Analyzing protein intermediate interactions in living E. coli cells using site-specific photo-crosslinking combined with chemical crosslinking

1. Dong, H., Xiang, Q., Gu, Y., Wang, Z., Paterson,

N.G., Stansfeld, P.J., He, C., Zhang, Y., Wang,

W., and Dong, C. (2014). Structural basis for

outer membrane lipopolysaccharide insertion.

Nature 511, 52–56. https://doi.org/10.1038/

nature13464.

2. Qiao, S., Luo, Q., Zhao, Y., Zhang, X.C., and

Huang, Y. (2014). Structural basis for

lipopolysaccharide insertion in the bacterial

outer membrane. Nature 511, 108–111. https://

doi.org/10.1038/nature13484.

3. Bakelar, J., Buchanan, S.K., and Noinaj, N.

(2016). The structure of the b-barrel assembly

machinery complex. Science 351, 180–186.

https://doi.org/10.1126/science.aad3460.

4. Gu, Y., Li, H., Dong, H., Zeng, Y., Zhang, Z.,

Paterson, N.G., Stansfeld, P.J., Wang, Z.,

Zhang, Y., Wang, W., and Dong, C. (2016).

Structural basis of outer membrane

protein insertion by the BAM complex.

Nature 531, 64–69. https://doi.org/10.1038/

nature17199.

5. Tomasek, D., and Kahne, D. (2021). The

assembly of b-barrel outer membrane proteins.

Curr. Opin. Microbiol. 60, 16–23. https://doi.

org/10.1016/j.mib.2021.01.009.

6. Narita, S.i., Masui, C., Suzuki, T., Dohmae, N.,

and Akiyama, Y. (2013). Protease homolog BepA

(YfgC) promotes assembly and degradation of

b-barrel membrane proteins in Escherichia coli.

Proc. Natl. Acad. Sci. USA 110, E3612–E3621.

https://doi.org/10.1073/pnas.1312012110.

7. Chin, J.W., and Schultz, P.G. (2002). In vivo

photocrosslinking with unnatural amino Acid

mutagenesis. Chembiochem 3, 1135–1137.

https://doi.org/10.1002/1439-7633(20021104)

3:11<1135::AID-CBIC1135>3.0.CO;2-M.

8. Miyazaki, R., Akiyama, Y., and Mori, H. (2020). A

photo-cross-linking approach to monitor

STAR Protocols 4, 102178, June 16, 2023

13

ll

Protocol

OPEN ACCESS

protein dynamics in living cells. Biochim.

Biophys. Acta Gen. Subj. 1864, 129317. https://

doi.org/10.1016/j.bbagen.2019.03.003.

and the b-barrel assembly machinery complex.

Mol. Microbiol. 106, 760–776. https://doi.org/

10.1111/mmi.13844.

9. Young, T.S., Ahmad, I., Yin, J.A., and Schultz,

P.G. (2010). An enhanced system for unnatural

amino acid mutagenesis in E. coli. J. Mol. Biol.

395, 361–374. https://doi.org/10.1016/j.jmb.

2009.10.030.

12. Green, M., and Sambrook, J. (2012). Molecular

Cloning: A Laboratory Manual, Fourth Edition

(Cold Spring Harbor Laboratory Press).

10. Miyazaki, R., Watanabe, T., Yoshitani, K., and

Akiyama, Y. (2021). Edge-strand of BepA

interacts with immature LptD on the b-barrel

assembly machine to direct it to on- and offpathways. Elife 10, e70541. https://doi.org/10.

7554/eLife.70541.

13. Gunasinghe, S.D., Shiota, T., Stubenrauch,

C.J., Schulze, K.E., Webb, C.T., Fulcher, A.J.,

Dunstan, R.A., Hay, I.D., Naderer, T., Whelan,

D.R., et al. (2018). The WD40 protein BamB

mediates coupling of BAM complexes into

assembly precincts in the bacterial outer

membrane. Cell Rep. 23, 2782–2794. https://

doi.org/10.1016/j.celrep.2018.04.093.

11. Daimon, Y., Iwama-Masui, C., Tanaka, Y.,

Shiota, T., Suzuki, T., Miyazaki, R., Sakurada, H.,

Lithgow, T., Dohmae, N., Mori, H., et al. (2017).

The TPR domain of BepA is required for

productive interaction with substrate proteins

14. Jumper, J., Evans, R., Pritzel, A., Green, T.,

Figurnov, M., Ronneberger, O.,

´dek, A.,

Tunyasuvunakool, K., Bates, R., Zı

Potapenko, A., et al. (2021). Highly accurate

protein structure prediction with AlphaFold.

14

STAR Protocols 4, 102178, June 16, 2023

Nature 596, 583–589. https://doi.org/10.1038/

s41586-021-03819-2.

15. Evans, R., O’Neill, M., Pritzel, A., Antropova, N.,

´dek, A., Bates, R.,

Senior, A., Green, T., Zı

Blackwell, S., Yim, J., et al. (2022). Protein

complex prediction with AlphaFold-Multimer.

Preprint at bioRxiv. https://doi.org/10.1101/

2021.10.04.463034.

16. Ryu, Y., and Schultz, P.G. (2006). Efficient

incorporation of unnatural amino acids into

proteins in Escherichia coli. Nat. Methods

3, 263–265. https://doi.org/10.1038/

nmeth864.

17. Yang, Y., Song, H., and Chen, P.R. (2016).

Genetically encoded photocrosslinkers for

identifying and mapping protein-protein

interactions in living cells. IUBMB Life 68,

879–886. https://doi.org/10.1002/iub.1560.

...