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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.

Predicting the shapes of protein complexes through collision cross section measurements and database searches Thumbnail


Authors

Michael Landreh

Cagla Sahin

Joseph Gault

Samira Sadeghi

Chester Lee Drum

Povilas Uzdavinys

David Drew

Timothy M Allison

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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