Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2019 Jan 2;91(1):142-155.
doi: 10.1021/acs.analchem.8b05014. Epub 2018 Dec 6.

Evolution of Structural Biology through the Lens of Mass Spectrometry

Upneet Kaur  1 , Danté T Johnson  1 , Emily E Chea  1 , Daniel J Deredge  1 , Jessica A Espino  1 , Lisa M Jones  1
Affiliations
Review

Evolution of Structural Biology through the Lens of Mass Spectrometry

Upneet Kaur et al. Anal Chem. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1.
Figure 1.
Varying resolution of different biophysical techniques. NMR and cryo-EM are mainly applicable for macromolecules, and light microscopy and electron tomography are mainly applicable in tissues, cells, and organelles. Mass spectrometry has a dynamic range providing structural information from tissues to macromolecules.
Figure 2.
Figure 2.
MS analysis of AmtB nanodisc. Panels A and B show the representative mass spectrum and deconvoluted spectrum. Four species are identified and highlighted, including AmtB with a large number of lipids (red), AmtB with ionic contact lipids (yellow), AmtB monomer (green), and MSP (blue). Panel C combines the mass spectra at different collision voltages, and panel D is a summation across all collision voltages. Reprinted from Marty, M. T.; Hoi, K. K.; Robinson, C. V. Acc Chem Res 2016, 49 (11), 2459–2467 (ref 12). Copyright 2016 American Chemical Society.
Figure 3.
Figure 3.
Analysis of MDa virus-like particles on the modified mass spectrometer. During an MS1 scan, the charge-reduced Cp180 (a) shows a well-resolved charge state envelope centered on ~30 000 m/z. To further shift ions to higher m/z values and demonstrate the full capability of the instrument, the noncharge-reduced Cp180 (b) charge state envelope was subjected to increasing HCD collision energies. At a collision energy of 250 V, the MS2 products extend to 50 000 m/z (c). At maximal HCD, 300 V (d), the production mass spectrum shows further fragmentation of the Cp180 assembly and ions up 70 000 m/z. The mass resolution is high enough to baseline-resolve these different dissociation products even at this high m/z value (d, left inset). At the highest m/z, the mass resolution is greater than 500 (d, right inset). Reprinted from Fort, K. L.; van de Waterbeemd, M.; Boll, D.; Reinhardt-Szyba, M.; Belov, M. E.; Sasaki, E.; Zschoche, R.; Hilvert, D.; Makarov, A. A.; Heck, A. J. R. Analyst 2018, 143 (1), 100–105 (ref 10), with permission of The Royal Society of Chemistry.
Figure 4.
Figure 4.
Illustration of the collision-induced unfolding analysis workflow for intact antibodies. (a) Selected antibody ions are unfolded through collisional heating, resulting in increased drift times; (b) drift-time data for a single protein charge state are tracked at each collision energy; (c) a collision-induced unfolding “fingerprint” is projected as a contour plot, where intensities for the features observed are denoted by a color-coded axis. Once complied, fingerprint data are compared using custom software in order to detect differences. Reprinted from Tian, Y.; Han, L.; Buckner, A. C.; Ruotolo, B. T. Analytical Chemistry 2015, 87 (22), 11509–11515 (ref 25). Copyright 2015 American Chemical Society.
Figure 5.
Figure 5.
Illustration of a proteoform: A term describing the complexity of a single-molecule protein species including genetic variation, alternative splicing of RNA, single-nucleotide polymorphisms (SNPs) in regions of genes coding for amino acids, and post-translational modifications that are explicitly defined in a specific combination.
Figure 6.
Figure 6.
