Yelle R B, Park N S, Ichiye T
Department of Biochemistry/Biophysics, Washington State University, Pullman 99164-4660, USA.
Proteins. 1995 Jun;22(2):154-67. doi: 10.1002/prot.340220208.
Molecular dynamics simulations of Clostridium pasteurianum rubredoxin in the oxidized and reduced forms have been performed. Good agreement between both forms and crystal data has been obtained (rms deviation of backbone atoms of 1.06 and 1.42 A, respectively), which was due in part to the use of explicit solvent and counterions. The reduced form exhibits an unexpected structural change: the redox site becomes much more solvent-accessible, so that water enters a channel between the surface and the site, but with little actual structural rearrangement (the rms deviation of backbone atoms between the oxidized and reduced is 0.77 A). The increase in solvent accessibility is also seen, although to a much lesser extent, between the oxidized and reduced crystal structures of Pyrococcus furiosus rubredoxin, but no high resolution crystal or nuclear magnetic resonance solution data exist for reduced C. pasteurianum rubredoxin. The electrostatic potential at the iron site and fluctuations in the potential, which contribute to both the redox and electron transfer properties, have also been evaluated for both the oxidized and the reduced simulations. These results show that the backbone plays a significant role (62-70 kcal/mol/e) and the polar side chains contribute relatively little (0-4 kcal/mol/e) to the absolute electrostatic potential at the iron of rubredoxin for both forms. However, both groups contribute significantly to the change in redox state by becoming more polarized and more densely packed around the redox site upon reduction. Furthermore, these results show that the solvent becomes much more polarized in the reduced form than in the oxidized form, even excluding the penetrating water. Finally, the simulation indicates that the contribution of the charged side chains to the electrostatic potential is largely canceled by that of the counterions.
对氧化态和还原态巴氏梭菌红素氧还蛋白进行了分子动力学模拟。两种形态与晶体数据之间取得了良好的一致性（主链原子的均方根偏差分别为1.06 Å和1.42 Å），这部分归因于使用了显式溶剂和抗衡离子。还原态呈现出意想不到的结构变化：氧化还原位点变得更易被溶剂接触，以至于水进入表面与该位点之间的通道，但实际结构重排很少（氧化态和还原态之间主链原子的均方根偏差为0.77 Å）。尽管程度要小得多，但在激烈火球菌红素氧还蛋白的氧化态和还原态晶体结构之间也观察到了溶剂可及性的增加，不过目前还没有还原态巴氏梭菌红素氧还蛋白的高分辨率晶体或核磁共振溶液数据。对于氧化态和还原态模拟，还评估了铁位点处的静电势以及电势波动，它们对氧化还原和电子转移性质都有贡献。这些结果表明，对于两种形态的红素氧还蛋白，主链对铁处的绝对静电势起显著作用（62 - 70千卡/摩尔/电子），而极性侧链的贡献相对较小（0 - 4千卡/摩尔/电子）。然而，在还原时，这两组基团通过在氧化还原位点周围变得更加极化和紧密堆积，对氧化还原状态的变化都有显著贡献。此外，这些结果表明，即使不考虑渗透水，还原态的溶剂极化程度也比氧化态高得多。最后，模拟表明带电侧链对静电势的贡献在很大程度上被抗衡离子的贡献抵消了。
