Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
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Nature Publishing Group
2016
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| Online Access: | https://eprints.nottingham.ac.uk/37911/ |
| _version_ | 1848795558411501568 |
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| author | Manzi, Lucio Barrow, Andrew S. Scott, Daniel Layfield, Robert Wright, Timothy G. Moses, John E. Oldham, Neil J. |
| author_facet | Manzi, Lucio Barrow, Andrew S. Scott, Daniel Layfield, Robert Wright, Timothy G. Moses, John E. Oldham, Neil J. |
| author_sort | Manzi, Lucio |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T19:34:00Z |
| format | Article |
| id | nottingham-37911 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:34:00Z |
| publishDate | 2016 |
| publisher | Nature Publishing Group |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-379112020-05-04T18:20:49Z https://eprints.nottingham.ac.uk/37911/ 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. 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. Nature Publishing Group 2016-11-16 Article PeerReviewed Manzi, Lucio, Barrow, Andrew S., Scott, Daniel, Layfield, Robert, Wright, Timothy G., Moses, John E. and Oldham, Neil J. (2016) Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions. Nature Communications, 7 (13288). ISSN 2041-1723 http://www.nature.com/articles/ncomms13288 doi:10.1038/ncomms13288 doi:10.1038/ncomms13288 |
| spellingShingle | Manzi, Lucio Barrow, Andrew S. Scott, Daniel Layfield, Robert Wright, Timothy G. Moses, John E. Oldham, Neil J. Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| title | Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| title_full | Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| title_fullStr | Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| title_full_unstemmed | Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| title_short | Carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| title_sort | carbene footprinting accurately maps binding sites in protein–ligand and protein–protein interactions |
| url | https://eprints.nottingham.ac.uk/37911/ https://eprints.nottingham.ac.uk/37911/ https://eprints.nottingham.ac.uk/37911/ |