Computional study of the spectral tuning and photoreaction of photoactive yellow protein

本文对光活性黄蛋白（PYP）的性质进行了阐述。1)我们开发了一种量子化学方法，可以评估光感受器蛋白（如PYP和视网膜蛋白）的最大吸收。在这种方法中，整个蛋白质被分解成两部分：区域I被量子力学处理，只包括一个发色团，区域II（周围的蛋白质部分）被经典静电处理。该方法的一个特点是可以明确地考虑蛋白质部分的电子极化效应。通过这种方法，我们发现蛋白质基质的电子极化在PYP和视网膜蛋白（如细菌视紫红质和盐视紫红质）的光谱调谐中起决定性作用。2)对PYP、PYP_L和PYP_M中间产物的暗态进行了10 ns分子动力学模拟。结果表明，在三种状态中，PYP_M在溶液中的分子波动最大。因此，形成了一个通道，以允许水在蛋白质的外部和内部之间交换。主成分分析结果表明，PYP_M具有特征性的低频振动运动，即铰链弯曲运动。我们推断，这种运动有助于结合转导，换句话说，有助于信号转导的激活。3)建立了蛋白质中可电离基团的全量子化学pKa计算方法，并将其应用于细菌视紫红质（bR）。基于该方法的计算成功地再现了bR基态和M中间体下视网膜希夫碱对Asp85的相对pKa值。结果表明，Tbr89是驱动bR第一个质子转移步骤的关键残基。

In this study, we clarified the following points concerning the properties of photoactive yellow protein (PYP). 1) We developed a quantum chemical methodology that can evaluate the absorption maximum of a photoreceptor protein such as PYP and retinal proteins. In this method, the entire protein is decomposed into two parts : region I is treated quantum mechanically and includes only a chromophore, and region II (the surrounding protein part) is treated by classical electrostatics. A feature of this method is that the electronic polarization effect of the protein part can be explicitly taken into account. Using this method, we indicated that the electronic polarization of the protein matrix is a decisive role in spectral tuning of PYP and retinal proteins such as bacteriorhodopsin and halorhodopsin. 2) 10 ns molecular dynamics simulations were carried out for the dark state of PYP, and the PYP_L and PYP_M intermediates. It was indicated that among the three states PYP_M has the largest molecular fluctuation in solution. As a result, a channel is formed to allow water exchange between the exterior and interior of the protein. In addition, the results of principal component analysis indicated that the PYP_M has a characteristic low frequency vibrational motion, namely a hinge bending motion. It was inferred that this motion contributes to binding to transduction, in other words, to the activation of signal transduction. 3) We developed a full quantum chemical methodology of pKa calculation of ionizable groups in proteins and applied it to bacteriorhodopsin (bR). The calculation based on this method successfully reproduced the relative pKa values of retinal Schiff base to Asp85 in both the bR ground state and the M intermediate. It was concluded that Tbr89 is a key residue driving the first proton transfer step in bR.