S residues corresponding to the oxidatively modified spinach residues (Table 1) are highlighted. These oxidized residues are shown as spheres superimposed on Fexinidazole Monomer I of the T. vulcanus structure. For clarity, only the D1 and D2 proteins and their associated cofactors are shown. A. the view from outside Monomer I, looking towards the dimeric complex from within the plane of the membrane. B. the view from Monomer II looking towards its interface with Monomer I within the plane of the membrane. The D1 protein is shown in pale green and the D2 protein is shown in pale yellow. The oxidatively modified residues of D1 are shown in dark green while those of D2 are shown in orange. Various cofactors of both D1 and D2 are labeled and colored pale green or yellow, respectively. PheoD1 is shown in bright green. The non-heme iron is shown in bright red. The Mn4O5Ca cluster and its associated chloride ions are labeled as the OEC. Figs. 2? were produced using PYMOL [53]. doi:10.1371/MedChemExpress 1418741-86-2 journal.pone.0058042.gOxidized Amino Acids on the Reducing Side of PS IIFigure 3. Detail of the Oxidized Residues in the Vicinity of QA. A close-up of the QA ?Non-Heme Iron ?QB region is shown. The T. vulcanus residues corresponding to the oxidatively modified spinach residues (Table 15900046 1) are highlighted and labeled. The D1 protein is shown in pale green and the D2 protein is shown in pale yellow. The 
oxidatively modified residues of D1 are shown in dark green while those of D2 are shown in orange, with the 
individual modified residues being labeled. QA is shown in yellow, QB in green and the non-heme iron is shown in bright red. doi:10.1371/journal.pone.0058042.gFigure 4. Detail of the Oxidized Residues in the Vicinity of PheoD1. The T. vulcanus residues corresponding to the oxidatively modified spinach residues (Table 1) are highlighted and labeled. The D1 protein is shown in pale green and the D2 protein is shown in pale yellow. The oxidatively modified residues of D1 are shown in dark green, with the individual modified residues being labeled. PheoD1 is shown in bright green, QA is shown in yellow, QB in green and the nonheme iron is shown in bright red. For clarity, modified residues in the vicinity of QA (and detailed in Fig. 3) are not shown. doi:10.1371/journal.pone.0058042.glifetime (t1/2<2 hr [42]). Interestingly, no oxidative modifications in the vicinity of the Mn4O5Ca cluster were observed on the D1 protein on this same plant material. Again, it is possible that D1 modifications in the vicinity of the metal cluster (or, perhaps, P680) may trigger D1 turnover and, consequently, limit the detection and/or accumulation of such putative oxidative modifications. While no modified residues were observed in the immediate vicinity of QB, we cannot rule out, at this time, the possibility that this site could also contribute to reducing-side ROS production. Additionally, since we did not collect mass spectrometry data on the cytochrome b559 a and b subunits or on the other low molecular mass subunits in the vicinity of this cytochrome, we cannot comment on their ability to produce ROS. We also cannot speculate on the relative rate of ROS production by PheoD1 or QA (or other putative ROS-producing sites). We have no quantitative data as to the proportion of modified amino acid residues present at any of the observed positions. Indeed, such quantification would 26001275 be difficult to obtain given the different hydophobicity of the unmodified vs. modified peptides and their conse.S residues corresponding to the oxidatively modified spinach residues (Table 1) are highlighted. These oxidized residues are shown as spheres superimposed on monomer I of the T. vulcanus structure. For clarity, only the D1 and D2 proteins and their associated cofactors are shown. A. the view from outside Monomer I, looking towards the dimeric complex from within the plane of the membrane. B. the view from Monomer II looking towards its interface with Monomer I within the plane of the membrane. The D1 protein is shown in pale green and the D2 protein is shown in pale yellow. The oxidatively modified residues of D1 are shown in dark green while those of D2 are shown in orange. Various cofactors of both D1 and D2 are labeled and colored pale green or yellow, respectively. PheoD1 is shown in bright green. The non-heme iron is shown in bright red. The Mn4O5Ca cluster and its associated chloride ions are labeled as the OEC. Figs. 2? were produced using PYMOL [53]. doi:10.1371/journal.pone.0058042.gOxidized Amino Acids on the Reducing Side of PS IIFigure 3. Detail of the Oxidized Residues in the Vicinity of QA. A close-up of the QA ?Non-Heme Iron ?QB region is shown. The T. vulcanus residues corresponding to the oxidatively modified spinach residues (Table 15900046 1) are highlighted and labeled. The D1 protein is shown in pale green and the D2 protein is shown in pale yellow. The oxidatively modified residues of D1 are shown in dark green while those of D2 are shown in orange, with the individual modified residues being labeled. QA is shown in yellow, QB in green and the non-heme iron is shown in bright red. doi:10.1371/journal.pone.0058042.gFigure 4. Detail of the Oxidized Residues in the Vicinity of PheoD1. The T. vulcanus residues corresponding to the oxidatively modified spinach residues (Table 1) are highlighted and labeled. The D1 protein is shown in pale green and the D2 protein is shown in pale yellow. The oxidatively modified residues of D1 are shown in dark green, with the individual modified residues being labeled. PheoD1 is shown in bright green, QA is shown in yellow, QB in green and the nonheme iron is shown in bright red. For clarity, modified residues in the vicinity of QA (and detailed in Fig. 3) are not shown. doi:10.1371/journal.pone.0058042.glifetime (t1/2<2 hr [42]). Interestingly, no oxidative modifications in the vicinity of the Mn4O5Ca cluster were observed on the D1 protein on this same plant material. Again, it is possible that D1 modifications in the vicinity of the metal cluster (or, perhaps, P680) may trigger D1 turnover and, consequently, limit the detection and/or accumulation of such putative oxidative modifications. While no modified residues were observed in the immediate vicinity of QB, we cannot rule out, at this time, the possibility that this site could also contribute to reducing-side ROS production. Additionally, since we did not collect mass spectrometry data on the cytochrome b559 a and b subunits or on the other low molecular mass subunits in the vicinity of this cytochrome, we cannot comment on their ability to produce ROS. We also cannot speculate on the relative rate of ROS production by PheoD1 or QA (or other putative ROS-producing sites). We have no quantitative data as to the proportion of modified amino acid residues present at any of the observed positions. Indeed, such quantification would 26001275 be difficult to obtain given the different hydophobicity of the unmodified vs. modified peptides and their conse.