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Genetically encoded bioorthogonal tryptophan decaging in living cells

Abstract

Tryptophan (Trp) plays a critical role in the regulation of protein structure, interactions and functions through its π system and indole N–H group. A generalizable method for blocking and rescuing Trp interactions would enable the gain-of-function manipulation of various Trp-containing proteins in vivo, but generating such a platform remains challenging. Here we develop a genetically encoded N1-vinyl-caged Trp capable of rapid and bioorthogonal decaging through an optimized inverse electron-demand Diels–Alder reaction, allowing site-specific activation of Trp on a protein of interest in living cells. This chemical activation of a genetically encoded caged-tryptophan (Trp-CAGE) strategy enables precise activation of the Trp of interest underlying diverse important molecular interactions. We demonstrate the utility of Trp-CAGE across various protein families, such as catalase-peroxidases and kinases, as translation initiators and posttranslational modification readers, allowing the modulation of epigenetic signalling in a temporally controlled manner. Coupled with computer-aided prediction, our strategy paves the way for bioorthogonal Trp activation on more than 28,000 candidate proteins within their native cellular settings.

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Fig. 1: Design of the bioorthogonal Trp-caging/decaging chemistry.
Fig. 2: Development of the bioorthogonal Trp-caging/decaging chemistry.
Fig. 3: Validating Trp-CAGE in vitro and in living cells.
Fig. 4: Establishment of the Trp-CAGE-based general protein activation platform.
Fig. 5: Applying Trp-CAGE for manipulating epigenetic reader proteins in living cells.

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Data availability

Data relating to the materials and methods, optimization studies, experimental procedures, DFT calculations, crystallographic data for vyW, NMR spectra and mass spectrometry are available in the Article or its Supplementary Information. Uncropped gels/blots and MS–MS data are provided in the related source data. Proteomics data are available via ProteomeXchange with the identifier PXD048817. Crystallographic data for vyW have been deposited at the Cambridge Crystallographic Data Centre, under the deposition number CCDC 2327816. Copies of the data can be obtained free of charge via https://www.ccdc.cam.ac.uk/structures/. Source data are provided with this paper.

Code availability

The source codes for Python used for measuring Trp–ligand distances are available in Supplementary Note 1.

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Acknowledgements

This work was supported by the Ministry of Science and Technology (2021YFA1302603 to P.R.C., 2019YFA09006600 to S.L., 2019YFA0904201, 2022YFA1304700 to X.F.), the National Natural Science Foundation of China (21937001, 22137001, 91753000 to P.R.C., 22222705, 92253302, 22361142828 to S.L., 22222701, 22077004, 92253301 to X.F., 22207095 to W.D. and 22207005 to Y.Z.), the Beijing Natural Science Foundation (Z200010 to P.R.C.), the Postdoctoral Program for Innovative Talents (BX20200005 to Y.Z.), the Feng Foundation of Biomedical Research to S.L., and the New Cornerstone Science Foundation through the New Cornerstone Investigator Program and the XPLORER Prize to P.R.C.

Author information

Authors and Affiliations

Authors

Contributions

P.R.C., S.L., X.F., Y.Z. and W.D. conceived the study. Y.Z. conducted chemistry development, protein decaging validation, and RLuc, src, KatG and eIF4E decaging experiments. W.D. developed the computational pipeline, aaRS direct evolution, and mCherry and epigenetic reader decaging experiments. Y.C. and C.L. assisted with computational design and decaging experiments. Y.S. contributed to the chemical synthesis and biochemical experiments. Y.Z., W.D., X.F., S.L. and P.R.C. wrote the paper with inputs from all authors.

Corresponding authors

Correspondence to Xinyuan Fan, Shixian Lin or Peng R. Chen.

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Nature Chemistry thanks Christopher Chang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Design and Establishment of Trp-CAGE.

A, Overview of caging and decaging strategies. Strategies for π system caging and decaging remain undeveloped. B, Trp interactions. Caging π interaction is necessary for covering all Trp interactions. C, Caging group evaluation for Trp π system. Unlike previous reported caging groups, vinyl group weakened Trp π system via conjugation. D, Nonlinear regressions of one phase decay was used during kinetic fitting. The calculation formula of fitted curve, half-life, and second-order rate constants K2 were shown. E, F, G, H, I, Kinetic fitted curve for iEDDA reaction between vyW and Tz 4, 10, 12, 13, 14, respectively. Tzs (1 mM) was treated with a ten-fold excess of vyW in PBS. Characteristic Tz peak absorbance at 520 nm disappears upon reaction, and was tracked over time (30 min) by absorbance scans using a Synergy H4 microplate reader. Reaction data were processed using GraphPad Prism 9.0 and fit to nonlinear regressions of one phase decay.

