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Ion mobility-mass spectrometry reveals conformational flexibility in the deubiquitinating enzyme USP5

Scott, Daniel; Layfield, Robert; Oldham, Neil J.

Authors

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



Abstract

Many proteins exhibit conformation flexibility as part of their biological function, whether through the presence of a series of well-defined states or by the existence of intrinsic disorder. Ion mobility spectrometry, in combination with MS (IM–MS), offers a rapid and sensitive means of probing ensembles of protein structures through measurement of gas-phase collisional cross sections. We have applied IM–MS analysis to the multidomain deubiquitinating enzyme ubiquitin specific protease 5 (USP5), which is believed to exhibit significant conformational flexibility. Native ESI–MS measurement of the 94-kDa USP5 revealed two distinct charge-state distributions: [M + 17H]+ to [M + 21H]+ and [M + 24H]+ to [M + 29H]+. The collisional cross sections of these ions revealed clear groupings of 52 ± 4 nm2 for the lower charges and 66 ± 6 nm2 for the higher charges. Molecular dynamics simulation of a compact form of USP5, based on a crystal structure, produced structures of 53–54 nm2 following 2 ns in the gas phase, while simulation of an extended form (based on small-angle X-ray scattering data) led to structures of 64 nm2. These data demonstrate that IM–MS is a valuable tool in studying proteins with different discrete conformational states.

Citation

Scott, D., Layfield, R., & Oldham, N. J. (2015). Ion mobility-mass spectrometry reveals conformational flexibility in the deubiquitinating enzyme USP5. Proteomics, 15(16), https://doi.org/10.1002/pmic.201400457

Journal Article Type Article
Acceptance Date Jan 14, 2015
Publication Date Mar 9, 2015
Deposit Date Jul 1, 2016
Publicly Available Date Jul 1, 2016
Journal Proteomics
Print ISSN 1615-9853
Electronic ISSN 1615-9861
Publisher Wiley
Peer Reviewed Peer Reviewed
Volume 15
Issue 16
DOI https://doi.org/10.1002/pmic.201400457
Keywords electrospray ionisation, ion mobility-mass spectrometry, protein conformation, ubiquitin specific protease 5
Public URL http://eprints.nottingham.ac.uk/id/eprint/34559
Publisher URL http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400457/abstract
Related Public URLs http://www.interscience.wiley.com/
Copyright Statement Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://eprints.nottingham.ac.uk/end_user_agreement.pdf





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