Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center

  1. Gai Nishikawa
  2. Yu Sugo
  3. Keisuke Saito
  4. Hiroshi Ishikita  Is a corresponding author
  1. Department of Applied Chemistry, The University of Tokyo, Japan
  2. Research Center for Advanced Science and Technology, The University of Tokyo, Japan
9 figures, 6 tables and 4 additional files

Figures

Electron-transfer pathways along the L- and M-branches in PbRC from B. viridis.

The PbRC is composed of the L (red), M (blue), H (gold), and C (yellow) subunits. [PLPM]: BChlb pair; BL and BM: accessory BChlb; HL and HM: BPheob; QA: primary quinone (menaquinone); Fe: non-heme Fe complex.

Figure 2 with 1 supplement
Em profiles in the XFEL structures for dataset a.

(a) 0 ps. (b) 5 ps. (c) 300 ps.

Figure 2—figure supplement 1
Em values calculated solving the linear Poisson-Boltzmann equation and LUMO energy levels calculated using a QM/MM approach in the dark-state structure.
Em profiles in the XFEL structures for dataset b.

(a) 0 ps. (b) 1 ps. (c) 5 ps. (d) 20 ps. (e) 300 ps. (f) 8 μs.

Residue pairs that are responsible for Em(BL)>Em(BM).
Residue pairs that are responsible for Em(HL)>Em(HM).
Time-dependent Em changes for BChlb and BPheob in the XFEL structures.

(a) Dataset a. (b) Dataset b. ΔEm denotes the Em shift with respect to the dark-state structure. Black solid lines: PL; black dotted lines: PM; blue solid lines BL; blue dotted lines: BM; red solid lines: HL; red dotted lines: HM.

Time-dependent changes in the lowest frequency out-of-plane modes of the chlorin rings in the XFEL structures (dataset a). (a) PL. (b) PM. (c) BL. (d) BM. (e) HL. (f) HM. (g) Typical lowest frequency out-of-plane modes of the chlorin rings.

Sad: saddling (red); ruf: ruffling (blue); dom: doming (green); wav(x, y): waving (x, y) (gray, dark blue); pro: propellering (orange). Solid and dotted lines indicate L- and M-branches, respectively. See Supplementary file 1 for the absolute values in the dark state for dataset a.

Time-dependent changes in the lowest frequency out-of-plane modes of the chlorin rings in the XFEL structures (dataset b). (a) PL. (b) PM. (c) BL. (d) BM. (e) HL. (f) HM.

Sad: saddling (red); ruf: ruffling (blue); dom: doming (green); wav(x, y): waving (x, y) (gray, dark blue); pro: propellering (orange). Solid and dotted lines indicate L- and M-branches, respectively. See Supplementary file 2 for the absolute values in the dark state for dataset b Figure 8—source data 1.

Time-dependent Em changes for QA in the XFEL structures.

(a) Dataset a. (b) Dataset b. ΔEm denotes the Em shift with respect to the dark-state structure. Note that the calculated Em(QA) values for dataset a and dataset b in the dark structure are –223 mV and –209 mV, respectively, which are comparable to experimentally measured values of –150 mV for PbRC from B. viridis (menaquinone) (Prince et al., 1976) and –180 mV for PbRC from R. sphaeroides (ubiquinone) (Prince and Dutton, 1976).

Tables

Table 1
Contributions of the L/M residue pairs that are responsible for Em(BL)>Em(BM) (more than 10 mV) in the dark-state structure (mV).

Difference: [contribution of subunit L to Em(BL)] + [contribution of subunit M to Em(BL)] – [contribution of subunit L to Em(BM)] – [contribution of subunit M to Em(BM)].

Subunit LEm(BL)Em(BM)Subunit MEm(BL)Em(BM)Difference
Phe-L181017Tyr-M20839–325
His-L144–8–2Glu-M171–14–4525
Asn-L1585–6Thr-M185–3–412
Table 2
Contributions of the L/M residue pairs that are responsible for Em(HL)>Em(HM) (more than 10 mV) in the dark-state structure (mV).

