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

Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

Authors

Lucio Manzi

Andrew S. Barrow

TIMOTHY WRIGHT TIM.WRIGHT@NOTTINGHAM.AC.UK
Professor of Physical and Theoretical Chemistry

John E. Moses

NEIL OLDHAM neil.oldham@nottingham.ac.uk
Professor of Biomolecular Spectrometry



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.

Citation

Manzi, L., Barrow, A. S., Scott, D., Layfield, R., Wright, T. G., Moses, J. E., & Oldham, N. J. (2016). Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions. Nature Communications, 7, https://doi.org/10.1038/ncomms13288

Journal Article Type Article
Acceptance Date Sep 20, 2016
Publication Date Nov 16, 2016
Deposit Date Nov 1, 2016
Publicly Available Date Nov 23, 2016
Journal Nature Communications
Electronic ISSN 2041-1723
Publisher Nature Publishing Group
Peer Reviewed Peer Reviewed
Volume 7
Article Number 13288
DOI https://doi.org/10.1038/ncomms13288
Public URL http://eprints.nottingham.ac.uk/id/eprint/37911
Publisher URL http://www.nature.com/articles/ncomms13288
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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