Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre

Båth, Petra; Banacore, Analia; Borjesson, Per; Bosman, Robert; Wickstrand, Cecilia; Safari, Cecilia; Dods, Robert; Ghosh, Swagatha; Dahl, Peter; Ortolani, Giorgia; Úlfarsdóttir, Tinna Björg; Hammarin, Greger; Garcia-Bonete, Maria-Jose; Vallejos, Adams; Ostojić, Lucija; Edlund, Petra; Linse, Johanna-Barbara; Andersson, Rebecka; Nango, Eriko; Owada, Shigeki; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Nureki, Osamu; Luo, Fangjia; James, Daniel; Nass, Karol; Johnson, Philip J. M.; Knopp, G.; Ozerov, Dmitry; Cirelli, Claudio; Milne, Christopher J.; Iwata, So; Brändén, Gisela; Neutze, Richard

doi:10.1107/s2059798322004144

Cited by 9 publications

(12 citation statements)

References 72 publications

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“…The computation was based on the electrostatic continuum model, solving the linear Poisson− Boltzmann equation with the MEAD program. 31 The difference in electrostatic energy between the two protonation states, 24 (c) R. sphaeroides (PDB code, 3I4D). 27 The H-bond distances are summarized in Table S1.…”

Section: Protonation Patternmentioning

confidence: 99%

“…In the Q B -bound B. viridis PbRC structures, Asn-L213 forms an H-bond with Ser-L223, the direct proton donor to Q B , whereas Asp-M43 does not form an H-bond with Ser-L223 (e.g., 2.25 Å structure). In addition, no water molecule is identified between Asp-M43 and Ser-L223.…”

Section: Introductionmentioning

confidence: 99%

“…19 However, the proton is localized predominantly at the proton donor moiety in standard H-bonds. Only when the pK a values of the proton donor and acceptor moieties are nearly equal (e.g., via electron transfer 10,12,20 In the Q B -bound B. viridis PbRC structures, Asn-L213 forms an H-bond with Ser-L223, the direct proton donor to Q B , whereas Asp-M43 does not form an H-bond with Ser-L223 (e.g., 2.25 Å structure 24 ). In addition, no water molecule is identified between Asp-M43 and Ser-L223.…”

Section: Introductionmentioning

confidence: 99%

“…Only when the pK a values of the proton donor and acceptor moieties are nearly equal (e.g., via electron transfer 10,12,20 or conformational changes 21 ) does a low-barrier H-bond form, facilitating proton transfer. 22,23 This In the Q B -bound B. viridis PbRC structures, Asn-L213 forms an H-bond with Ser-L223, the direct proton donor to Q B , whereas Asp-M43 does not form an H-bond with Ser-L223 (e.g., 2.25 Å structure 24 ). In addition, no water molecule is identified between Asp-M43 and Ser-L223.…”

Section: Introductionmentioning

confidence: 99%

“…(a) T. tepidum (PDB code, 5Y5S). 26 (b) B. viridis (PDB code, 7Q7Q) 24. (c) R. sphaeroides (PDB code, 3I4D) 27.…”

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confidence: 99%

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Mechanism of Asparagine-Mediated Proton Transfer in Photosynthetic Reaction Centers

Sugo

Ishikita

2023

Biochemistry

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In photosynthetic reaction centers from purple bacteria (PbRCs), light-induced charge separation leads to the reduction of the terminal electron acceptor quinone, QB. The reduction of QB to QB •– is followed by protonation via Asp-L213 and Ser-L223 in PbRC from Rhodobacter sphaeroides. However, Asp-L213 is replaced with nontitratable Asn-L222 and Asn-L213 in PbRCs from Thermochromatium tepidum and Blastochloris viridis, respectively. Here, we investigated the energetics of proton transfer along the asparagine-involved H-bond network using a quantum mechanical/molecular mechanical approach. The potential energy profile for the H-bond between H3O+ and the carbonyl O site of Asn-L222 shows that the proton is predominantly localized at the Asn-L222 moiety in the T. tepidum PbRC protein environment, easily forming the enol species. The release of the proton from the amide −NH2 site toward Ser-L232 via tautomerization suffers from the energy barrier. Upon reorientation of Asn-L222, the enol −OH site forms a short low-barrier H-bond with Ser-L232, facilitating protonation of QB •– in a Grotthuss-like mechanism. This is a basis of how asparagine or glutamine side chains function as acceptors/donors in proton transfer pathways.

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Section: Protonation Patternmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…(a) T. tepidum (PDB code, 5Y5S). 26 (b) B. viridis (PDB code, 7Q7Q) 24. (c) R. sphaeroides (PDB code, 3I4D) 27.…”

mentioning

confidence: 99%

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Mechanism of Asparagine-Mediated Proton Transfer in Photosynthetic Reaction Centers

Sugo

Ishikita

2023

Biochemistry

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Absolute and non-invasive determination of the electron bunch length in a free electron laser using a bunch compressor monitor

Orlandi

2024

Sci Rep

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In a linac driven Free Electron Laser (FEL), the shot-to-shot and non-invasive monitoring of the electron bunch length is normally ensured by Bunch Compressor Monitors (BCMs). The bunch-length dependent signal of a BCM results from the detection and integration—over a given frequency band—of the temporal coherent enhancement of the radiation spectral energy emitted by the electron beam while experiencing a longitudinal compression. In this work, we present a method that permits to express the relative variation of the bunch length as a function of the relative statistical fluctuations of the BCM and charge signals. Furthermore, in the case of a BCM equipped with two detectors simultaneously operating in two distinct wavelength bands, the method permits an absolute determination of the electron bunch length. The proposed method is beneficial to a FEL. Thanks to it, the machine compression feedback can be tuned against the absolute measurement of the bunch length rather than a bunch-length dependent signal. In a CW-superconducting-linac driven FEL, it can offer the precious opportunity to implement a fully non-invasive and absolute diagnostics of the bunch length.

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Machine learning based longitudinal virtual diagnostics at SwissFEL

Bettoni,

Orlandi,

Salomone

et al. 2024

Review of Scientific Instruments

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The bunch length in a linac driven Free Electron Laser (FEL) is a major parameter to be characterized to optimize the final accelerator performance. In linear machines, this observable is typically determined from the beam imaged on a screen located downstream of a Transverse Deflecting Structure (TDS) used to impinge a time dependent kick along the longitudinal coordinate of the beam. This measurement is typically performed during the machine setup and only sporadically to check the beam duration, but it cannot be continuously repeated because it is time consuming and invasive. A non-invasive method to determine the electron bunch length has already been presented in the past. This method is based on the analysis of the synchrotron radiation light spot emitted by the bunch passing through a magnetic chicane, provided that the energy chirp impinged on the bunch by the upstream radio frequency structures is known. In order to overcome a systematic discrepancy affecting the synchrotron radiation monitor based results compared to the absolute TDS based ones, we implemented and optimized a machine learning approach to predict the bunch length downstream of the two SwissFEL compression stages—from about 10 fs up to about 2 ps—as well as the beam longitudinal profile at the first one.

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Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre

Cited by 9 publications

References 72 publications

Mechanism of Asparagine-Mediated Proton Transfer in Photosynthetic Reaction Centers

Mechanism of Asparagine-Mediated Proton Transfer in Photosynthetic Reaction Centers

Absolute and non-invasive determination of the electron bunch length in a free electron laser using a bunch compressor monitor

Machine learning based longitudinal virtual diagnostics at SwissFEL

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