Abstract
One of the primary objectives in chemistry research is to observe atomic motions during reactions in real time. Although X-ray free-electron lasers (XFELs) have facilitated the capture of reaction intermediates using time-resolved serial femtosecond crystallography (TR-SFX), only a few natural photoactive proteins have been investigated using this method, mostly due to the lack of suitable phototriggers. Here we report the genetic encoding of a xanthone amino acid (FXO), as an efficient phototrigger, into a rationally designed human liver fatty-acid binding protein mutant (termed XOM), which undergoes photo-induced C–H bond transformation with high selectivity and quantum efficiency. We solved the structures of XOM before and 10–300 ns after flash illumination, at 1.55–1.70 Å resolutions, and captured the elusive excited-state intermediates responsible for precise C–H bond activation. We expect that most redox enzymes can now be investigated by TR-SFX, using our method, to reveal reaction intermediates key for their efficiency and selectivity.
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Data availability
Data supporting the main findings of this study are included in the Article, Supplementary Information and source data. Data are also available from the corresponding author upon reasonable request. The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the following IDs: FABP1–63FXO, 7DZL; XOM ground state (Shanghai synchrotron radiation data), 7DZJ; XOM crosslinked state (Shanghai synchrotron radiation data), 7DZK; XFEL XOM ground state, 7DZE; 10-ns intermediate state, 7DZF; 30-ns intermediate state, 7DZG; 100-ns intermediate state, 7DZH; 300-ns intermediate state 7DZI. A figshare dataset for this Article is also available on figshare at https://figshare.com/s/87f814f13408b4fb0fff38. Source data are provided with this Paper.
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Acknowledgements
We thank Y. Wang for helping with the protein crystallization drop set with Mosquito Crystal, S.S. Zang for helping with NMR spectra determination, J.H. Li for helping with CD spectra determination and Z.S. Xie and L.L. Niu for MS spectra determination. We thank the staff from Beamline BL17B or BL18U1 at Shanghai Synchrotron Radiation Facility (SSRF) for crystallography data collection. We thank SACLA staff for helping with the XFEL experiments conducted at BL2 of SACLA, with the approval of the Japan Synchrotron Radiation Research Institute (proposals nos. 2018B8016, 2019B8008 and 2020B8064). We are grateful for financial support from the National Science Foundation of China under awards nos. 22193023, 22121003, 91953202 and 21837005, the National Key Research and Development Program of China under awards nos. 2017YFA0503704, 2017YFA0503700 and 2019YFA0904101, CAS Project for Young Scientists in Basic Research, YSBR-015, and the Sanming Project of Medicine in Shenzhen (no. SZSM201811092). We thank the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED (grant no. JP20am0101070 to S.I.) and acknowledge financial support from JSPS KAKENHI (grant no. JP18H02394 to E.N.).
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J.W. and J.-R.S. conceived the study and designed the experiments. X.L. performed most of the experiments and, together with J.W., wrote the manuscript; modifications were made by J.-R.S. and others. P.L. evolved the FXORS. Z.X., C.C. and Y.Z. synthesized the FXO compounds. X.L., Z.X., L.J., Y.X., M.Y. and X.Z. expressed, purified and crystallized the XOM. X.L., H.L., Z.X., M.Y., K.K., Y.N., S.K., H.Y., N.M., E.N., F.L., S.O., L.-J.Y. and J.-R.S. performed the XFEL experiments. H.L. processed the diffraction images. H.L. and L.-J.Y. analysed the structure.
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Nature Chemistry thanks Claudiu Stan and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Supplementary materials and methods, Figs. 1–21, Tables 1–5, and Movies 1–3.
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Unprocessed gels of Fig. 1c.
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Liu, X., Liu, P., Li, H. et al. Excited-state intermediates in a designer protein encoding a phototrigger caught by an X-ray free-electron laser. Nat. Chem. 14, 1054–1060 (2022). https://doi.org/10.1038/s41557-022-00992-3
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DOI: https://doi.org/10.1038/s41557-022-00992-3
