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Oxidized amino acid residues in the vicinity of Q(A) and Pheo(D1) of the photosystem II reaction center: putative generation sites of reducing-side reactive oxygen species.

Frankel LK, Sallans L, Limbach PA, Bricker TM - PLoS ONE (2013)

Bottom Line: A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem.In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues (239)F, (241)Q, (242)E and the D2 residues (238)P, (239)T, (242)E and (247)M) and PheoD1 (D1 residues (130)E, (133)L and (135)F).These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana, United States of America.

ABSTRACT
Under a variety of stress conditions, Photosystem II produces reactive oxygen species on both the reducing and oxidizing sides of the photosystem. A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem. In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues (239)F, (241)Q, (242)E and the D2 residues (238)P, (239)T, (242)E and (247)M) and PheoD1 (D1 residues (130)E, (133)L and (135)F). These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.

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Example Mass Spectrometry Data from the Unmodified Peptide.235AFNPTQAEETYSMVTAN252R and the Oxidatively Modified Peptide 235AFNPTQAEETYS247M+16 VTAN252R of the D2 Protein A. Top, spectrum of the collision-induced dissociation (CID) of the unmodified peptide 235AFNPTQAEETYSMVTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified 235AFNPTQAEETYS247M+16 VTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. For comparison the b13+–b17+ ions of the unmodified peptide are highlighted in blue and those of the modified peptide are highlighted in cyan. All b ions longer than b12+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This indicates that 247M contains an oxidative modification. Additionally, the y6+–y15+ions of the unmodified peptide are highlighted in green, while those of the modified peptide are highlighted in yellow. All y ions longer than y5+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This verifies that 247M contains an oxidative modification. The p values for the unmodified and modified peptide were 10−13 and 10−11, respectively.
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pone-0058042-g001: Example Mass Spectrometry Data from the Unmodified Peptide.235AFNPTQAEETYSMVTAN252R and the Oxidatively Modified Peptide 235AFNPTQAEETYS247M+16 VTAN252R of the D2 Protein A. Top, spectrum of the collision-induced dissociation (CID) of the unmodified peptide 235AFNPTQAEETYSMVTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified 235AFNPTQAEETYS247M+16 VTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. For comparison the b13+–b17+ ions of the unmodified peptide are highlighted in blue and those of the modified peptide are highlighted in cyan. All b ions longer than b12+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This indicates that 247M contains an oxidative modification. Additionally, the y6+–y15+ions of the unmodified peptide are highlighted in green, while those of the modified peptide are highlighted in yellow. All y ions longer than y5+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This verifies that 247M contains an oxidative modification. The p values for the unmodified and modified peptide were 10−13 and 10−11, respectively.

Mentions: Fig. 1 illustrates the quality of the mass spectrometry data used for the identification of oxidized amino acid residues in the D1 and D2 proteins. In this figure the MS/MS data collected for the D2 peptide 235A–252R are illustrated. In Fig. 1A, the data from the unmodified peptide are illustrated, while in Fig. 1B, data from the peptide bearing oxidized 247M are shown. In this example and others (Figs. S1–S2), both modified and unmodified versions of the target peptide were identified; in another example only the modified peptide was detected (Fig. S3). Using a p value ≤0.00001 assured extremely high quality peptide identifications with nearly complete y- and b-ion series being observed.


Oxidized amino acid residues in the vicinity of Q(A) and Pheo(D1) of the photosystem II reaction center: putative generation sites of reducing-side reactive oxygen species.

Frankel LK, Sallans L, Limbach PA, Bricker TM - PLoS ONE (2013)

Example Mass Spectrometry Data from the Unmodified Peptide.235AFNPTQAEETYSMVTAN252R and the Oxidatively Modified Peptide 235AFNPTQAEETYS247M+16 VTAN252R of the D2 Protein A. Top, spectrum of the collision-induced dissociation (CID) of the unmodified peptide 235AFNPTQAEETYSMVTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified 235AFNPTQAEETYS247M+16 VTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. For comparison the b13+–b17+ ions of the unmodified peptide are highlighted in blue and those of the modified peptide are highlighted in cyan. All b ions longer than b12+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This indicates that 247M contains an oxidative modification. Additionally, the y6+–y15+ions of the unmodified peptide are highlighted in green, while those of the modified peptide are highlighted in yellow. All y ions longer than y5+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This verifies that 247M contains an oxidative modification. The p values for the unmodified and modified peptide were 10−13 and 10−11, respectively.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585169&req=5

pone-0058042-g001: Example Mass Spectrometry Data from the Unmodified Peptide.235AFNPTQAEETYSMVTAN252R and the Oxidatively Modified Peptide 235AFNPTQAEETYS247M+16 VTAN252R of the D2 Protein A. Top, spectrum of the collision-induced dissociation (CID) of the unmodified peptide 235AFNPTQAEETYSMVTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum (above) are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. B. Top, spectrum of the CID dissociation of the modified 235AFNPTQAEETYS247M+16 VTAN252R. Various identified ions are labeled. Bottom, table of all predicted masses for the y- and b- ions generated from this peptide sequence. Ions identified in the CID spectrum are shown in red. The b'++, b'+ y'++ and y'+ ions are generated by the neutral loss of water while the b*++, b*+ y*++ and y*+ ions are generated from the loss of ammonia. For comparison the b13+–b17+ ions of the unmodified peptide are highlighted in blue and those of the modified peptide are highlighted in cyan. All b ions longer than b12+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This indicates that 247M contains an oxidative modification. Additionally, the y6+–y15+ions of the unmodified peptide are highlighted in green, while those of the modified peptide are highlighted in yellow. All y ions longer than y5+ in the modified peptide are 16 Da larger than the corresponding ions observed from the unmodified peptide. This verifies that 247M contains an oxidative modification. The p values for the unmodified and modified peptide were 10−13 and 10−11, respectively.
Mentions: Fig. 1 illustrates the quality of the mass spectrometry data used for the identification of oxidized amino acid residues in the D1 and D2 proteins. In this figure the MS/MS data collected for the D2 peptide 235A–252R are illustrated. In Fig. 1A, the data from the unmodified peptide are illustrated, while in Fig. 1B, data from the peptide bearing oxidized 247M are shown. In this example and others (Figs. S1–S2), both modified and unmodified versions of the target peptide were identified; in another example only the modified peptide was detected (Fig. S3). Using a p value ≤0.00001 assured extremely high quality peptide identifications with nearly complete y- and b-ion series being observed.

Bottom Line: A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem.In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues (239)F, (241)Q, (242)E and the D2 residues (238)P, (239)T, (242)E and (247)M) and PheoD1 (D1 residues (130)E, (133)L and (135)F).These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana, United States of America.

ABSTRACT
Under a variety of stress conditions, Photosystem II produces reactive oxygen species on both the reducing and oxidizing sides of the photosystem. A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem. In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues (239)F, (241)Q, (242)E and the D2 residues (238)P, (239)T, (242)E and (247)M) and PheoD1 (D1 residues (130)E, (133)L and (135)F). These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.

Show MeSH
Related in: MedlinePlus