Native Top-Down Mass Spectrometry and Ion Mobility MS for Characterizing the Cobalt and Manganese Metal Binding of α-Synuclein Protein
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Structural characterization of intrinsically disordered proteins (IDPs) has been a major challenge in the field of protein science due to limited capabilities to obtain full-length high-resolution structures. Native ESI-MS with top-down MS was utilized to obtain structural features of protein-ligand binding for the Parkinson’s disease-related protein, α-synuclein (αSyn), which is natively unstructured. Binding of heavy metals has been implicated in the accelerated formation of αSyn aggregation. Using high-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry, native top-down MS with various fragmentation methods, including electron capture dissociation (ECD), collisional activated dissociation (CAD), and multistage tandem MS (MS3), deduced the binding sites of cobalt and manganese to the C-terminal region of the protein. Ion mobility MS (IM-MS) revealed a collapse toward compacted states of αSyn upon metal binding. The combination of native top-down MS and IM-MS provides structural information of protein-ligand interactions for intrinsically disordered proteins.
KeywordsNative mass spectrometry α-Synuclein Metal binding Protein-ligand complex Top-down mass spectrometry Electron capture dissociation Electrospray ionization
Parkinson’s disease (PD) is a neurodegenerative disorder that results in impairment of movement function, including motor skills that affect speech and breathing [1, 2, 3]. One of the pathogenic hallmarks of PD is the deposition of α-synuclein (αSyn) protein as an amyloid, known as Lewy bodies, in dopaminergic neurons [2, 4, 5]. This pathogenic feature, called synucleinopathies, can also be linked to dementia and other symptoms such as multiple system atrophy (MSA) [6, 7]. The normal functions of αSyn in the brain remain largely unknown. Some studies have reported that αSyn is involved in lipid binding [8, 9] and promotes SNARE-mediated vesicle fusion . It may play a role in neurotransmitter regulation [11, 12, 13, 14].
Divalent and trivalent heavy metals, such as aluminum, copper, cobalt, manganese, cadmium, and iron, have been shown to accelerate αSyn aggregation [40, 41, 42]. It is believed that metal binding triggers structural changes of the protein toward more compact states via charge neutralization, leading to neurodegenerative disease progression [41, 43]. Binding of copper by αSyn has been widely studied [44, 45, 46, 47, 48, 49]. Copper binds to two regions of αSyn, the N-terminus and His-50, although the Cu-binding to His-50 is debated [34, 42]. Cu-binding is not found on the N-terminus for N-terminal acetylated forms of αSyn . The αSyn binding to other transition metals, including cobalt, manganese, iron, and nickel are far less studied, but the available data to date suggests that cobalt and manganese bind to the acidic C-terminal tail, particularly Asp-121 and Glu-123, with lower affinity than copper [51, 52]. Co/Mn-binding to αSyn is measured to be in the millimolar range, whereas Cu-binding is in the micromolar range .
In this report, we demonstrate the applicability of native mass spectrometry (MS) approaches with electrospray ionization (ESI) to provide important structural information on the binding of cobalt and manganese to α-synuclein. Native ESI-MS has been demonstrated to be an effective experimental platform to interrogate the structures of proteins , protein-ligand interactions , and large protein complexes [56, 57, 58]. Structural features, such as the elucidation of metal binding sites, have been revealed using top-down MS with electron capture dissociation (ECD) and collisionally activated dissociation (CAD) [57, 59]. Generally hydrophobic and weak non-covalent interactions involving ligand binding do not survive the energetic dissociation process of vibrational activation-based CAD. Previously, we have demonstrated that such weak interactions can be maintained under radical activation-based ECD conditions, allowing ligand binding sites to be elucidated . But in the case of metal binding, which mainly involves charge-charge interactions, such electrostatic interactions are strengthened in the gas phase due to low dielectric constant , and supported by computational modeling . Other ligands that interact with proteins through strong electrostatic forces, such as nucleotides (e.g., ATP), can be analyzed using CAD conditions [62, 63]. Our earlier native top-down MS studies of αSyn revealed the binding sites of weakly bound (solution Kd in the 10−3–10−6 M range) organic ligands using ECD [39, 55]. Herein, we used both ECD and CAD to identify the sites of Mn- and Co-binding to αSyn. Despite the millimolar binding affinity of Co-/Mn-binding to αSyn, Co-/Mn-binding might be involved in the aggregation pathway by forming transient folded intermediates. Ion mobility mass spectrometry (IM-MS) provided additional structural and conformation information that may play a role in amyloid fibrillation [8, 64].
