KINKED DNA & CRYSTALLOGRAPHY: SIMULATED ANNEALING OF ECORI ENDONUCLEASE

扭结的DNA

• 批准号: 6295111
• 负责人: JOHN M ROSENBERG
• 金额: $ 1.17万
• 依托单位: MELLON PITTS CORPORATION (MPC CORP)
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-09-30 至 1999-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6295111
• 关键词: biological products; biomedical resource; genetics

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.

我们提出了一系列的模拟，这些模拟将利用 新近确定的Eco RI和Eco RV内切酶AS的结构 以及我们最近完成的DNA-Eco的初步模拟 RI情结。我们对同源DNA-Eco RI的初步模拟 核酸内切酶复合体使用6A显性水作为 总共大约有15,000个原子。我们使用Amber 4.0进行了模拟 该复合体为170 ps，目前正在分析弹道。 具体目标是：1.推广初步模拟 原生复合体从目前170 ps的精选到最终持续时间 为500 ps。2.模拟脱脂蛋白(在没有DNA的情况下) 使用类似协议的250 ps。3.模拟同源DNA-Eco RV 复数(4RVE)为250 ps。