MacGowan Stuart A, Senge Mathias O
School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
Biochim Biophys Acta. 2016 Apr;1857(4):427-42. doi: 10.1016/j.bbabio.2016.02.001. Epub 2016 Feb 3.
The structural data for the Fenna-Matthews-Olson (FMO) protein indicate that the bacteriochlorophylls (BChls) display a significant degree of conformational heterogeneity of their peripheral substituents and the protein-induced nonplanar skeletal deformations of the tetrapyrrole macrocycle. As electronic properties of chromophores are altered by such differences, a conformational effect may influence the site-energies of specific pigments and thus play a role in mediating the excitation energy transfer dynamics, but this has not yet been established. The difficulty of assessing this question is shown to be partly the result of the inability of the sequential truncation approach usually employed to account for interactions between the conformations of the macrocycle and its substituents and an alternative approach is suggested. By assigning the BChl atoms to meaningful atom groups and performing all possible permutations of partial optimizations in a full-factorial design, where each group is either frozen in the crystal geometry or optimized in vacuo, followed by excited state calculations on each resulting structure (PM6//ZIndo/S), the specific effects of the conformations of each BChl component as well as mutual interactions between the molecular fragments on the site-energy can be delineated. This factorial relaxation procedure gives different estimates of the macrocycle conformational perturbation than the approach of sequentially truncating the BChl periphery. The results were evaluated in the context of published site-energies for the FMO pigments from three species to identify how conformational effects contribute to their distribution and instances of cross-species conservation and functional divergence of the BChl nonplanarity conformational contribution are described.
芬纳 - 马修斯 - 奥尔森（FMO）蛋白的结构数据表明，细菌叶绿素（BChls）的外围取代基呈现出显著程度的构象异质性，并且存在蛋白质诱导的四吡咯大环平面外骨架变形。由于发色团的电子特性会因这些差异而改变，构象效应可能会影响特定色素的位点能量，从而在介导激发能量传递动力学中发挥作用，但这一点尚未得到证实。评估这个问题的困难部分源于通常采用的顺序截断方法无法解释大环及其取代基构象之间的相互作用，因此提出了一种替代方法。通过将BChl原子分配到有意义的原子组，并在全因子设计中对部分优化进行所有可能的排列，其中每个组要么固定在晶体几何结构中，要么在真空中进行优化，然后对每个所得结构进行激发态计算（PM6//ZIndo/S），可以描绘出每个BChl组分构象以及分子片段之间相互作用对位点能量的具体影响。这种因子松弛程序给出的大环构象扰动估计与顺序截断BChl外围的方法不同。在已发表的来自三个物种的FMO色素位点能量的背景下对结果进行了评估，以确定构象效应如何影响它们的分布，并描述了BChl非平面性构象贡献的跨物种保守和功能差异实例。
