Pizzitutti Francesco, Sétif Pierre, Marchi Massimo
Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France.
J Am Chem Soc. 2003 Dec 10;125(49):15224-32. doi: 10.1021/ja0370286.
This paper reports on extensive molecular dynamics simulations (about 40 ns in total) in both the reduced and the oxidized states of Ferredoxin from Cyanobacterium Anabaena PCC7119. These calculations have provided us with the free energy profile of the phi(47) backbone angle which controls the "CO in" to "CO out" transition of Cys46 in the reduced and oxidized Fd7119. Our main motivation has been to identify the time scales involved in the reduction of Fd and single out the amino acid residues crucially affecting the conformational change and, thus, electron transfer. The free energy profiles obtained in this study are relevant to electron transfers in the PSI/Fd7119 and Fd7119/FNR complexes. Our findings based on hydrated ferredoxin simulations are that activated processes are to occur in the protein during electron transfer to and from ferredoxin. The relative stability and the activation barrier of the "CO in" to "CO out" transition can be modulated by the distance between the Ser47 and the Glu94 residues. In our calculations, for short distances, the "CO in" state is favored in the reduced form, whereas for large distances, the "CO out" state becomes increasingly favored. Accordingly, conformational changes in Fd7119 when bound to PSI or FNR can have crucial effects on the kinetics of the electron transfer. Our simulations also show that the hydrogen bond between between Ser47(OG) and Cys46(O) is essential to lock in the "CO out" state. This finding explains why only the Ser47Thr Fd7119 mutant sustains electron transfer activity, as only residues serine and threonine can form a specific hydrogen bond with Cys46(O). Finally, our simulations predict that Phe65 has a large probability of being in close contact with the Cys46(O) at the top of the conformational free energy barrier. This carbonyl/phenyl ring interaction can then facilitate the de-localization of the Fd's electron toward the Pi orbitals of Phe65 aromatic ring which is thought to be crucial to the Fd7119/FNR electron transfer
本文报道了对来自蓝藻鱼腥藻PCC7119的铁氧化还原蛋白在还原态和氧化态下进行的广泛分子动力学模拟（总计约40纳秒）。这些计算为我们提供了控制还原态和氧化态Fd7119中Cys46的“CO入”到“CO出”转变的phi(47)主链角的自由能分布。我们的主要动机是确定参与Fd还原的时间尺度，并找出对构象变化进而对电子转移有至关重要影响的氨基酸残基。本研究中获得的自由能分布与PSI/Fd7119和Fd7119/FNR复合物中的电子转移相关。我们基于水合铁氧化还原蛋白模拟的发现是，在与铁氧化还原蛋白之间进行电子转移期间，蛋白质中会发生活化过程。“CO入”到“CO出”转变的相对稳定性和活化能垒可通过Ser47和Glu94残基之间的距离来调节。在我们的计算中，对于短距离，“CO入”状态在还原形式中更受青睐，而对于长距离，“CO出”状态越来越受青睐。因此，Fd7119与PSI或FNR结合时的构象变化可能对电子转移动力学产生关键影响。我们的模拟还表明，Ser47(OG)和Cys46(O)之间的氢键对于锁定“CO出”状态至关重要。这一发现解释了为什么只有Ser47Thr Fd7119突变体保持电子转移活性，因为只有丝氨酸和苏氨酸残基能与Cys46(O)形成特定氢键。最后，我们的模拟预测，在构象自由能垒顶部，Phe65与Cys46(O)紧密接触的概率很大。这种羰基/苯环相互作用随后可促进Fd的电子向Phe65芳香环的π轨道离域，这被认为对Fd7119/FNR电子转移至关重要