Recombinant full-length α-synuclein (amino acids 1–140) and its trunctated polypeptides (amino acids 1–60, 61–140, and 96–140) were purchased from rPeptide (Bogard, GA). Proteins were further desalted by exchange with 20 mM ammonium acetate using 10 kDa MWCO Amicon centrifugal filters (MilliporeSigma; Burlington, MA). Cobalt acetate and manganese acetate were purchased from Sigma (St. Louis, MO) and resuspended in 20 mM ammonium acetate. Metals were added to the αSyn solution at the appropriate protein:metal concentration ratio. The final concentration of αSyn was kept at 10 μM in 20 mM ammonium acetate at pH 6.8. Samples were loaded into nano-ESI Au/Pd-coated borosilicate emitters (Thermo Scientific; San Jose, CA) for mass spectrometry analysis.
Top-down mass spectrometry experiments were performed with a Bruker Solarix 15-Tesla Fourier transform ion cyclotron resonance (FT-ICR) instrument and an Infinity ICR cell (Billerica, MA). To generate ions, the ESI voltage was set to ca. 1000 V to deliver protein sample at a flow rate of 50 nL/min. The capillary source temperature was 180 °C. The ion optic voltages were set to the following: deflector plate, 200 V; capillary exit, 180 V; funnel, 120 V; skimmer, 30 V.
For ECD-MS/MS experiments, precursor ions were isolated by the quadrupole and transferred into the FT-ICR cell for ECD fragmentation and ion detection. The estimated resolving power was set to 400,000 at m/z 400. For CAD-MS/MS, CAD was performed in the collision cell remote from the ICR cell. CAD fragments were transferred to and detected by the ICR cell. The CAD voltage was adjusted to a range between 8 and 15 V, depending on the isolated charge states. A supplemental skimmer voltage of up to 30 V was included for additional collisional activation to enhance ECD fragmentation. (Activated ion ECD from supplemental infrared radiation was not used.) Pseudo-MS3 experiments  for further fragmentation of MS2 product ions were conducted by a combination of the nozzle-skimmer CAD (NS-CAD) and CAD or ECD. NS-CAD was used as the unbiased first stage MS/MS (i.e., collisional activation of all ions), followed by CAD or ECD of selected NS-CAD products as the second stage MS/MS. MS2 and MS3 fragments were manually assigned against the theoretical fragments indicated by Protein Prospector (University of California, San Francisco; http://prospector.ucsf.edu/prospector/mshome.htm) and visually displayed using MATLAB (MathWorks, Natick, MA).
Ion Mobility Mass Spectrometry
IM-MS was performed with a Waters Synapt G2 HDMS quadrupole traveling wave ion mobility (TWIM) orthogonal time-of-flight mass spectrometer (Waters; Manchester, UK). For IM-MS experiments, αSyn and αSyn-metal samples were prepared to have a final concentration of 20 μM in 20 mM ammonium acetate. CoCl2 and MnCl2 were used to prepare αSyn-Co(II) (1:8 M ratio) and αSyn-Mn(II) (1:10 M ratio). Analyte solutions were inserted into Au-/Pd-coated borosilicate emitters (Thermo Scientific) nano-ESI-MS. A nano-ESI capillary voltage of 1.3 kV, cone voltage of 20 V, and source temperature of 50 °C were used for the experiments. For MS experiments, the settings of the instrument were trap bias, 45 V; IMS bias, 3 V; trap collision energy, 3 V; transfer collision energy, 0 V. The gas flow rates for the helium cell located before the IMS cell, and the IMS cell gas (N2) were 150 mL/min and 60 mL/min, respectively. The pressures of the helium cell and the IMS cell were 1.4 × 103 and 3.1 × 100 mbar, respectively. TWIM wave velocity and wave height were set to 500 m/s and 24 V, respectively. The experimental arrival times were converted into collision cross-section values by performing calibration using denatured ubiquitin, cytochrome c, and apo-myoglobin proteins of which collision cross section values were previously reported [8, 66, 67].