Reactivity of the DAU cross-linker with thiol groups, i.e., cysteine residues in proteins. As for other urea-based cross-linkers, two pairs of amine and isocyanate product ions are generated in (+)-ESI collisional activation (CID or HCD) experiments. Reprinted from Iacobucci, C.; Piotrowski, C.; Rehkamp, A.; Ihling, C. H.; Sinz, A. J Am Soc Mass Spectrom 2018 (ref 62).
Figure 7.
Figure 7.
Cross-linking-derived model for respirasome supercomplex CI2CIII2CIV2. (a) Cryo-EM-derived structure of respirasome CICIII2CIV (PDB: 5GUP) with cross-links identifying interactions between CI (gold ribbon) and CIII (purple ribbon) (NDUA2 K13, K75, and K98 linked to QCR2 K250), CIII homodimer (QCR2 K159 linked to QCR2 K159), and CI and CIV (teal-blue ribbon) (COX5A K189 linked to NDUA9 K68) displayed. Cross-linked sites are shown as space-filled residues. Residues connected by red lines agree with the structure, while residues connected by a yellow line exceed the maximum cross-linkable distance (42 Å). (b) Structure of a circular representation of the respirasome CI2CIII2CIV2, which agrees with all observed cross-linked sites. Reprinted from Chavez, J. D.; Lee, C. F.; Caudal, A.; Keller, A.; Tian, R.; Bruce, J. E. Cell Syst 2018, 6 (1), 136–141 e5 (ref 95). Copyright 2018 Cell.
Figure 8.
Figure 8.
Overview of the photolytic covalent labeling workflow, for peptide labeling. (a) Proteolytic digestion of protein generates a population of unlabeled peptides. (b) Equilibration of peptides with substituted diazirines in aqueous solution. Diazirine labeling reagents used in this study include 3,3′-azibutan-1-ol, 3,3′-azibutyl-1 ammonium, and 4,4′-azipentan-1-oate. (c) Photolysis at λ = 355 nm to generate reactive carbenes that insert into chemically accessible regions of peptide. Photolysis is constrained to a sub-microliter volume in a windowed UV-transparent capillary that supports flash-freezing in liquid nitrogen. (d) Localization of carbene insertion sites within peptides using high-resolution MS/MS data analyzed in the Mass Spec Studio software package. Reprinted from Ziemianowicz, D. S.; Bomgarden, R.; Etienne, C.; Schriemer, D. C. J Am Soc Mass Spectrom 2017, 28 (10), 2011–2021 (ref 106). Copyright 2018 Journal of The American Society for Mass Spectrometry.
Figure 9.
Figure 9.
(a) Rosetta score versus RMSD to the native structure plots for 20 000 models generated using Rosetta ab initio for each of the four benchmark proteins. The top scoring model is represented as a star on each plot. (b) The top scoring models from the Rosetta score versus RMSD distributions in A (color) superimposed on the respective native model (gray). (c) Rosetta score + hrf_ms_labeling versus RMSD to the native structure plots for each of the four benchmark proteins after rescoring with the new score term. The top scoring model is represented as a star on each plot. (d) The top scoring models from the Rosetta score + hrf_ms_labeling rescoring distributions in C (color) superimposed on the respective native model (gray). Reprinted from Aprahamian, M. L.; Chea, E. E.; Jones, L. M.; Lindert, S. 2018, 90 (12), 7721–7729 (ref 116). Copyright 2018 American Chemical Society.
See this image and copyright information in PMC

References

    1. Boeri Erba E; Petosa C Protein Sci. 2015, 24 (8), 1176–1192. - PMC - PubMed
    1. Chen B; Brown KA; Lin Z; Ge Y Anal. Chem 2018, 90 (1), 110–127. - PMC - PubMed
    1. Kanu AB; Dwivedi P; Tam M; Matz L; Hill HH Jr. J. Mass Spectrom 2008, 43 (1), 1–22. - PubMed
    1. Sinz A Angew. Chem. Int. Ed 2018, 57 (22), 6390–6396. - PubMed
    1. Chavez JD; Bruce JE Curr. Opin. Chem. Biol 2019, 48, 8–18. - PMC - PubMed

Publication types