Global Profiling of Functional Histidines in Live Cells Using Small-molecule Photosensitizer and Chemical Probe Relay Labelling

Overview

Journal Nat Chem

Specialty Chemistry

Date 2024 Jun 4

PMID 38834725

Authors

Yansheng Zhai

Xinyu Zhang

Zijing Chen

Dingyuan Yan

Lin Zhu

Zhe Zhang

Xianghe Wang

Kailu Tian

Yan Huang

Xi Yang

Wen Sun

Dong Wang

Yu-Hsuan Tsai

Tuoping Luo

Gang Li

Affiliations

Soon will be listed here.

Abstract

Recent advances in chemical proteomics have focused on developing chemical probes that react with nucleophilic amino acid residues. Although histidine is an attractive candidate due to its importance in enzymatic catalysis, metal binding and protein-protein interaction, its moderate nucleophilicity poses challenges. Its modification is frequently influenced by cysteine and lysine, which results in poor selectivity and narrow proteome coverage. Here we report a singlet oxygen and chemical probe relay labelling method that achieves high selectivity towards histidine. Libraries of small-molecule photosensitizers and chemical probes were screened to optimize histidine labelling, enabling histidine profiling in live cells with around 7,200 unique sites. Using NMR spectroscopy and X-ray crystallography, we characterized the reaction mechanism and the structures of the resulting products. We then applied this method to discover unannotated histidine sites key to enzymatic activity and metal binding in select metalloproteins. This method also revealed the accessibility change of histidine mediated by protein-protein interaction that influences select protein subcellular localization, underscoring its capability in discovering functional histidines.

Citing Articles

Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome.

Becker A, Biletch E, Kennelly J, Julio A, Villaneuva M, Nagari R bioRxiv. 2024; .

PMID: 39229057 PMC: 11370482. DOI: 10.1101/2024.08.20.608660.

References

Liu Y, Patricelli M, Cravatt B . Activity-based protein profiling: the serine hydrolases. Proc Natl Acad Sci U S A. 1999; 96(26):14694-9. PMC: 24710. DOI: 10.1073/pnas.96.26.14694. View

Cravatt B, Wright A, Kozarich J . Activity-based protein profiling: from enzyme chemistry to proteomic chemistry. Annu Rev Biochem. 2008; 77:383-414. DOI: 10.1146/annurev.biochem.75.101304.124125. View

Long J, Cravatt B . The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem Rev. 2011; 111(10):6022-63. PMC: 3192302. DOI: 10.1021/cr200075y. View

Kidd D, Liu Y, Cravatt B . Profiling serine hydrolase activities in complex proteomes. Biochemistry. 2001; 40(13):4005-15. DOI: 10.1021/bi002579j. View

Patricelli M, Szardenings A, Liyanage M, Nomanbhoy T, Wu M, Weissig H . Functional interrogation of the kinome using nucleotide acyl phosphates. Biochemistry. 2007; 46(2):350-8. DOI: 10.1021/bi062142x. View

Zhao Q, Ouyang X, Wan X, Gajiwala K, Kath J, Jones L . Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes. J Am Chem Soc. 2017; 139(2):680-685. PMC: 5858558. DOI: 10.1021/jacs.6b08536. View

Kato D, Boatright K, Berger A, Nazif T, Blum G, Ryan C . Activity-based probes that target diverse cysteine protease families. Nat Chem Biol. 2006; 1(1):33-8. DOI: 10.1038/nchembio707. View

Saghatelian A, Jessani N, Joseph A, Humphrey M, Cravatt B . Activity-based probes for the proteomic profiling of metalloproteases. Proc Natl Acad Sci U S A. 2004; 101(27):10000-5. PMC: 454150. DOI: 10.1073/pnas.0402784101. View

Hekmat O, Kim Y, Williams S, He S, Withers S . Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi. J Biol Chem. 2005; 280(42):35126-35. DOI: 10.1074/jbc.M508434200. View

10.

Kumar S, Zhou B, Liang F, Wang W, Huang Z, Zhang Z . Activity-based probes for protein tyrosine phosphatases. Proc Natl Acad Sci U S A. 2004; 101(21):7943-8. PMC: 419536. DOI: 10.1073/pnas.0402323101. View

11.

Bachovchin D, Brown S, Rosen H, Cravatt B . Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes. Nat Biotechnol. 2009; 27(4):387-94. PMC: 2709489. DOI: 10.1038/nbt.1531. View

12.

Nomura D, Long J, Niessen S, Hoover H, Ng S, Cravatt B . Monoacylglycerol lipase regulates a fatty acid network that promotes cancer pathogenesis. Cell. 2010; 140(1):49-61. PMC: 2885975. DOI: 10.1016/j.cell.2009.11.027. View

13.

Weerapana E, Wang C, Simon G, Richter F, Khare S, Dillon M . Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature. 2010; 468(7325):790-5. PMC: 3058684. DOI: 10.1038/nature09472. View

14.

Hacker S, Backus K, Lazear M, Forli S, Correia B, Cravatt B . Global profiling of lysine reactivity and ligandability in the human proteome. Nat Chem. 2017; 9(12):1181-1190. PMC: 5726523. DOI: 10.1038/nchem.2826. View

15.

Hahm H, Toroitich E, Borne A, Brulet J, Libby A, Yuan K . Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nat Chem Biol. 2019; 16(2):150-159. PMC: 6982592. DOI: 10.1038/s41589-019-0404-5. View

16.

Lin S, Yang X, Jia S, Weeks A, Hornsby M, Lee P . Redox-based reagents for chemoselective methionine bioconjugation. Science. 2017; 355(6325):597-602. PMC: 5827972. DOI: 10.1126/science.aal3316. View

17.

Ma N, Hu J, Zhang Z, Liu W, Huang M, Fan Y . 2-Azirine-Based Reagents for Chemoselective Bioconjugation at Carboxyl Residues Inside Live Cells. J Am Chem Soc. 2020; 142(13):6051-6059. DOI: 10.1021/jacs.9b12116. View

18.

Bach K, Beerkens B, Zanon P, Hacker S . Light-Activatable, 2,5-Disubstituted Tetrazoles for the Proteome-wide Profiling of Aspartates and Glutamates in Living Bacteria. ACS Cent Sci. 2020; 6(4):546-554. PMC: 7181327. DOI: 10.1021/acscentsci.9b01268. View

19.

Gutteridge A, Thornton J . Understanding nature's catalytic toolkit. Trends Biochem Sci. 2005; 30(11):622-9. DOI: 10.1016/j.tibs.2005.09.006. View

20.

Dokmanic I, Sikic M, Tomic S . Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination. Acta Crystallogr D Biol Crystallogr. 2008; 64(Pt 3):257-63. DOI: 10.1107/S090744490706595X. View