Source data

Extended Data Fig. 2 Screening, optimization, and validation of Trp-CAGE.

A, The amber suppression efficiency of vyW by the indicated chPheRSs was tested by a GFP reporter assay (n = 2). B, The chPheRS mutants by rational design for vyW recognition. Rational mutations were labelled light brown. C, In vitro optimization of decaging conditions on GFP protein. 100 μL of GFP variant (10 μM) in PBS was treated with Tz at 37 °C for 60 min. The yields were calculated based on relative intensity of substrate and product peaks in LC-MS. D, the activity of wild-type Rluc-WT, RLuc-261-W variant and RLuc-261-vyW variant with/without Tz treatment. Error bars represent ± standard error of the mean (n = 3). Two-tailed t test was used. ****P < 0.0001. E, The decaging of RLuc-261-vyW in different incubation times. The activation signal can be observed after 1 min of Tz treatment, and the signal reached to 50% of maximum activation within 10–15 min. Error bars represent ± standard error of the mean (n = 3 biologically independent samples). Two-tailed t test was used. ****P < 0.0001. F, Summarized Km of RLuc-WT, RLuc-261-W and RLuc-261-vyW. The Km were generated by Michaelis–Menten analysis with Graphpad Prism 9.0. G, RLuc catalysed luminescence process. The peroxide intermediate is crucial for the final product generation. H, The crystal structure of coelenterazine binding to RLuc (PDB code: 7QXR). F261 is close to the heterocycle core of coelenterazine. I, the incorporated vyW may react with peroxide intermediate, thus preventing the formation of the final luminescent product. J, The Prilezhaev oxidation reaction.

Source data

Extended Data Fig. 3 Investigation of potential cross reactivity of strained intermediate and the rationale of choosing tetrazines.

A, Protein pull-down experiment. GFP-D190-vyW was expressed in E. coli, 100 μM Tz 4 was added to trigger the formation of the strained intermediate. The proteins were pulled down with His beads after decaging for 1 h. B, The intact-MS analysis of pull-downed protein samples in the 5000 to 80000 Da range. Around 70% of GFP-190-vyW was rescued in living E. coli cells. C, Gel analysis of pull-downed protein samples. No obvious cross-linked band was detected (n = 2 biologically independent experiments). D, MS/MS analysis of pull-downed samples. The non-linked, decaged vyW>W mutant peptide was detected with high confidence. E, The rationale of choosing tetrazines on various proteins.

Source data

Extended Data Fig. 4 Computer-aided screening of proteins with key tryptophan residue(s).

A, The top10 ligands families from the screening. The X-axis represent the ligand types in every family. The counts of every family were shown in right. B, The function analysis of proteins from screening. The top15 functions of name were shown. C, The detailed categories of ligand in amino acids and its modifications family. The counts of every ligand were shown. D, The detailed categories of ligand in cofactors family. The counts of every ligand were shown.

Extended Data Fig. 5 Optimization and application of Trp-CAGE as a general protein activation platform.

A, LC–MS characterization of mCherry-vyW before and after decaging with Tz 10. The LC-MS peak for mCherry-vyW was labelled in the figure, which indicated that the chromophore of mCherry-92-vyW was not formed (Calculated MW of unmatured mCherry-92-vyW is 27641 Da, and the observed MW is 27644 Da). When decaging with Tz, the major peak was shifted. The molecular weight of this peak was identical with maturated mCherry (decgaing vinyl group and formatting chromophore, the calculated and observed MWs are both 27593 Da). B, Time dependent fluorescence intensity increase of rescued mCherry. C, Evaluating katG decaing efficiency of different Tzs. Asymmetric Tz 13 is the most efficient one among tested. Error bars represent ±standard error of the mean (n = 3 biologically independent samples). D, Schematic of allosteric regulation of Src. Created with BioRender.com. E, Evaluating src decaing efficiency of different Tzs. Asymmetric Tz 12 is the most efficient (n = 2 biologically independent experiments). F, Western blotting analysis of in vivo src-428-vyW decaging (n = 2 biologically independent experiments). G, Schematic of eIF4E activation mediated c-myc upregulation. H, Western blotting analysis of eIF4E-46-vyW, eIF4E-56-vyW decaging in HEK 293T (n = 2 biologically independent experiments). I, Western blotting analysis of eIF4E-102-vyW, eIF4E-166-vyW decaging in HEK 293T cells (n = 2 biologically independent experiments).

