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Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers

Author

Listed:
  • Jian-Hua Wang

    (National Institute of Biological Sciences (NIBS)
    Tsinghua University)

  • Yu-Liang Tang

    (Peking University)

  • Zhou Gong

    (Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences)

  • Rohit Jain

    (University of Massachusetts Medical School)

  • Fan Xiao

    (Peking University)

  • Yu Zhou

    (National Institute of Biological Sciences (NIBS)
    Tsinghua University)

  • Dan Tan

    (National Institute of Biological Sciences (NIBS))

  • Qiang Li

    (Peking University)

  • Niu Huang

    (National Institute of Biological Sciences (NIBS)
    Tsinghua University)

  • Shu-Qun Liu

    (Yunnan University)

  • Keqiong Ye

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Chun Tang

    (Peking University
    Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences)

  • Meng-Qiu Dong

    (National Institute of Biological Sciences (NIBS)
    Tsinghua University)

  • Xiaoguang Lei

    (Peking University)

Abstract

Chemical cross-linking of proteins coupled with mass spectrometry is widely used in protein structural analysis. In this study we develop a class of non-hydrolyzable amine-selective di-ortho-phthalaldehyde (DOPA) cross-linkers, one of which is called DOPA2. Cross-linking of proteins with DOPA2 is 60–120 times faster than that with the N-hydroxysuccinimide ester cross-linker DSS. Compared with DSS cross-links, DOPA2 cross-links show better agreement with the crystal structures of tested proteins. More importantly, DOPA2 has unique advantages when working at low pH, low temperature, or in the presence of denaturants. Using staphylococcal nuclease, bovine serum albumin, and bovine pancreatic ribonuclease A, we demonstrate that DOPA2 cross-linking provides abundant spatial information about the conformations of progressively denatured forms of these proteins. Furthermore, DOPA2 cross-linking allows time-course analysis of protein conformational changes during denaturant-induced unfolding.

Suggested Citation

  • Jian-Hua Wang & Yu-Liang Tang & Zhou Gong & Rohit Jain & Fan Xiao & Yu Zhou & Dan Tan & Qiang Li & Niu Huang & Shu-Qun Liu & Keqiong Ye & Chun Tang & Meng-Qiu Dong & Xiaoguang Lei, 2022. "Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28879-4
    DOI: 10.1038/s41467-022-28879-4
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    References listed on IDEAS

    as
    1. Rebecca Beveridge & Johannes Stadlmann & Josef M. Penninger & Karl Mechtler, 2020. "A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    2. Alexander X. Jones & Yong Cao & Yu-Liang Tang & Jian-Hua Wang & Yue-He Ding & Hui Tan & Zhen-Lin Chen & Run-Qian Fang & Jili Yin & Rong-Chang Chen & Xing Zhu & Yang She & Niu Huang & Feng Shao & Keqio, 2019. "Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    3. Katherine Henzler-Wildman & Dorothee Kern, 2007. "Dynamic personalities of proteins," Nature, Nature, vol. 450(7172), pages 964-972, December.
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    Cited by:

    1. Ting Wang & Shiyun Ma & Guanghui Ji & Guoli Wang & Yang Liu & Lei Zhang & Ying Zhang & Haojie Lu, 2024. "A chemical proteomics approach for global mapping of functional lysines on cell surface of living cell," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Yida Jiang & Xinghe Zhang & Honggang Nie & Jianxiong Fan & Shuangshuang Di & Hui Fu & Xiu Zhang & Lijuan Wang & Chun Tang, 2024. "Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    3. Ying Zhu & Kerem Can Akkaya & Julia Ruta & Nanako Yokoyama & Cong Wang & Max Ruwolt & Diogo Borges Lima & Martin Lehmann & Fan Liu, 2024. "Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    4. Jiangnan Zheng & Zhendong Zheng & Changying Fu & Yicheng Weng & An He & Xueting Ye & Weina Gao & Ruijun Tian, 2023. "Deciphering intercellular signaling complexes by interaction-guided chemical proteomics," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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