Department of Physics, City College of New York, New York, NY, 10031, USA.
Center for Materials Science, Zewail City of Science and Technology, Ahmed Zewail Road, 6th of October City, Giza, 12578, Egypt.
J Biol Inorg Chem. 2018 Mar;23(2):285-293. doi: 10.1007/s00775-017-1530-8. Epub 2017 Dec 27.
Superoxide dismutases (SOD) are vital enzymes for disproportionation of superoxide molecules in mammals. Despite the high similarity between the Mn-SOD and Fe-SOD, they are inactive if the metals in the active sites are exchanged. Here, we use DFT, QM/MM and Monte Carlo sampling to optimize the crystal structure and to calculate the mid-point potential for the native and substituted Mn/Fe-SOD. The optimized DFT and QM/MM structures of the Mn-SOD show a major conformational change for the conserved TYR34 compared to the X-ray structure. These changes reduce the distance between TYR34 and Mn ion to 2.59 Å, which yields a lower reduction potential for the Mn. On contrary, there is no significant difference between optimized and crystal structures in the Fe-SOD. The calculated E values starting from the DFT structures of the active sites show similar pattern, in good agreement with those observed experimentally. However, the calculated E values starting with the QM/MM structures that include the whole protein are significantly higher due to the desolvation penalty. In addition, the pK values for the water ligand in the reduced state Mn(II) and Fe(II) were calculated. The water pK in Mn-SOD is higher than that in Fe-SOD by 3.5 pH units, which is similar to the shift measured experimentally. Finally, we investigated the role of HIS30 and the effect of its protonation state on the E values.
超氧化物歧化酶（SOD）是哺乳动物中超氧阴离子分子歧化的重要酶。尽管 Mn-SOD 和 Fe-SOD 之间具有高度相似性，但如果活性位点中的金属交换，它们就会失去活性。在这里，我们使用 DFT、QM/MM 和蒙特卡罗采样来优化晶体结构，并计算天然和取代的 Mn/Fe-SOD 的中点电位。与 X 射线结构相比，优化的 Mn-SOD 的 DFT 和 QM/MM 结构显示出保守的 TYR34 发生了主要的构象变化。这些变化将 TYR34 和 Mn 离子之间的距离缩小到 2.59 Å，从而降低了 Mn 的还原电位。相反，在 Fe-SOD 中，优化后的结构与晶体结构之间没有明显差异。从活性位点的 DFT 结构开始计算的 E 值表现出相似的模式，与实验观察到的值非常吻合。然而，从包括整个蛋白质的 QM/MM 结构开始计算的 E 值由于去溶剂化罚分而显著升高。此外，还计算了还原态 Mn(II)和 Fe(II)中配体水的 pK 值。Mn-SOD 中的水 pK 值比 Fe-SOD 高 3.5 pH 单位，与实验测量的位移相似。最后，我们研究了 HIS30 的作用及其质子化状态对 E 值的影响。
