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

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.

Metal migration and subunit swapping in ALS-linked SOD1: Zn2+ transfer between mutant and wild-type occurs faster than the rate of heterodimerization

“…We used semi-soft ionization conditions (30% acetonitrile, 100 mM formic acid) that dissociate the dimer, but preserve metal binding, thus allowing us to determine which subunit is binding metals ( 44 ). Protein samples were washed into MQ and metalated prior to heterodimerization.…”

“…The mass spectra of the 4Zn-SOD1 had several peaks which correlated to the 1Zn or 2Zn/subunit species with or without a sulfate adduct (Zn 2+ = +65 Da, SO 4 2− = +96 Da). As a monomer, the maximum number of Zn 2+ is 2 as there are only two metal-binding active sites per monomer ( 44 ) (additional weak sites presumably exist elsewhere on the surface of the protein) ( 36 , 45 , 46 ). Note that trace mass spectral signals of apo-SOD1 are observed in 4Zn-SOD1 samples ( Fig.…”

Mass spectrometric insights into protein aggregation

“…In a recent example, IM-MS was applied to assess the misfolding pathway of bovine Cu/Zn-superoxide dismutase (SOD1), with dysregulation of this enzyme of significance in a range of neurodegenerative disorders. Through systematic denaturation of the holodimer by manipulation of solution conditions, elongation was first observed, followed by dissociation to holo-, single-metal, and finally extremely extended apo-monomeric SOD1 units, with loss of the metal cofactors found to be critical to destabilization [ 41 ].…”

Molecular and Structural Characterization of Isomeric Compounds in Atmospheric Organic Aerosol Using Ion Mobility-Mass Spectrometry

“…IM-MS is a powerful postionization separation technique that separates gas-phase ions based on their mobility through an inert buffer gas such as N 2 . , Ions are pulsed into the low electric field drift tube and separated in a few milliseconds in the gas phase based on their collision cross sections, mass-to-charge ratio ( m / z ), and charge states. − Analyte identification in this measurement is aided by converting the ion-specific drift time (DT) values, t D , into the collision cross section (CCS) using the Mason–Schamp equation. − Ion mobility measurements provide an additional level of fingerprinting for SOA components using the CCS as a structural descriptor and enable the gas-phase separation of isomers in complex mixtures. , In certain cases, measured CCS offers the molecular description of the gas-phase three-dimensional (3D) configuration of ions formed in ionization, , which has been used for studying the folding and unfolding of protein complexes − and structures of DNA molecules. , The mobility of ions in IM-MS is affected by the charging effects in electrospray ionization (ESI), which often generates several ionized states of analyte molecules such as protonated and deprotonated species along with cation or anion adducts. The mode of ionization influences the conformation and selectivity of ionized analytes.…”