Results and Discussion
ESI-MS and MS2 of Unbound α-Synuclein
ESI-MS of Metal-Bound α-Synuclein
Binding of cobalt and manganese to αSyn were readily observed by native ESI-MS (Fig. 2). Protein:metal concentration ratios were optimized between 1:5 and 1:10, with the protein concentration kept at 10 μM. Gentle ion source conditions were used to minimize disruption of metal binding. The deconvoluted mass spectrum of unbound αSyn displayed monoisotopic and average masses at 14452 and 14,460 Da, respectively. Native ESI-MS of αSyn incubated with cobalt showed a mass (monoisotopic) of 14,509 Da, which corresponds to the mass of αSyn with one bound cobalt (Supplemental Table S1). A mass of 14,505 Da was measured for αSyn incubated with manganese, which agrees with a single manganese bound to αSyn (Supplemental Table S2). A second bound cobalt and manganese cation was also observed, but other studies indicate that non-specific metal binding is observed for αSyn [40, 41, 51]. This work will exclusively focus on the characterization of the 1:1 protein-metal complexes.
Because αSyn contains several acidic residues, the protein is negatively charged at physiological pH (pI ~ 4.6). Binding of divalent metal cations could be expected to electrostatically neutralize some of the negative charge. It has been proposed that charge neutralization from metal binding might alter αSyn’s conformation and trigger protein fibrillation . Protein charge state distributions measured by ESI-MS have been used to monitor αSyn folding induced by Cu-binding . A closer examination of the ESI charge state distribution (CSD) showed little differences between the metal-free and metal-bound states, which could suggest that the global structure is not significantly changed upon metal binding. It has been widely considered that CSDs from native ESI-MS can be used to reflect a protein’s conformation [72, 73, 74, 75], where low charge states at high m/z represent compact conformers and the extended conformers yield high charge states found at low m/z. Because αSyn is natively unstructured at pH 7, small changes in its structure due to metal binding may be difficult to produce observable changes in its CSD. Ion mobility mass spectrometry (IM-MS), however, may reflect changes in structure due to metal binding (vide infra).
Cobalt Binds to C-Terminal Unstructured Tail of α-Synuclein
If the Co-binding site is at the C-terminus, CAD of the αSyn-cobalt complex may yield more information for metal binding due to extensive fragmentation near the C-terminus. Backbone cleavage from CAD was 61%, higher than for apo-αSyn. There are some differences evident in the CAD map for αSyn-Co compared to that for apo-αSyn (Fig. 4b), and this is perhaps due to a structural change upon cobalt binding to the C-terminal region. Overall, we observed more abundant apo- and holo-y-ions for the αSyn-Co complex than for apo-αSyn. The following apo-fragments were identified: b115, b116, and y127 (with low intensity). Also we observed b126+Co, b127+Co, b137+Co, y21+Co and y24+Co holo-products. With backbone cleavages from CAD and ECD, we confirmed that the cobalt-binding region is between residues 119DPDNEAYE126. Sequence coverage increased to 96% when combining data from both ECD and CAD.
Manganese and Cobalt Share the Same Binding Site to α-Synuclein
Pseudo-MS3 to Further Probe Metal Binding of αSyn
Additional stages of MS/MS (e.g., MS3) can be useful, for example, to confirm product ion assignments or to further pinpoint the sites of modification. A “pseudo-MS3” experiment with the FT-ICR instrument was enabled to further probe the Co- and Mn-binding to αSyn. The potential on the skimmer in the atmosphere/vacuum interface was increased to fragment by CAD all ions generated by the ESI source. (This process was previously termed nozzle-skimmer dissociation (NSD)  and now sometimes called in-source CAD or IS-CAD.) Product ions generated by IS-CAD can be selected as precursors for further activation/dissociation, i.e., pseudo-MS3. Two product ions from each metal complex (y21+Co, y24+Co, y21+Mn, and y24+Mn) generated by IS-CAD were isolated for CAD-MS3 experiments.