Difference: [contribution of subunit L to Em(HL)] + [contribution of subunit M to Em(HL)] – [contribution of subunit L to Em(HM)] – [contribution of subunit M to Em(HM)].

Subunit LEm(HL)Em(HM)Subunit MEm(HL)Em(HM)Difference
Ala-L120–40Asn-M1470–4238
Asp-L218–2–22Trp-M2521020
Arg-L103773Arg-M13035917
Ala-L237–20Ser-M2713–1616
Lys-L110172Ala-M1370314
Val-L21915Thr-M25317111
His-L21110Arg-M24514411
Table 3
Residues that shift Em(HL) most significantly during putative electron transfer in the XFEL structures (dataset a) (mV).

The same residues are highlighted in the same colors for clarity.

Dataset aShiftShift
0–5 psSer-L1765Cys-M2104
Thr-M220–7BL–5
5–300 psBL7Gly-M2093
Gly-M211–11Leu-M212–8
Table 4
Residues that shift Em(HL) most significantly during putative electron transfer in the XFEL structures (dataset b) (mV).

The same residues are highlighted in the same colors for clarity.

Dataset bShiftShift
0–1 psSer-L2388Ser-L1767
BL–7Leu-M213–3
1–5 psGly-M2116Leu-M2135
Ser-L238–6Thr-M253–5
5–20 psBL12Thr-M2537
Leu-M213–4PM–3
20–300 psSer-L2383Gly-M2112
BL–10Glu-L212–4
300 ps to 8 μsGlu-L2124Leu-M2134
BL–6Gly-M211–5
Table 5
Induced out-of-plane distortion of HL and HM in the PbRC protein environment of the dark structure for dataset a in response to the reduction (Å).
SaddlingRufflingDomingWavingPropellering
B2uB1uA2uEg(x)Eg(y)A1u
HL0.180.35–0.100.13–0.110.13
HL0.240.35–0.090.12–0.120.13
(PL•+HL)(0.22)(0.36)(–0.07)(0.13)(–0.13)(0.13)
HL/HL difference0.060.000.01–0.01–0.010.00
HM0.060.40–0.200.370.120.19
HM0.120.38–0.220.330.090.22
(PL•+HM)(0.14)(0.38)(–0.22)(0.33)(0.10)(0.22)
HM/HM difference0.06–0.02–0.02–0.04–0.030.03
Table 6
Induced out-of-plane distortion of HL and HM in the PbRC protein environment of the dark structure for dataset b in response to the reduction (Å).
SaddlingRufflingDomingWavingPropellering
B2uB1uA2uEg(x)Eg(y)A1u
HL0.130.35–0.130.07–0.090.20
HL0.250.34–0.020.12–0.160.13
(PL•+HL)(0.23)(0.34)(–0.03)(0.12)(–0.16)(0.12)
HL/HL difference0.12–0.010.110.05–0.07–0.07
HM0.080.57–0.110.160.200.32
HM0.160.36–0.190.360.180.21
(PL•+HM)(0.16)(0.36)(–0.20)(0.36)(0.18)(0.21)
HM/HM difference0.08–0.21–0.080.20–0.02–0.11

Additional files

Supplementary file 1

Out-of-plane distortions in the PbRC protein environment of the dark structure for dataset a (Å).

https://cdn.elifesciences.org/articles/88955/elife-88955-supp1-v1.docx
Supplementary file 2

Out-of-plane distortions in the PbRC protein environment of the dark structure for dataset b (Å).

https://cdn.elifesciences.org/articles/88955/elife-88955-supp2-v1.docx
Supplementary file 3

Atomic charges of BChlb and BPheob.

https://cdn.elifesciences.org/articles/88955/elife-88955-supp3-v1.docx
MDAR checklist
https://cdn.elifesciences.org/articles/88955/elife-88955-mdarchecklist1-v1.docx

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Gai Nishikawa
  2. Yu Sugo
  3. Keisuke Saito
  4. Hiroshi Ishikita
(2023)
Absence of electron-transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center
eLife 12:RP88955.
https://doi.org/10.7554/eLife.88955.4