Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry
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Abstract
Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (Saccharomyces cerevisiae) and mammals (rat - Rattus norvegicus, rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.
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In relatively simple cases, native MS mass alone can suffice to indicate the number of monomers in a complex and determine differences in complex makeup.
“In relatively simple cases, this can suffice to indicate the number of monomers in a complex and determine differences in complex makeup.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [22]
Sharon and co-workers found novel sequence information on the alpha subunit of the rat 20S proteasome with complex-down analysis.
“Sharon and co-workers found novel sequence information on the alpha subunit of the rat 20S proteasome with complex-down analysis.22”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [22]
The rat 20S proteasome alpha subunit was found to have N-terminal acetylation and removal of the last two amino acids on the C-terminus, complementing data absent from cryo-EM.
“Notably, they found N-terminal acetylation and removal of the last two amino acids on the C-terminus, complementing data that was absent from cryo-EM, which did not have enough resolution to discern these features.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [22]
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High-Resolution Native Mass Spectrometry
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- Authors
- Vimer, S., Ben-Nissan, G., Morgenstern, D., Kumar-Deshmukh, F., Polkinghorn, C., Quintyn, R. S., Vasil’ev, Y. V., Beckman, J. S., Elad, N., Wysocki, V. H., & Sharon, M.
- Affiliations
- Weizmann Institute of Science (IL)
- Weizmann Institute of Science , , ,
- The Ohio State University (US)
- ECD for the Masses (United States) (US)
- Oregon State University (US)
- Corresponding author
- Sharon, Michal
- Venue
- ACS Central Science
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-04-10
- Volume
- 6
- Issue
- 4
- Pages
- 573-588
- ISSN
- 2374-7943 (ISSN-L)
- 2374-7951
- PMC
- PMC7181328
- OpenAlex
- W3015495420
- Cited by
- 63
- References
- 85
- Citations by year
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- FWCI
- 3.53
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Locations
- ACS Central Science (publishedVersion, cc-by)
- ChemRxiv (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Royal College of Surgeons in Ireland (submittedVersion, cc-by-nc)
- Funders
- National Institutes of Health (P41GM128577)
- Horizon 2020 Framework Programme (636752)
- Israel Science Foundation (300/17)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- 20S proteasome, native mass spectrometry, kinetic stability, human proteasome, Thermoplasma acidophilum, cryo-EM structure
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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