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Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions

Author

Listed:
  • Lucio Manzi

    (School of Chemistry, University of Nottingham, University Park)

  • Andrew S. Barrow

    (School of Chemistry, University of Nottingham, University Park)

  • Daniel Scott

    (School of Chemistry, University of Nottingham, University Park
    Queen’s Medical Centre, School of Life Sciences, University of Nottingham)

  • Robert Layfield

    (Queen’s Medical Centre, School of Life Sciences, University of Nottingham)

  • Timothy G. Wright

    (School of Chemistry, University of Nottingham, University Park)

  • John E. Moses

    (School of Chemistry, University of Nottingham, University Park)

  • Neil J. Oldham

    (School of Chemistry, University of Nottingham, University Park)

Abstract

Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

Suggested Citation

  • Lucio Manzi & Andrew S. Barrow & Daniel Scott & Robert Layfield & Timothy G. Wright & John E. Moses & Neil J. Oldham, 2016. "Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions," Nature Communications, Nature, vol. 7(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13288
    DOI: 10.1038/ncomms13288
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    Cited by:

    1. 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.

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