Research ArticlePLANT SCIENCES

Reactive oxygen species leave a damage trail that reveals water channels in Photosystem II

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Science Advances  17 Nov 2017:
Vol. 3, no. 11, eaao3013
DOI: 10.1126/sciadv.aao3013
  • Fig. 1 Example of product-ion (MS/MS) spectra that identify oxidative modifications of PSII residues.

    Product-ion (MS/MS) spectra of the oxidized CP43 peptide 362GPwLEPLRGPNGLDLD378K (top) and the unmodified form of the peptide (bottom). The oxidation (+15.9949 Da) was localized to 364W. Note that 372N contains the common deamidation modification (+0.9840 Da) according to both spectra. The fragment maps and corresponding labeled b- and y-ions show the convincing fragmentation series obtained at high mass accuracy (~0.02 Da), allowing highly confident peptide identification and unambiguous residue-level localization of the oxidative modification. Lowercase lettering in the amino acid sequence indicates the site of oxidation (see figs. S1 to S3 for additional example spectra). m/z, mass/charge ratio.

  • Fig. 2 Residues with oxidative modifications detected in this study.

    The modified residues on D1, D2, and CP43 were mapped onto the 1.9 Å crystal structure of PSII from T. vulcanus (PDB: 3WU2). Red, modified residues on the lumenal side of PSII; green, modified residues on the cytosolic side of PSII, in the vicinity of QA; purple, modified residues on the cytosolic side of PSII, in the vicinity of QB.

  • Fig. 3 Lumen-side oxidized residues detected in this study.

    (A) Depiction of the 42 lumen-side oxidized residues detected in this study (red). (B) Same depiction as in (A), but arm 1 is shown in red, arm 2 in purple, and arm 3 in yellow. (C) All the 255 lumen-side residues that were covered by MS in this study, plus the covered and oxidized CP47 residues discussed in the text (see table S3). Some residues are obscured by others and are not visible in this view. Red, oxidized residues; cyan, nonoxidized residues. (D) Same depiction as in (A), except that in this view, the surface-exposed residues are colored blue, and buried residues are colored red. Visual Molecular Dynamics (VMD) (66) was used to determine whether a residue is surface-exposed or buried. Throughout the figure, the Mn cluster is shown in green.

  • Fig. 4 Superposition of channels identified in previous MD studies onto the lumen-side oxidized residues.

    (A) A segment of the oxidized arm 1 residues partially surrounds water channel 3 (cyan; left) identified in MD studies (26, 27). The oxidized arm 2 residues partially surround water channel 4a (cyan; right) and oxygen channel 4ai (orange) identified by Vassiliev et al. (26, 27). The oxidized CP47 residues mentioned in the discussion are included in both parts of this figure (see movie S1 for a full rotation of this image about the y axis). (B) A closer view of the correspondence between oxidized arm 1 residues and channel 3 (26, 27). The 1.9 Å PSII crystal structure PDB: 3ARC was used for correspondence with channels in the study by Vassiliev et al. (26, 27). It should be noted that the depictions of channels 3, 4a, and 4ai in Figs. 4 and 5 are fixed-diameter representations. Because of the natural protein dynamics, the size and exact local shape of the actual accessible pathway within the protein complex may vary slightly from the depiction. (A) and (B): Red, arm 1 residues that correspond closely to channel 3; light purple, arm 2 residues; yellow, arm 3 residues; green, Mn cluster.

  • Fig. 5 Comparison of lumen-side oxidized residues detected by Bricker and co-workers (11, 13) and in the current study.

    (A) Lumen-side oxidized residues detected on the D1 and D2 proteins in the study by Kale et al. (11) and in arm 1 in this study and their correspondence to channel 3 (26). (B) D1/D2 arm 1 residues in this study and the additional oxidized CP47 residues identified in a targeted analysis based on the results of Frankel et al. (13) and their correspondence to channel 3 (26, 27). (C) Oxidized residues in the arm 3 region detected by Frankel et al. (13) and in the current study. Note: Some additional lumen-side residues detected by Frankel et al. (13) that are not relevant to this discussion are not shown in this figure. Gray, residues only found oxidized by Bricker and co-workers (11, 13); orange (A) and purple (C), residues found oxidized in the studies by Kale et al. (11) or Frankel et al. (13), respectively, and the current study; red, D1/D2 arm 1 residues; yellow, Cl (B) and arm 3 residues (C); cyan, channel 3 (26); green, Mn cluster.

  • Table 1 Correspondence between channels identified in computational studies and this work.

    Channel names are listed followed by the species they were assigned to conduct in the original study. Channels in the same column are nearly identical unless otherwise noted.


    Embedded Image

    *The authors calculated a high (~22 kcal/mol) activation energy barrier for water travel through this channel, rendering it “virtually impermeable” to water (see main text for discussion).

    †Encompasses approximately two-thirds of channel 1 length.

    ‡Encompasses approximately three-fourths of channel 2 length.

    §Encompasses approximately one-half of channel 5 length.

    ¶Encompasses approximately three-fourths of channel 4ci length.

    ||Encompasses approximately two-thirds of channel 5 length.

    Supplementary Materials

    • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/11/eaao3013/DC1

      fig. S1. Example 1 of product-ion (MS/MS) spectra detected that identify oxidative modifications of PSII residues.

      fig. S2. Example 2 of product-ion (MS/MS) spectra detected that identify oxidative modifications of PSII residues.

      fig. S3. Example 3 of product-ion (MS/MS) spectra detected that identify oxidative modifications of PSII residues.

      table S1. Oxidative modifications included as variable modifications in the MS database searches.

      table S2. Oxidative modifications of PSII detected in this study.

      table S3. List of oxidized peptides detected in this study.

      table S4. Oxidized residues that correspond to channels determined in previous MD studies.

      movie S1. Rotation of Fig. 4A about the y axis.

      Reference (67)

    • Supplementary Materials

      This PDF file includes:

      • fig. S1. Example 1 of product-ion (MS/MS) spectra detected that identify oxidative modifications of PSII residues.
      • fig. S2. Example 2 of product-ion (MS/MS) spectra detected that identify oxidative modifications of PSII residues.
      • fig. S3. Example 3 of product-ion (MS/MS) spectra detected that identify oxidative modifications of PSII residues.
      • table S1. Oxidative modifications included as variable modifications in the MS database searches.
      • table S2. Oxidative modifications of PSII detected in this study.
      • table S4. Oxidized residues that correspond to channels determined in previous MD studies.
      • Legend for movie S1
      • Reference (67)

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      Other Supplementary Material for this manuscript includes the following:

      • table S3 (Microsoft Excel format). List of oxidized peptides detected in this study.
      • movie S1 (.mp4 format). Rotation of Fig. 4A about the y axis.

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