Source data

Extended Data Fig. 6 Appling Trp-CAGE for manipulating epigenetic reader proteins.

A, LC-MS validation of reader domain decaging. B, The live cell imaging of CDYL1-chromo domain variants in HEK 293 T cells (n = 3). Scale bar: 10 μm. C, The live cell imaging of BAHCC1-BAH domain variants in HEK 293T cells (n = 3 biologically independent experiments). Scale bar: 10 μm. D-G, Appling Trp-CAGE to recusing function of caged CDY1-chromo domains (D, F) and CBX1-chromo domains (E, G) in vitro (D, E) and in live cells (F, G). MST analysis of affinity of CDY1 (D) and CBX1 (E) variants for H3K9me3 peptide. The data were fitted with a Kd model by MO.Affinity.Analysis Software (v2.3). Fraction bound = 1/(1 + (Kd/[D])), where [D] is the total concentration of the ligand peptide. WT proteins were used as a positive control. In the MST assay, H3K9me3 peptides were labelled by a fluorescent dye molecule, fluorescein isothiocyanate (FITC). Error bars represent ± standard error of the mean (n = 3 biologically independent samples). The live cell imaging of CDY1-chromo domain variants (F) and CBX1-chromo domains (G) in HEK 293T cells (n = 3 biologically independent experiments). Scale bar: 10 μm.

Source data

Extended Data Fig. 7 Quantification on the distribution of reader proteins and colocalization imaging with inhibitors.

A, C the procedure for quantifying the distribution of CDYL1 reader protein of H3K9me3 (A) and BAH reader protein of H3K27me3 (C). B, D the quantification results for CDYL1 (B) and BAH (D) at indicated conditions. Error bars represent ± standard error of the mean (n = 16, 13 and 13 cells for CDYL1-WT, CDYL1-vyW and CDYL1-vyW decaging; n = 11, 11 and 9 cells for BAH-WT, BAH-vyW and BAH-vyW decaging). E, the representative image of BAH variants in presence of H3K27me3 inhibitors of EED226 (20 μM) and EPZ6438 (5 μM), the reader proteins distribution was changed by inhibitors incubation. F, the quantification of distribution pattern in presence or absence of H3K27me3 inhibitors. One-Way ANOVA test was used. Error bars represent ± standard error of the mean (n = 11, 11 and 9 cells for BAH-WT, BAH-vyW and BAH-vyW decaging in absence of inhibitor; n = 13, 11 and 8 cells for BAH-WT, BAH-vyW and BAH-vyW decaging in presence of inhibitors respectively). Scale bar: 10 μm.

Source data

Extended Data Fig. 8 The logic flowchart of Trp-CAGE for protein activation in living systems.

To predict if one POI could be blocked and rescued by Trp-CAGE, an optimized protein–ligand complex structure was obtained from the PDB, and comparative modelling and/or ligand-docking were used when necessary. Trp–ligand distance (d) was calculated by Rosetta and used as filters to differentiate Trp interaction types. Hits with d > 5 A is sent to allosteric verification. DipyTz (Tz 4) is recommended to be firstly tested in the decaging step, further screening and treatment with less-hindered asymmetric Tzs (Tz 10, 12, 13, 14) may improve decaging efficiency.

Supplementary information

Supplementary Information

Supplementary materials and methods, Tables 1–3, Note 1 and Figs. 1–10.

Reporting Summary

Supplementary Data 1

CIF report for for the crystallographic data of vyW.

Supplementary Data 2

MS–MS analysis of non-linked, decaged vyW > W mutant peptides.

Supplementary Data 3

MS–MS analysis of pull-downed proteins/

Supplementary Data 4

The cross-linked peptides analysed by pLink.

Supplementary Data 5

The predicted proteins containing conserved Trp residues.

Supplementary Data 6

The primers and plasmids.

Supplementary Data 7

Crystallographic data for vyW.

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Zhu, Y., Ding, W., Chen, Y. et al. Genetically encoded bioorthogonal tryptophan decaging in living cells. Nat. Chem. 16, 533–542 (2024). https://doi.org/10.1038/s41557-024-01463-7

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