Michael Landreh
Predicting the shapes of protein complexes through collision cross section measurements and database searches
Landreh, Michael; Sahin, Cagla; Gault, Joseph; Sadeghi, Samira; Drum, Chester Lee; Uzdavinys, Povilas; Drew, David; Allison, Timothy M; Degiacomi, Matteo T.; Marklund, Erik G.
Authors
Cagla Sahin
Joseph Gault
Samira Sadeghi
Chester Lee Drum
Povilas Uzdavinys
David Drew
Timothy M Allison
Matteo Degiacomi matteo.t.degiacomi@durham.ac.uk
Part Time Teacher
Erik G. Marklund
Abstract
In structural biology, collision cross sections (CCSs) from ion mobility mass spectrometry (IM-MS) measurements are routinely compared to computationally or experimentally derived protein structures. Here, we investigate whether CCS data can inform about the shape of a protein in the absence of specific reference structures. Analysis of the proteins in the CCS database shows that protein complexes with low apparent densities are structurally more diverse than those with a high apparent density. Although assigning protein shapes purely on CCS data is not possible, we find that we can distinguish oblate- and prolate-shaped protein complexesby using the CCS, molecular weight, and oligomeric states to mine the Protein Data Bank (PDB) for potentially similar protein structures. Furthermore, comparing the CCS of a ferritin cage to the solution structures in the PDB reveals significant deviations caused by structural collapse on the gas phase. We then apply the strategy to an integral membrane protein by comparing the shapes of a prokaryotic and a eukaryotic sodium/proton antiporter homologue. We conclude that mining the PDB with IM-MS data is a time-effective way to derive low-resolution structural models.
Citation
Landreh, M., Sahin, C., Gault, J., Sadeghi, S., Drum, C. L., Uzdavinys, P., …Marklund, E. G. (2020). Predicting the shapes of protein complexes through collision cross section measurements and database searches. Analytical Chemistry, 92(18), 12297-12303. https://doi.org/10.1021/acs.analchem.0c01940
Journal Article Type | Article |
---|---|
Acceptance Date | Jul 14, 2020 |
Online Publication Date | Jul 14, 2020 |
Publication Date | Sep 15, 2020 |
Deposit Date | Jul 14, 2020 |
Publicly Available Date | Jul 14, 2021 |
Journal | Analytical Chemistry |
Print ISSN | 0003-2700 |
Electronic ISSN | 1520-6882 |
Publisher | American Chemical Society |
Peer Reviewed | Peer Reviewed |
Volume | 92 |
Issue | 18 |
Pages | 12297-12303 |
DOI | https://doi.org/10.1021/acs.analchem.0c01940 |
Public URL | https://durham-repository.worktribe.com/output/1266462 |
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Copyright Statement
This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.analchem.0c01940
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