Wibowo Fajar R, Rauch Christine, Trieb Michael, Liedl Klaus R
Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A6020 Innsbruck, Austria.
Biopolymers. 2005 Oct 15;79(3):128-38. doi: 10.1002/bip.20341.
MD simulations have been carried out to understand the dynamical behavior of the DNA substrate of the Thermus aquaticus DNA methyltransferase (M.TaqI) in the methylation process at N6 of adenine. As starting structures, an x-ray structure of M.TaqI in complex with DNA and cofactor analogue (PDB code: 1G 38) and free decamer d(GTTCGATGTC)(2) were taken. The x-ray structure shows two consecutive BII substates that are not observed in the free decamer. These consecutive BII substates are also observed during our simulation. Additionally, their facing backbones adopt the same conformations. These double facing BII substates are stable during the last 9 ns of the trajectories and result in a stretched DNA structure. On the other hand, protein-DNA contacts on 5' and 3' phosphodiester groups of the partner thymine of flipped adenine have changed. The sugar and phosphate parts of thymine have moved further into the empty space left by the flipping base without the influence of protein. Furthermore, readily high populated BII substates at the GpA step of palindromic tetrad TCGA rather than CpG step are observed in the free decamer. On the contrary, the BI substate at the GpA step is observed on the flipped adenine strand. A restrained MD simulation, reproducing the BI/BII pattern in the complex, demonstrated the influence of the unusual backbone conformation on the dynamical behavior of the target base. This finding along with the increased nearby interstrand phosphate distance is supportive to the N6-methylation mechanism.
已进行分子动力学（MD）模拟，以了解嗜热栖热菌DNA甲基转移酶（M.TaqI）的DNA底物在腺嘌呤N6甲基化过程中的动力学行为。以与DNA和辅因子类似物复合的M.TaqI的X射线结构（PDB代码：1G 38）和游离的十聚体d(GTTCGATGTC)(2)作为起始结构。X射线结构显示出在游离十聚体中未观察到的两个连续的BII亚状态。在我们的模拟过程中也观察到了这些连续的BII亚状态。此外，它们相对的主链采取相同的构象。这些双面对的BII亚状态在轨迹的最后9纳秒内是稳定的，并导致DNA结构伸展。另一方面，翻转腺嘌呤的配对胸腺嘧啶的5'和3'磷酸二酯基团上的蛋白质-DNA接触发生了变化。胸腺嘧啶的糖和磷酸部分在没有蛋白质影响的情况下进一步移入由翻转碱基留下的空白空间。此外，在游离十聚体中观察到，在回文四联体TCGA的GpA步而不是CpG步处，BII亚状态的占有率很高。相反，在翻转的腺嘌呤链上观察到GpA步处的BI亚状态。一个受限的MD模拟再现了复合物中的BI/BII模式，证明了异常主链构象对目标碱基动力学行为的影响。这一发现以及附近链间磷酸距离的增加支持了N6甲基化机制。
