Channelrhodopsins are photosensitive proteins that trigger flagella motion in single cell algae and have been successfully utilized in optogenetic applications. In optogenetics light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using QM/MM molecular dynamics, and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified TD-DFT. In contrast to previous reports, we found that different hydrogen-bonding networks—involving the retinal protonated Schiff base, the putative counterions E162 and D292 as well as water molecules—had only a small impact on the absorption spectrum. However, in case of deprotonated E162 increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factor was found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 % and 82 %, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.

中文翻译：

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确定通道视紫红质吸收光谱的结构因素：嵌合体C1C2的案例研究。

通道视紫红质是在单细胞藻类中触发鞭毛运动的光敏蛋白，已成功地用于光遗传学应用中。在光遗传学中，光用于激活活生物体中的神经细胞，这可以通过利用通道视紫红质的离子通道信号传导来实现。为此类应用量身定制通道视紫红质包括调节最大吸收。为了建立合理的设计并获得所需的光谱偏移，需要对吸收光谱有基本的了解。我们已经研究了嵌合C1C2作为该蛋白家族的代表，并且是具有可用晶体结构的第一成员。为此，我们使用QM / MM分子动力学对C1C2的构象进行了采样，并使用ADC（2）和简化的TD-DFT对轨迹的快照进行激励能量计算。与以前的报告相反，我们发现不同的氢键网络-涉及视网膜质子化席夫碱，推定的抗衡离子E162和D292以及水分子-对吸收光谱的影响很小。但是，在E162去质子化的情况下，与席夫碱氢键伙伴的距离增加，导致系统的蓝移。β-紫罗兰酮环的旋转被认为是另一个重要的贡献者。然而，发现最重要的因素是键长交替和键序交替，它们与最大吸收线性相关，分别高达62％和82％。