Molecular dynamics simulations of the cytochrome c3-rubredoxin complex from Desulfovibrio vulgaris.
Molecular dynamics simulations of the cytochrome c3-rubredoxin complex from Desulfovibrio vulgaris.
复制标题
普通脱硫弧菌细胞色素 c3-红氧还蛋白复合物的分子动力学模拟。
DOI：
10.1002/prot.340110207
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发表时间：
1991
期刊：
影响因子：
2.9
通讯作者：
Wampler,JE
中科院分区：
文献类型：
--
作者：
Stewart,DE;Wampler,JE
对硫酸盐还原菌普通硫酸盐弧菌的铁蛋白鲁布还蛋白与细胞色素3形成的络合物进行了分子动力学模拟。这些模拟既包括显式溶剂水分子，也包括不包括溶剂分子的模拟，使用与距离相关的介电常数来近似溶剂的屏蔽效应。这两种模拟的结果截然不同，表明环境影响的表现在这类模拟中很重要。例如，当显式溶剂水包括在内时，在非溶剂模拟中看不到两种蛋白质的显著适应性；事实上，在溶剂模拟中，复合体似乎变得更弱。尽管如此，铁-铁距离在解题模拟中比在非解题模拟中减小得更明显。研究发现，在这两种情况下，分子动力学都比单纯的能量最小化进一步优化了结构。
Molecular dynamics simulations have been carried out on the complex formed between the tetraheme cytochromec3and the iron protein rubredoxin from the sulfate‐reducing bacteriumDesulfovibrio vulgaris. These simulations were performed both with explicit solvent water molecules included, and without solvent molecules using a distance‐dependent dielectric constant to approximate the screening effects of solvent. The results of both simulations are strikingly different, indicating that the representation of environmental effects is important in such simulations. For example, a striking adaptation of the two proteins seen in the nonsolvated simulation is not seen when explicit solvent water is included; in fact, the complex appears to become weaker in the solvated simulation. Nonetheless, the iron–iron distance decreases more significantly in the solvated simulation than in the nonsolvated simulation. It was found that in both cases molecular dynamics optimized the structures further than energy minimization alone.