KINKED DNA & CRYSTALLOGRAPHY: SIMULATED ANNEALING OF ECORI ENDONUCLEASE

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。 扩展对 从目前的170 pS到最终持续时间的天然复合体 500 pS。 2. 模拟脱辅基蛋白（在没有DNA的情况下）， 250 pS使用类似的协议。 3. 模拟同源DNA-Eco RV 复合物（4RVE），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.