Soares C M, Martel P J, Mendes J, Carrondo M A
Instituto de Tecnologia Química e Biologica, Oeiras, Portugal.
Biophys J. 1998 Apr;74(4):1708-21. doi: 10.1016/S0006-3495(98)77882-8.
The tetraheme cytochrome c3 from Desulfovibrio vulgaris Hildenborough is studied using molecular dynamics simulation studies in explicit solvent. The high heme content of the protein, which has its core almost entirely made up of c-type heme, presents specific problems in the simulation. Instability in the structure is observed in long simulations above 1 ns, something that does not occur in a monoheme cytochrome, suggesting problems in heme parametrization. Given these stability problems, a partially restrained model, which avoids destruction of the structure, was created with the objective of performing free energy calculations of heme reduction, studies that require long simulations. With this model, the free energy of reduction of each individual heme was calculated. A correction in the long-range electrostatic interactions of charge groups belonging to the redox centers had to be made in order to make the system physically meaningful. Correlation is obtained between the calculated free energies and the experimental data for three of four hemes. However, the relative scale of the calculated energies is different from the scale of the experimental free energies. Reasons for this are discussed. In addition to the free energy calculations, this model allows the study of conformational changes upon reduction. Even if the precise details of the structural changes that take place in this system upon individual heme reduction are probably out of the reach of this study, it appears that these structural changes are small, similarly to what is observed for other redox proteins. This does not mean that their effect is minor, and one example is the conformational change observed in propionate D from heme I when heme II becomes reduced. A motion of this kind could be the basis of the experimentally observed cooperativity effects between heme reduction, namely positive cooperativity.
利用显式溶剂中的分子动力学模拟研究了来自希登伯勒脱硫弧菌的四血红素细胞色素c3。该蛋白质的血红素含量很高，其核心几乎完全由c型血红素组成，这在模拟中带来了特定问题。在超过1 ns的长时间模拟中观察到结构不稳定，而单血红素细胞色素不会出现这种情况，这表明血红素参数化存在问题。鉴于这些稳定性问题，创建了一个部分受限模型，该模型可避免结构破坏，目的是进行血红素还原的自由能计算，这类研究需要长时间模拟。利用该模型计算了每个血红素的还原自由能。为了使系统具有物理意义，必须对属于氧化还原中心的电荷基团的长程静电相互作用进行校正。计算得到的自由能与四个血红素中三个的实验数据之间存在相关性。然而，计算能量的相对尺度与实验自由能的尺度不同。对此进行了讨论。除了自由能计算外，该模型还允许研究还原时的构象变化。即使该系统中单个血红素还原时发生的结构变化的精确细节可能超出本研究的范围，但似乎这些结构变化很小，与其他氧化还原蛋白的情况类似。这并不意味着它们的影响很小，一个例子是当血红素II还原时，血红素I中丙酸D的构象变化。这种运动可能是实验观察到的血红素还原之间协同效应（即正协同效应）的基础。
