Molecular dynamics of substrate complexes with hamster cytochrome P450c17 (CYP17): mechanistic approach to understanding substrate binding and activities.
Molecular dynamics of substrate complexes with hamster cytochrome P450c17 (CYP17): mechanistic approach to understanding substrate binding and activities.
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仓鼠细胞色素 P450c17 (CYP17) 底物复合物的分子动力学：了解底物结合和活性的机械方法。
DOI：
10.1016/s0304-4165(02)00488-9
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发表时间：
2003
期刊：
影响因子：
--
通讯作者：
Auchus,RichardJ
中科院分区：
文献类型：
--
作者：
Mathieu,AxelP;LeHoux,JeanGuy;Auchus,RichardJ
来自不同动物物种的细胞色素P450 c17异构体具有不同的底物选择性，特别是对于17，20-裂解酶活性。特别地，人P450 c17选择性地产生脱氢表雄酮，几乎没有雄烯二酮（AD）。另一方面，CYP 450 c17以相当的速率产生这两种类固醇。因此，我们研究了计算分析是否可以解释活性曲线的差异。因此，我们将四种P450 c17底物--我们进行了分子动力学（MD）模拟的复合物和分析所得的轨迹，以确定与基板相互作用的氨基酸。从两个不同方向的基板，我们得到了两套绑定轨迹在每种情况下。第一组轨迹揭示了结合过程中发生的结构重排，而第二组轨迹反映了催化过程中的底物取向。我们的模型表明，底物选择性和与仓鼠P450 c17的结合需要三个不同的步骤：（1）在假定的底物入口识别底物，其特征在于在仓鼠P450 c17的表面含有带电残基R96和D116的口袋;（2）底物进入活性位点，在通过底物与血红素D-环丙酸酯基团、R96、R440和T306的可能的氢键结合所引导的中间位置;随后（3）逆时针旋转底物90°，将其定位在反应性的最佳位置，该过程可通过与仓鼠P450 c17的110-112区域的氢键结合来指导。与一些基板，我们得到的轨迹表明，主要扭曲的I-螺旋和开放的H-I环发生在基板结合。总之，这些建模练习提供了洞察可能发生的结构重组底物结合过程中，并表明，参与这一过程的三个不同步骤的氨基酸可能都有助于底物结合和活动。
The cytochrome P450c17 isoforms from various animal species have different substrate selectivity, especially for 17,20-lyase activity. In particular, the human P450c17 selectively produces dehydroepiandrosterone with little androstenedione (AD). Hamster P450c17, on the other hand, produces both of these steroids at comparable rates. We thus investigated if computational analysis could explain the difference in activity profiles. Therefore, we inserted the four P450c17 substrates—pregnenolone, progesterone, and their 17α-hydroxylated forms—inside our hamster P450c17 model, which we derived from our human P450c17 model based on the crystal structure of P450BMP. We performed molecular dynamics (MD) simulations on the complexes and analyzed the resultant trajectories to identify amino acids that interact with substrates. Starting with substrates in two different orientations, we obtained two sets of binding trajectories in each case. The first set of trajectories reveal structural rearrangements that occur during binding, whereas the second set of trajectories reflects substrate orientations during catalysis. Our modeling suggests that three distinct steps are required for substrate selectivity and binding to the hamster P450c17: (1) recognition of the substrate at the putative substrate entrance, characterized by a pocket at the surface of the hamster P450c17 containing charged residues R96 and D116; (2) entry of the substrate into the active site, in an intermediate position directed by possible hydrogen bonding of the substrates with the heme D-ring propionate group, R96, R440, and T306; followed by (3) 90° counterclockwise rotation of the substrates, positioning them in optimal position for reactivity, a process that may be directed by hydrogen bonding to the 110–112 region of the hamster P450c17. With some substrates, we obtained trajectories which suggest that major distortions in the I-helix and opening of the H–I loop occur during substrate binding. In conclusion, these modeling exercises provide insight to possible structural reorganizations that occur during substrate binding and suggest that amino acids that participate in three distinct steps of this process may all contribute to substrate binding and activity.