Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla and C.S.I.C.), Spain.
Bioelectrochemistry. 2009 Nov;77(1):43-52. doi: 10.1016/j.bioelechem.2009.06.003. Epub 2009 Jun 16.
Many fleeting macromolecular interactions, like those being involved in electron transport, are essential in biology. However, little is known about the behaviour of the partners and their dynamics within their short-lived complex. To tackle such issue, we have performed molecular dynamics simulations on an electron transfer complex formed by plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Besides simulations of the isolated partners, two independent trajectories of the complex were calculated, starting from the two different conformations in the NMR ensemble. The first one leads to a more stable ensemble with a shorter distance between the metal sites of the two partners. The second experiences a significant drift of the complex conformation. Analyses of the distinct calculations show that the conformation of cytochrome f is strained upon binding of its partner, and relaxes upon its release. Interestingly, the principal component analysis of the trajectories indicates that plastocyanin displays a concerted motion with the small domain of cytochrome f that can be attributed to electrostatic interactions between the two proteins.
许多短暂的大分子相互作用，如参与电子传递的相互作用，在生物学中是必不可少的。然而，对于伴侣的行为及其在短暂复合物中的动力学，我们知之甚少。为了解决这个问题，我们对来自蓝藻 Phormidium laminosum 的质体蓝蛋白和细胞色素 f 形成的电子转移复合物进行了分子动力学模拟。除了对分离的伴侣进行模拟外，还从 NMR 集合中的两种不同构象计算了复合物的两个独立轨迹。第一个轨迹导致具有更短金属位点距离的更稳定的集合。第二个经历了复合物构象的显著漂移。对不同计算的分析表明，细胞色素 f 的构象在与其伴侣结合时受到应变，在释放时会松弛。有趣的是，轨迹的主成分分析表明，质体蓝蛋白与细胞色素 f 的小结构域表现出协同运动，这可以归因于两种蛋白质之间的静电相互作用。
