Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy.
J Mol Graph Model. 2011 Jun;29(7):915-9. doi: 10.1016/j.jmgm.2011.03.001. Epub 2011 Mar 8.
The massive computational resources available in the framework of a grid paradigm approach represent an emerging tool in the bioinformatics field. In this paper, we used the above approach in the rapid determination of the interactions between the ring-hydroxylating dioxygenase, comprised six enzymatic subunits, and polycyclic aromatic hydrocarbons (PAHs) in their optimal positions. The results were obtained by simulating enzyme dynamics at 300 K through molecular dynamics calculations. For the first time, the equilibrated structure of the dioxygenase revealed a network of channels throughout the enzyme that were sufficiently large to allow a flow of small ions or molecules from the inner core of the complex to its exterior surface. The ring-hydroxylating dioxygenase was able to interact with some of the studied PAHs. Additionally, not only the number of aromatic rings but also the PAH shape were critical in predicting the ability of the dioxygenase to interact with these types of molecules. Docking calculations shed light on a new possible binding site that is far from the enzymatic one, which is potentially interesting in considering the stability of the enzyme itself.
网格范例方法中可用的大量计算资源代表了生物信息学领域中的一种新兴工具。在本文中，我们在快速确定包含六个酶亚基的环羟基化双加氧酶与多环芳烃（PAHs）在其最佳位置之间的相互作用时使用了上述方法。通过分子动力学计算在 300 K 下模拟酶动力学获得了结果。首次，双加氧酶的平衡结构揭示了贯穿整个酶的通道网络，这些通道足够大，可以允许从小分子或离子从复合物的核心流到其外表面。环羟基化双加氧酶能够与一些研究中的 PAHs 相互作用。此外，不仅芳香环的数量，而且 PAH 的形状对于预测双加氧酶与这些类型的分子相互作用的能力至关重要。对接计算揭示了一个远离酶的新的可能结合位点，这对于考虑酶本身的稳定性可能是很有趣的。
