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79952484641
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note
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18 The structural diagram was prepared using PYMOL (www.pymol.org) and VMD. All graphs were plotted using the XMGRACE program (http://plasma-gate.weizmann.ac.il/Grace). The overall conformational stability of the HDAC8 protein was established by calculating the Ca root-mean-squared-deviation (RMSD) over the course of a 20 ns dynamics simulation. After an initial increase, the Cα RMSD was constant, at 1.65 Å. The flexible regions of the protein were also calculated using the root mean squared fluctuation (RMSF). The fluctuations are relatively small in helices present in the core of the protein, with increased degree of fluctuation in the loops connecting helices.
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