Influence of the Protein Environment on the Electronic Excitation of Chromophores in the Phycoerythrin 545 Light-Harvesting Complex: A Combined MD-QM/MM Method with Polarized Protein-Specific Charge Scheme
Influence of the Protein Environment on the Electronic Excitation of Chromophores in the Phycoerythrin 545 Light-Harvesting Complex: A Combined MD-QM/MM Method with Polarized Protein-Specific Charge Scheme
复制标题
蛋白质环境对藻红蛋白 545 光捕获复合物中发色团电子激发的影响：结合 MD-QM/MM 方法与极化蛋白质特异性电荷方案
DOI：
10.1021/acs.jpcb.8b11764
复制
发表时间：
2019
影响因子：
3.3
通讯作者：
Mo Yan
中科院分区：
文献类型：
--
作者：
Tong Zhengqing;Huai Zhe;Mei Ye;Mo Yan
为了更好地了解波动的蛋白质环境如何影响PE 545捕光天线系统中发色团的位点能量排序，我们沿着分子动力学（MD）轨迹进行了量子力学/分子力学（QM/MM）计算。极化蛋白质特定电荷（PPC）计划中采用的MD模拟和QM/MM计算的蛋白质环境的更真实的描述。用ZINDO/S-CIS计算得到的位能梯与通过同时拟合稳态光谱和瞬态吸收光谱从实验中提取的最佳模型吻合得很好。比较了三种电荷方案的组合，以阐明蛋白质环境如何调节发色团的位点能量。结果表明，蛋白质环境发挥的多重作用，例如，通过微调发色团的构象或通过特定的色素-蛋白质相互作用，都是至关重要的网站能量安排。此外，我们研究了个别环境的影响，发现极性残基和水分子对能量转移的贡献最大。
To gain better insight into how the fluctuating protein environment influences the site energy ordering of the chromophores in PE545 light-harvesting antenna system, we carried out quantum mechanics/molecular mechanics (QM/MM) calculations along the molecular dynamics (MD) trajectory. The Polarized Protein-Specific Charge (PPC) scheme was adopted in both the MD simulation and the QM/MM calculations for a more realistic description of the protein environment. The deduced site energy ladder calculated using ZINDO/S-CIS agrees well with the best model extracted from experiments by a simultaneous fit of the steady-state spectra and transient absorption spectra. Three combinations of charge schemes were compared to elucidate how the protein environment modulates the site energy of chromophores. The result indicates that the multiroles that the protein environment is playing, for instance, by fine-tuning of the conformation of chromophores or by specific pigment–protein interactions, are both crucial for site energy arrangement. Furthermore, we investigated the effects of individual environments and found that the polar residues and water molecules contribute most to the energy shifts.