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

光活性黄色蛋白的光谱调谐和光反应的计算研究

• 批准号: 12680653
• 负责人: SAKURAI Minoru
• 金额: $ 2.18万
• 依托单位: Tokyo Institute of Technology
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2000
• 资助国家: 日本
• 起止时间: 2000 至 2002
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-12680653/
• 关键词: photoactive yellow protein; molecular dynamics simulation; QM; MM method; pKa calculation; retinal protein; rhodopsin; photocycle; ロドプシン; シグナル伝達; 光反応サイクル; 動的構造; 振動解析; バクテリオロドプシン; オプシンシフト; 溶媒効果

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.

在这项研究中，我们阐明了有关光活性黄蛋白（PYP）特性的以下几点。 1）我们开发了一种量子化学方法，可以评估感光蛋白（例如PYP和视网膜蛋白）的最大吸收。在这种方法中，整个蛋白质被分解为两个部分：区域I对量子进行了机械处理，并且仅包括发色团，而区域II（周围蛋白质部分）通过经典静电治疗。该方法的一个特征是可以明确考虑蛋白质部分的电子极化效应。使用这种方法，我们指出蛋白质基质的电子极化是在PYP和视网膜蛋白（例如细菌紫红质和卤代淡op蛋白）的光谱调节中的决定性作用。 2）对PYP的黑暗状态进行了10个NS分子动力学模拟，PYP_L和PYP_M中间体进行了。据表明，在这三个状态中，pyp_m在溶液中具有最大的分子波动。结果，形成通道以允许蛋白质外部和内部之间的水交换。此外，主成分分析的结果表明，PYP_M具有特征性的低频振动运动，即铰链弯曲运动。据推断，这种运动有助于与转导的结合，换句话说，与信号转导的激活。 3）我们开发了蛋白质可离子基团的PKA计算的完整量子化学方法论，并将其应用于细菌紫红素（BR）。基于此方法的计算成功地重现了在BR基态和M中间体的视网膜Schiff碱基的相对PKA值与Asp85的相对PKA值。得出的结论是，TBR89是驱动BR中第一个质子转移步骤的关键残基。

项目成果

Minoru Sakurai, Keiko Sakata, Shino Saito, Sawako Nakajima, Yoshio Inoue: "Decisive Role of Electronic Polarization of the Protein Environment in Determining the Absorption Maximum of Halorhodopsin"Journal of the American Chemical Society. 125. 3108-3102

Minoru Sakurai、Keiko Sakata、Shino Saito、Sawako Nakajima、Yoshio Inoue：“蛋白质环境的电子极化在确定嗜盐视紫红质吸收最大值中的决定性作用”美国化学会杂志。

M.Yoda, H.Houjou, Y.Inoue, M.Sakurai: "Spectral Tuning of Photoactive Yellow Protein. Theoretical and Experimental Analysis of Medium Effects on the Absorption Spectrum of the Chromophore"Journal of Physical Chemistry B. 105. 9887-9895 (2001)

M.Yoda，H.Houjou，Y.Inoue，M.Sakurai：“光活性黄色蛋白的光谱调谐。介质对发色团吸收光谱影响的理论和实验分析”物理化学杂志 B.105.9887-9895

M. Shiozawa, N. Kamiya, J. Higo, Y. Inoue, M. Sakurai: "Evidence for Large Structural Fluctuations of the Photobleached Intermediate of Photoactive Yellow Protein in Solution"Journal of American Chemical Society. 123. 7445-7446 (2001)

M. Shiozawa、N. Kamiya、J. Higo、Y. Inoue、M. Sakurai：“溶液中光漂白中间体光活性黄色蛋白的大结构波动的证据”美国化学会杂志。

K.Ohno, N.Kamiya, N.Asakwa, Y.Inoue, M.Sakurai: "Application of an integrated MOZYME+DFT method to pKa calculations for protein"Chem. Physics Letters. 341. 387-392 (2001)

K.Ohno、N.Kamiya、N.Asakwa、Y.Inoue、M.Sakurai：“集成 MOZYME DFT 方法在蛋白质 pKa 计算中的应用”Chem。

Sawako Nakajima, Kazuki Ohno, Yoshio Inoue, Minoru Sakurai: "Quantum Chemical Study of the pKa Control Mechanism for the Active Center in Bacteriorhodopsin and Its M Intermediate"Journal of Physical Chemistry B. (印刷中). (2003)

Sawako Nakajima、Kazuki Ohno、Yoshio Inoue、Minoru Sakurai：“细菌视紫红质及其 M 中间体活性中心的 pKa 控制机制的量子化学研究”物理化学杂志 B.（出版中）。