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.
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