Molecular dynamics of the P450cam-Pdx complex reveals complex stability and novel interface contacts
Molecular dynamics of the P450cam-Pdx complex reveals complex stability and novel interface contacts
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DOI：
10.1002/pro.2583
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发表时间：
2015-01-01
期刊：
影响因子：
8
通讯作者：
Poulos, Thomas L.
中科院分区：
文献类型：
--
作者：
Hollingsworth, Scott A.;Poulos, Thomas L.
细胞色素P450 cam催化樟脑的立体和区域特异性羟基化为5-外羟基樟脑。用于樟脑氧化的两个电子由Pdx（putidaredoxin）提供，Pdx是一种含Fe 2S 2的蛋白质。最近的两个晶体结构的P450 cam-Pdx复合物，一个解决了与共价交联的帮助下，一个没有，提供了一个结构图片的氧化还原伙伴的相互作用。为了研究复合物结构的稳定性和最近的晶体结构之间的微小差异，对交联结构进行了100纳秒的分子动力学（MD）模拟，所述交联结构在计算机上突变为野生型并且去除了接头分子。复合物在模拟过程中是稳定的，尽管构象变化包括P450 cam的C螺旋进一步向Pdx的移动允许在整个模拟过程中保持稳定的复合物界面处形成许多新的接触。虽然在模拟中丢失了几个次要的晶体接触，但之前实验研究的所有主要接触都保持不变。平衡的MD结构包含类似于交联和非共价结构以及新鉴定的相互作用的接触的混合物。最后，MD模拟中P450 cam Asp 251-Arg 186离子对的重组反映了在更混杂的CYP 101 D1中观察到的离子对，并表明Asp 251-Arg 186离子对可能很重要。
Cytochrome P450cam catalyzes the stereo and regiospecific hydroxylation of camphor to 5-exo-hydroxylcamphor. The two electrons for the oxidation of camphor are provided by putidaredoxin (Pdx), a Fe2S2 containing protein. Two recent crystal structures of the P450cam-Pdx complex, one solved with the aid of covalent cross-linking and one without, have provided a structural picture of the redox partner interaction. To study the stability of the complex structure and the minor differences between the recent crystal structures, a 100 nanosecond molecular dynamics (MD) simulation of the cross-linked structure, mutated in silico to wild type and the linker molecule removed, was performed. The complex was stable over the course of the simulation though conformational changes including the movement of the C helix of P450cam further toward Pdx allowed for the formation of a number of new contacts at the complex interface that remained stable throughout the simulation. While several minor crystal contacts were lost in the simulation, all major contacts that had been experimentally studied previously were maintained. The equilibrated MD structure contained a mixture of contacts resembling both the cross-linked and noncovalent structures and the newly identified interactions. Finally, the reformation of the P450cam Asp251-Arg186 ion pair in the MD simulation mirrors the ion pair observed in the more promiscuous CYP101D1 and suggests that the Asp251-Arg186 ion pair may be important.