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From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain
Chemical Science ( IF 7.6 ) Pub Date : 2021-09-09 , DOI: 10.1039/d1sc03000k Shaima Hashem 1 , Veronica Macaluso 1 , Michele Nottoli 1 , Filippo Lipparini 1 , Lorenzo Cupellini 1 , Benedetta Mennucci 1
Chemical Science ( IF 7.6 ) Pub Date : 2021-09-09 , DOI: 10.1039/d1sc03000k Shaima Hashem 1 , Veronica Macaluso 1 , Michele Nottoli 1 , Filippo Lipparini 1 , Lorenzo Cupellini 1 , Benedetta Mennucci 1
Affiliation
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Photoreceptor proteins bind a chromophore, which, upon light absorption, modifies its geometry or its interactions with the protein, finally inducing the structural change needed to switch the protein from an inactive to an active or signaling state. In the Blue Light-Using Flavin (BLUF) family of photoreceptors, the chromophore is a flavin and the changes have been connected with a rearrangement of the hydrogen bond network around it on the basis of spectroscopic changes measured for the dark-to-light conversion. However, the exact conformational change triggered by the photoexcitation is still elusive mainly because a clear consensus on the identity not only of the light activated state but also of the dark one has not been achieved. Here, we present an integrated investigation that combines microsecond MD simulations starting from the two conflicting crystal structures available for the AppA BLUF domain with calculations of NMR, IR and UV-Vis spectra using a polarizable QM/MM approach. Thanks to such a combined analysis of the three different spectroscopic responses, a robust characterization of the structure of the dark state in solution is given together with the uncovering of important flaws of the most popular molecular mechanisms present in the literature for the dark-to-light activation.
中文翻译：
从晶体学数据到光感受器的溶液结构：AppA BLUF 域的案例
光感受器蛋白与发色团结合，在光吸收后，发色团改变其几何形状或其与蛋白质的相互作用，最终诱导将蛋白质从非活性状态转变为活性状态或信号传导状态所需的结构变化。在蓝光黄素 (BLUF) 光感受器家族中，发色团是黄素，并且根据暗光转换测量的光谱变化，这些变化与其周围氢键网络的重排有关。然而，光激发引发的确切构象变化仍然难以捉摸，主要是因为对于光激活态和暗激活态的身份尚未达成明确的共识。在这里，我们提出了一项综合研究，该研究将从 AppA BLUF 域可用的两种相互冲突的晶体结构开始进行微秒 MD 模拟，并使用可偏振 QM/MM 方法计算 NMR、IR 和 UV-Vis 光谱。由于对三种不同光谱响应的综合分析，给出了溶液中暗态结构的可靠表征，同时揭示了暗态到暗态文献中最流行的分子机制的重要缺陷。光激活。
更新日期：2021-09-17
中文翻译：
从晶体学数据到光感受器的溶液结构：AppA BLUF 域的案例
光感受器蛋白与发色团结合，在光吸收后，发色团改变其几何形状或其与蛋白质的相互作用，最终诱导将蛋白质从非活性状态转变为活性状态或信号传导状态所需的结构变化。在蓝光黄素 (BLUF) 光感受器家族中，发色团是黄素，并且根据暗光转换测量的光谱变化，这些变化与其周围氢键网络的重排有关。然而，光激发引发的确切构象变化仍然难以捉摸，主要是因为对于光激活态和暗激活态的身份尚未达成明确的共识。在这里，我们提出了一项综合研究，该研究将从 AppA BLUF 域可用的两种相互冲突的晶体结构开始进行微秒 MD 模拟，并使用可偏振 QM/MM 方法计算 NMR、IR 和 UV-Vis 光谱。由于对三种不同光谱响应的综合分析，给出了溶液中暗态结构的可靠表征，同时揭示了暗态到暗态文献中最流行的分子机制的重要缺陷。光激活。
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