State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science , East China Normal University , Shanghai 200062 , China.
NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China.
J Phys Chem B. 2019 Mar 7;123(9):2040-2049. doi: 10.1021/acs.jpcb.8b11764. Epub 2019 Feb 21.
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.
为了更深入地了解波动的蛋白质环境如何影响 PE545 光捕获天线系统中发色团的位置能量排序，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。在 MD 模拟和 QM/MM 计算中都采用了极化蛋白特定电荷（PPC）方案，以更真实地描述蛋白质环境。使用 ZINDO/S-CIS 推断出的位置能梯级与通过稳态光谱和瞬态吸收光谱的同时拟合从实验中提取的最佳模型非常吻合。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置能。结果表明，蛋白质环境起着多种作用，例如微调发色团的构象或通过特定的色素-蛋白质相互作用，对位置能排列都至关重要。此外，我们研究了单个环境的影响，发现极性残基和水分子对能量位移的贡献最大。
