SIMULATIONS OF KINKED DNA & ANNEALING OF DNA ECO RI & RV ENDONUCLEASE COMPLEX

我们提出了一系列的模拟，将利用 最近确定的EcoRI和EcoRV内切核酸酶的结构为 以及我们最近完成的DNA-Eco的初步模拟 RI复合体。 我们对同源DNA-Eco RI的初步模拟 核酸内切酶复合物采用了6 A明确的水壳， 总共约有15,000个原子。 我们使用AMBER 4.0来模拟 170 pS的复合体，目前正在分析轨迹。 具体目标是：（1）扩展了初步的模拟， 从目前的170 pS到最终持续时间的天然复合体 （2）模拟脱辅基蛋白（在不存在DNA的情况下）， （3）模拟同源DNA-Eco RV 复合物（4 RVE），250 pS。

We propose a series of simulations that will take advantage of recently determined structures for Eco RI and Eco RV endonucleases as well as our recently completed preliminary simulation of the DNA-Eco RI complex. Our preliminary simulation of the cognate DNA-Eco RI endonuclease complex employed a 6 A shell of explicit water for a total of approximately 15,000 atoms. We used AMBER 4.0 to simulate the complex for 170 pS and are currently analyzing the trajectory. The specific aims are: (1) extend the preliminary simulation of the native complex from its current curation of 170 pS to a final duration of 500 pS; (2) simulate the apo-protein (in the absence of DNA) for 250 pS using a similar protocol; (3) simulate the cognate DNA-Eco RV complex (4RVE) for 250 pS.