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Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins

Author

Listed:
  • Tamar Tayri-Wilk

    (The Hebrew University of Jerusalem
    The Hebrew University of Jerusalem)

  • Moriya Slavin

    (The Hebrew University of Jerusalem)

  • Joanna Zamel

    (The Hebrew University of Jerusalem)

  • Ayelet Blass

    (The Hebrew University of Jerusalem)

  • Shon Cohen

    (The Hebrew University of Jerusalem)

  • Alex Motzik

    (The Hebrew University of Jerusalem)

  • Xue Sun

    (The Hebrew University of Jerusalem)

  • Deborah E. Shalev

    (The Hebrew University of Jerusalem
    Azrieli College of Engineering)

  • Oren Ram

    (The Hebrew University of Jerusalem)

  • Nir Kalisman

    (The Hebrew University of Jerusalem)

Abstract

Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein–protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies.

Suggested Citation

  • Tamar Tayri-Wilk & Moriya Slavin & Joanna Zamel & Ayelet Blass & Shon Cohen & Alex Motzik & Xue Sun & Deborah E. Shalev & Oren Ram & Nir Kalisman, 2020. "Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16935-w
    DOI: 10.1038/s41467-020-16935-w
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    Cited by:

    1. Andrew R. M. Michael & Bruno C. Amaral & Kallie L. Ball & Kristen H. Eiriksson & David C. Schriemer, 2024. "Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Yuwan Chen & Wen Zhou & Yufei Xia & Weijie Zhang & Qun Zhao & Xinwei Li & Hang Gao & Zhen Liang & Guanghui Ma & Kaiguang Yang & Lihua Zhang & Yukui Zhang, 2023. "Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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