Chapter 4 ā Page 130 protein complexes, and explains the higher average RMSD, although the precise extent of the pivot di ered over time (during the simulation, as the protein conformation fluctuates) and between the simulation replicas. The pivot is clearest when aligning the native and oxidized version of the protein based on only the receptor chains, i.e. the protein chains that were not oxidized, which is shown in Figure 3b. Figure 3: Oxidation-induced structural changes in the proteins. (a) RMSD of the CĪ± atoms of the native and oxidized protein complexes. (b) Cartoon view of representative frames (i.e., one of their replicas) for the native (blue) and oxidized (orange) protein complexes, aligned based on the non-oxidized receptors. The arrows highlight how the ligands have shifted in the oxidized structure.
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