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these circumstances is often representative of the enzymatically-Reduce SSB or the final stage of processing radiation-induced SSBs, just prior to the start on the repair phase. The PARP-one protein was represented in entire atomic resolution only for the areas actively Employed in the co-crystallization experiments, specially, the two Zn fingers Zn1 and Zn2. In a number of the MD simulations we held them physically related by their 13-a.a. linker, even though in other simulations we produced them act independently to simulate a PARP-one dimer.

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following 500ns MD simulation, the DNA appears nearly straight plus the gap closed, with little if any area for Zn2 and Zn1 to make contacts Using the SSB ends, as it might be noticed from the plots in Fig. 3b,c. to grasp If your initial orientation of Zn1-two could play a task from the SSB opening and kinking, we for that reason proceeded with manually adjusting the orientation with the protein into distinct interacting configurations, as defined in another part.

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