The data for the Mn-complexes y21+Mn and y24+Mn showed similar results (Fig. 6c, d), yet there were some differences compared to the Co-complexes. From the pseudo-MS3 experiments, as for Co-binding, the Mn-binding site appears to be at residues 132GYQDYE137. But there is a distinct backbone cleavage at Glu-137 (relative to the full-length sequence) that yields Mn-bound b-ions (b18+Mn from y21+Mn precursor, and b21+Mn from y24+Mn precursor). Binding of manganese may induce reconfiguration or increase stabilization around the secondary binding site, which might explain why the fragment at Glu-137/Pro-138 yielded the highest abundance observed. The Pro-128/Ser-129 cleavage from y24+Mn showed more metal-bound fragment than with cobalt, suggesting the Mn-migration was more complete. The remaining product ions were similar to that found for cobalt-binding. Overall, the results from MS/MS and MS3 confirmed that cobalt and manganese have similar αSyn-binding sites.
MS/MS of Truncated αSyn Confirmed Metal Binding Sites
Aside from full-length αSyn, three truncated αSyn variants (1–60, 61–140, and 96–140) were characterized. αSyn(1–60) covers the N-terminal helical amphipathic region. αSyn(96–140) has only the C-terminal acidic region, which is mainly unfolded. αSyn(61–140) contains both the NAC and acidic regions. As expected, cobalt and manganese binds to both the 61–140 and 96–140 fragments, but not to the N-terminal 1–60 fragment (data not shown). These results confirmed the C-terminal binding regions, which were shared between the two metals. Top-down MS/MS experiments by ECD and CAD of Co/Mn-bound αSyn(61–140) and αSyn(96–140) were performed; the identified binding site was the same as for the full-length protein.
Metal Binding-Induced Structural Changes Observed by Ion Mobility Spectrometry
Native top-down mass spectrometry and ion mobility MS were used to provide in-depth structural information on the binding of divalent metal ions, Co and Mn, to α-synuclein, an intrinsically disordered protein. ECD, CAD, and pseudo-MS3 (IS-CAD/CAD-MS3) techniques were able to identify the binding sites of cobalt and manganese to the protein. Because the binding of Co and Mn to αSyn is governed by electrostatic interactions, the metal-protein interactions appeared to be highly stable in the gas phase and they survived higher-energy dissociation methods such as CAD. Sequence coverage was greatly improved by combining CAD and ECD data. Top-down MS revealed that Co and Mn share similar binding locations, with the primary and secondary binding sites, 119DPDNEAYE126 and 132GYQDY136, respectively, found at the C-terminal end. However, other weaker binding sites might be present along the polypeptide backbone. Different metals have different binding sites to αSyn and their interactions can cause unique structural changes [41, 52]. Previously, we reported the binding of Cu(II) to regions mainly near the N-terminus and residues 45–56 (wherein His-50 is located), whereas the C-terminal residues showed negligible interaction with Cu(II) . We postulated that a conformational strain in the αSyn–Cu(II) complex modulates the fibrillation pathway, thereby mediating the formation of highly cell-transmissible, cytotoxic αSyn fibrils with short lengths. Mn-/Co-binding can influence protein folding, which may be important factors for neurodegenerative diseases. Newer activation/dissociation methods, such as surface induced dissociation (SID)  and UV photodissociation (UVPD) [83, 84], should provide additional useful tools for MS-characterization of protein-ligand complexes. Top-down MS and IM-MS are complementary biophysical tools to elucidate the structural changes induced by protein-ligand interactions.
This study received support from the US National Institutes of Health (R01GM103479, S10RR028893, S10OD018504 to J.A.L.); the US Department of Energy (DE-FC02-02ER63421 to J.A.L.); the Development and Promotion of Science and Technology Talents Project (DPST) and Royal Thai Government (to P.W.); the Rachadapisek Sompot Fund, Chulalongkorn University (to P.W.); the National Research Foundation of Korea (NRF) (NRF-2016R1A2B4013089 and 20100020209 to H.I.K.); Korea University Future Research Grant (to H.I.K.); and the Ministry of Science, ICT and Future Planning (CAP-15-10-KRICT to H.I.K.).
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