Utilizing Ion Mobility-Mass Spectrometry to Investigate the Unfolding Pathway of Cu/Zn Superoxide Dismutase

Overview

Journal Front Chem

Specialty Chemistry

Date 2021 Feb 26

PMID 33634076

Citations 5

Authors

Karen E Butler

Yoshihiko Takinami

Adam Rainczuk

Erin S Baker

Blaine R Roberts

Affiliations

Soon will be listed here.

Abstract

Native mass spectrometry has emerged as a powerful tool for structural biology as it enables the evaluation of molecules as they occur in their physiological conditions. Ion mobility spectrometry-mass spectrometry (IMS-MS) has shown essential in these analyses as it allows the measurement of the shape of a molecule, denoted as its collision cross section (CCS), and mass. The structural information garnered from native IMS-MS provides insight into the tertiary and quaternary structure of proteins and can be used to validate NMR or crystallographic X-ray structures. Additionally, due to the rapid nature (millisecond measurements) and ability of IMS-MS to analyze heterogeneous solutions, it can be used to address structural questions not possible with traditional structural approaches. Herein, we applied multiple solution conditions to systematically denature bovine Cu/Zn-superoxide dismutase (SOD1) and assess its unfolding pathway from the holo-dimer to the holo-monomer, single-metal monomer, and apo-monomer. Additionally, we compared and noted 1-2% agreement between CCS values from both drift tube IMS and trapped IMS for the SOD1 holo-monomer and holo-dimer. The observed CCS values were in excellent agreement with computational CCS values predicted from the homo-dimer crystal structure, showcasing the ability to use both IMS-MS platforms to provide valuable structural information for molecular modeling of protein interactions and structural assessments.

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References

Zhuang X, Liu S, Zhang R, Song F, Liu Z, Liu S . Identification of unfolding and dissociation pathways of superoxide dismutase in the gas phase by ion-mobility separation and tandem mass spectrometry. Anal Chem. 2014; 86(23):11599-605. DOI: 10.1021/ac502253t. View

Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H . The Protein Data Bank. Nucleic Acids Res. 1999; 28(1):235-42. PMC: 102472. DOI: 10.1093/nar/28.1.235. View

Testa L, Brocca S, Grandori R . Charge-surface correlation in electrospray ionization of folded and unfolded proteins. Anal Chem. 2011; 83(17):6459-63. DOI: 10.1021/ac201740z. View

Hayward L, Rodriguez J, Kim J, Tiwari A, Goto J, Cabelli D . Decreased metallation and activity in subsets of mutant superoxide dismutases associated with familial amyotrophic lateral sclerosis. J Biol Chem. 2002; 277(18):15923-31. DOI: 10.1074/jbc.M112087200. View

ABERNETHY J, Steinman H, Hill R . Bovine erythrocyte superoxide dismutase. Subunit structure and sequence location of the intrasubunit disulfide bond. J Biol Chem. 1974; 249(22):7339-47. View

McAlary L, Harrison J, Aquilina J, Fitzgerald S, Kelso C, Benesch J . Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt Bridge Formation. Anal Chem. 2019; 92(2):1702-1711. DOI: 10.1021/acs.analchem.9b01699. View

Marklund E, Degiacomi M, Robinson C, Baldwin A, Benesch J . Collision cross sections for structural proteomics. Structure. 2015; 23(4):791-9. DOI: 10.1016/j.str.2015.02.010. View

Stathopulos P, Rumfeldt J, Scholz G, Irani R, Frey H, Hallewell R . Cu/Zn superoxide dismutase mutants associated with amyotrophic lateral sclerosis show enhanced formation of aggregates in vitro. Proc Natl Acad Sci U S A. 2003; 100(12):7021-6. PMC: 165823. DOI: 10.1073/pnas.1237797100. View

Hough M, Strange R, Hasnain S . Conformational variability of the Cu site in one subunit of bovine CuZn superoxide dismutase: the importance of mobility in the Glu119-Leu142 loop region for catalytic function. J Mol Biol. 2000; 304(2):231-41. DOI: 10.1006/jmbi.2000.4186. View

10.

Rhoads T, Lopez N, Zollinger D, Morre J, Arbogast B, Maier C . Measuring copper and zinc superoxide dismutase from spinal cord tissue using electrospray mass spectrometry. Anal Biochem. 2011; 415(1):52-8. PMC: 3118564. DOI: 10.1016/j.ab.2011.03.029. View

11.

Li H, Sheng Y, McGee W, Cammarata M, Holden D, Loo J . Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. Anal Chem. 2017; 89(5):2731-2738. PMC: 5495147. DOI: 10.1021/acs.analchem.6b02377. View

12.

McCord J, Fridovich I . Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein). J Biol Chem. 1969; 244(22):6049-55. View

13.

Arnesano F, Banci L, Bertini I, Martinelli M, Furukawa Y, OHalloran T . The unusually stable quaternary structure of human Cu,Zn-superoxide dismutase 1 is controlled by both metal occupancy and disulfide status. J Biol Chem. 2004; 279(46):47998-8003. DOI: 10.1074/jbc.M406021200. View

14.

Banci L, Bertini I, Cramaro F, Del Conte R, Viezzoli M . Solution structure of Apo Cu,Zn superoxide dismutase: role of metal ions in protein folding. Biochemistry. 2003; 42(32):9543-53. DOI: 10.1021/bi034324m. View

15.

Banci L, Bertini I, Cramaro F, Del Conte R, Viezzoli M . The solution structure of reduced dimeric copper zinc superoxide dismutase. The structural effects of dimerization. Eur J Biochem. 2002; 269(7):1905-15. DOI: 10.1046/j.1432-1033.2002.02840.x. View

16.

Ray S, Nowak R, Strokovich K, Brown Jr R, Walz T, Lansbury Jr P . An intersubunit disulfide bond prevents in vitro aggregation of a superoxide dismutase-1 mutant linked to familial amytrophic lateral sclerosis. Biochemistry. 2004; 43(17):4899-905. DOI: 10.1021/bi030246r. View

17.

Heck A, van den Heuvel R . Investigation of intact protein complexes by mass spectrometry. Mass Spectrom Rev. 2004; 23(5):368-89. DOI: 10.1002/mas.10081. View

18.

Rolland A, Prell J . Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry. Trends Analyt Chem. 2020; 116:282-291. PMC: 6979403. DOI: 10.1016/j.trac.2019.04.023. View

19.

Xian F, Hendrickson C, Marshall A . High resolution mass spectrometry. Anal Chem. 2012; 84(2):708-19. DOI: 10.1021/ac203191t. View

20.

Doucette P, Whitson L, Cao X, Schirf V, Demeler B, Valentine J . Dissociation of human copper-zinc superoxide dismutase dimers using chaotrope and reductant. Insights into the molecular basis for dimer stability. J Biol Chem. 2004; 279(52):54558-66. DOI: 10.1074/jbc.M409744200. View