects between the QM and the MM subsystems. A good agreement with experiments is found for all the three spectra. Moreover, we find a transient H-bond network within the binding pocket of the biliverdin chromophore that, unexpectedly, does not significantly affect the spectra. In parallel, we characterize the vibrations that are more strongly coupled to the biliverdin excitation, confirming the important role of the hydrogen-out-of-plane mode of its vinyl C-H together with the expected C[double bond, length as m-dash]C stretching of the double bond involved in the photoisomerization.
我们首次全面地从多尺度计算角度研究了乏养菌生色团的基态的共振拉曼、吸收和圆二色光谱。模拟了所有组成部分的光谱，包括远红和蓝带的能量位置和线宽。为了实现这一目标，我们结合了长达 4.5 μs 的水合二聚生色团的分子动力学模拟和混合量子力学/分子力学（QM/MM）模型，该模型考虑了 QM 和 MM 子系统之间的静电和相互极化效应。三种光谱都与实验结果吻合良好。此外，我们在胆绿素发色团的结合口袋内发现了一个瞬态氢键网络，出乎意料的是，它对光谱没有显著影响。同时，我们对与胆绿素激发更强烈耦合的振动进行了特征描述，证实了其乙烯基 C-H 的面外模式以及参与光致异构化的双键的预期 C[双键，长度为破折号]C 拉伸的重要作用。
