Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.
J Phys Chem B. 2013 Apr 25;117(16):4263-73. doi: 10.1021/jp305033d. Epub 2012 Oct 5.
Structure-based calculations are combined with quantitative modeling of spectra and energy transfer dynamics to detemine the energy transfer scheme of the PE545 principal light-harvesting antenna of the cryptomonad Rhodomonas CS24. We use a recently developed quantum-mechanics/molecular mechanics (QM/MM) method that allows us to account for pigment-protein interactions at atomic detail in site energies, transition dipole moments, and electronic couplings. In addition, conformational flexibility of the pigment-protein complex is accounted for through molecular dynamics (MD) simulations. We find that conformational disorder largely smoothes the large energetic differences predicted from the crystal structure between the pseudosymmetric pairs PEB50/61C-PEB50/61D and PEB82C-PEB82D. Moreover, we find that, in contrast to chlorophyll-based photosynthetic complexes, pigment composition and conformation play a major role in defining the energy ladder in the PE545 complex, rather than specific pigment-protein interactions. This is explained by the remarkable conformational flexibility of the eight bilin pigments in PE545, characterized by a quasi-linear arrangement of four pyrrole units. The MD-QM/MM site energies allow us to reproduce the main features of the spectra, and minor adjustments of the energies of the three red-most pigments DBV19A, DBV19B, and PEB82D allow us to model the spectra of PE545 with a similar quality compared to our original model (model E from Novoderezhkin et al. Biophys. J.2010, 99, 344), which was extracted from the spectral and kinetic fit. Moreover, the fit of the transient absorption kinetics is even better in the new structure-based model. The largest difference between our previous and present results is that the MD-QM/MM calculations predict a much smaller gap between the PEB50/61C and PEB50/61D sites, in better accord with chemical intuition. We conclude that the current adjusted MD-QM/MM energies are more reliable in order to explore the spectral properties and energy transfer dynamics in the PE545 complex.
基于结构的计算与光谱和能量转移动力学的定量建模相结合，以确定隐甲藻 Rhodomonas CS24 的 PE545 主要光捕获天线的能量转移方案。我们使用最近开发的量子力学/分子力学 (QM/MM) 方法，该方法允许我们在原子细节上考虑色素-蛋白相互作用，包括在位置能量、跃迁偶极矩和电子耦合中。此外，通过分子动力学 (MD) 模拟来考虑色素-蛋白复合物的构象灵活性。我们发现构象无序在很大程度上平滑了从晶体结构预测的 PEB50/61C-PEB50/61D 和 PEB82C-PEB82D 伪对称对之间的大能量差异。此外，我们发现，与基于叶绿素的光合作用复合物相比，色素组成和构象在定义 PE545 复合物中的能量梯级中起着主要作用，而不是特定的色素-蛋白相互作用。这可以解释为 PE545 中的八个类胡萝卜素色素具有显著的构象灵活性，其特征是四个吡咯单元的准线性排列。MD-QM/MM 位置能量使我们能够再现光谱的主要特征，并且对三个最红的色素 DBV19A、DBV19B 和 PEB82D 的能量进行微小调整，使我们能够用与我们原始模型（Novoderezhkin 等人的模型 E，Biophys. J.2010, 99, 344）相似的质量模拟 PE545 的光谱，该模型是从光谱和动力学拟合中提取的。此外，新结构基础模型中的瞬态吸收动力学拟合甚至更好。我们之前和现在的结果之间的最大区别是，MD-QM/MM 计算预测 PEB50/61C 和 PEB50/61D 位点之间的差距要小得多，这更符合化学直觉。我们得出结论，为了探索 PE545 复合物的光谱性质和能量转移动力学，当前调整后的 MD-QM/MM 能量更可靠。
