Shenoy V S, Ichiye T
Department of Biochemistry/Biophysics, Washington State University, Pullman 99164-4660.
Proteins. 1993 Oct;17(2):152-60. doi: 10.1002/prot.340170205.
A theoretical investigation of the protein contribution to the redox potential of the iron-sulfur protein rubredoxin is presented. Structures of the oxidized and reduced forms of the protein were obtained by energy minimizing the oxidized crystal structure of Clostridium pasteurianum rubredoxin with appropriate charges and parameters. By including 102 crystal waters, structures close to the original crystal structure were obtained (rms difference of 1.16 A), even with extensive minimization, thus allowing accurate calculations of comparative energies. Our calculations indicate an energy change of about -60 kcal/mol (2.58 eV) in the protein alone upon reduction. This energy change was due to both the change in charge of the redox site and the subsequent relaxation of the protein. An energy minimization procedure for the relaxation gives rms differences between the oxidized and reduced states of about 0.2 A. The changes were small and occurred in both the backbone and sidechain mainly near the Fe-S center but contributed about -16 kcal/mol (0.69 eV) to the total protein contribution. Although the neglect of certain effects such as electronic polarization may make the relaxation energies calculated an upper limit, the results indicate that protein relaxation contributes substantially to the redox potential.
本文对蛋白质对铁硫蛋白红素氧还蛋白氧化还原电位的贡献进行了理论研究。通过使用适当的电荷和参数对巴氏梭菌红素氧还蛋白的氧化晶体结构进行能量最小化，获得了该蛋白氧化态和还原态的结构。通过包含102个结晶水，即使经过广泛的最小化处理，仍获得了与原始晶体结构接近的结构（均方根差异为1.16 Å），从而能够准确计算比较能量。我们的计算表明，仅蛋白质还原时能量变化约为-60千卡/摩尔（2.58电子伏特）。这种能量变化是由于氧化还原位点电荷的变化以及随后蛋白质的弛豫。弛豫的能量最小化程序给出氧化态和还原态之间的均方根差异约为0.2 Å。这些变化很小，主要发生在主链和侧链中靠近Fe-S中心的位置，但对蛋白质的总贡献约为-16千卡/摩尔（0.69电子伏特）。尽管忽略某些效应（如电子极化）可能会使计算出的弛豫能量成为上限，但结果表明蛋白质弛豫对氧化还原电位有很大贡献。
