Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Enas  N. Yousef; Ramakrishna Sesham; Jacob  W. McCabe; Rajpal Vangala; Laurence A. Angel

doi:10.3791/60102

JoVE Journal > Chemistry

化学

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published: September 07, 2019

doi:

10.3791/60102

Enas N. Yousef¹, Ramakrishna Sesham¹, Jacob W. McCabe¹, Rajpal Vangala¹, Laurence A. Angel¹

¹Department of Chemistry,Texas A&M University-Commerce

Summary

Ion mobility-mass spectrometry and molecular modeling techniques can characterize the selective metal chelating performance of designed metal-binding peptides and the copper-binding peptide methanobactin. Developing new classes of metal chelating peptides will help lead to therapeutics for diseases associated with metal ion misbalance.

Abstract

Electrospray ionization (ESI) can transfer an aqueous-phase peptide or peptide complex to the gas-phase while conserving its mass, overall charge, metal-binding interactions, and conformational shape. Coupling ESI with ion mobility-mass spectrometry (IM-MS) provides an instrumental technique that allows for simultaneous measurement of a peptide’s mass-to-charge (m/z) and collision cross section (CCS) that relate to its stoichiometry, protonation state, and conformational shape. The overall charge of a peptide complex is controlled by the protonation of 1) the peptide’s acidic and basic sites and 2) the oxidation state of the metal ion(s). Therefore, the overall charge state of a complex is a function of the pH of the solution that affects the peptides metal ion binding affinity. For ESI-IM-MS analyses, peptide and metal ions solutions are prepared from aqueous-only solutions, with the pH adjusted with dilute aqueous acetic acid or ammonium hydroxide. This allows for pH dependence and metal ion selectivity to be determined for a specific peptide. Furthermore, the m/z and CCS of a peptide complex can be used with B3LYP/LanL2DZ molecular modeling to discern binding sites of the metal ion coordination and tertiary structure of the complex. The results show how ESI-IM-MS can characterize the selective chelating performance of a set of alternative methanobactin peptides and compare them to the copper-binding peptide methanobactin.

Introduction

Copper and zinc ions are essential for living organisms and crucial to processes including oxidative protection, tissue growth, respiration, cholesterol, glucose metabolism, and genome reading¹. To enable these functions, groups such as the thiolate of Cys, imidazole of His²^,³, (more rarely) thioether of methionine, and carboxylate of Glu and Asp selectively incorporate metals as cofactors into the active sites of metalloenzymes. The similarity of these coordination groups raises an intriguing question regarding how the His and Cys ligands selectively incorporate either Cu(I/II) or Zn(II) to ensure correct functioning.

Selective binding is often accomplished by acquisition and trafficking peptides, which control Zn(II) or Cu(I/II) ion concentrations⁴. Cu(I/II) is highly reactive and causes oxidative damage or adventitious binding to enzymes, so its free concentration is tightly regulated by copper chaperones and copper-regulating proteins that transport it safely to various locations in the cell and tightly control its homeostasis⁵^,⁶. Disruption of copper metabolism or homeostasis is directly implicated in Menkes and Wilson’s disease⁷ as well as cancers⁷ and neural disorders, such as prion⁸ and Alzheimer’s disease⁹.

Wilson’s disease is associated with increased copper levels in the eyes, liver and sections of the brain, where the redox reactions of Cu(I/II) produces reactive oxygen species, causing hepatolenticular and neurological degeneration. Existing chelation therapies are the small thiol amino acid penicillamine and triethylenetetramine. Alternatively, the methanotrophic copper-acquisition peptides methanobactin (mb)¹⁰^,¹¹ exhibit therapeutic potential because of their high binding affinity for Cu(I)¹². When the methanobactin (mb-OB3b) from Methylosinus trichosporium OB3b was studied in an animal model of Wilson’s disease, copper was efficiently removed from the liver and excreted through the bile¹³. In vitro experiments confirmed that mb-OB3b could chelate the copper from the copper metallothionein contained in the liver cytosol¹³. Laser ablation inductively coupled plasma mass spectrometry imaging techniques have investigated the spatial distribution of copper in Wilson’s disease liver samples¹⁴^,¹⁵^,¹⁶ and shown that mb-OB3b removes the copper with short treatment periods of only 8 days¹⁷.

The mb-OB3b will also bind with other metal ions, including Ag(I), Au(III), Pb(II), Mn(II), Co(II), Fe(II), Ni(II), and Zn(II)¹⁸^,¹⁹. Competition for the physiological Cu(I) binding site is exhibited by Ag(I) because it can displace Cu(I) from the mb-OB3b complex, with both Ag(I) and Ni(II) also showing irreversible binding to Mb which cannot be displaced by Cu(I)¹⁹. Recently, a series of alternative methanobactin (amb) oligopeptides with the 2His-2Cys binding motif have been studied²⁰^,²¹, and their Zn(II) and Cu(I/II) binding properties characterized. Their primary amino acid sequences are similar, and they all contain the 2His-2Cys motif, Pro and an acetylated N-terminus. They mainly differ from mb-OB3b because the 2His-2Cys motif replaces the two enethiol oxazolone binding sites of mb-OB3b.

Electrospray ionization coupled with ion mobility-mass spectrometry (ESI-IM-MS) provides for a powerful instrumental technique for determining the metal-binding properties of peptides because it measures their mass-to-charge (m/z) and collision cross section (CCS) while conserving their mass, charge, and conformational shape from the solution-phase. The m/z and CCS relate to the peptides stoichiometry, protonation state, and conformational shape. Stoichiometry is determined because the identity and number of each element present in the species is explicitly identified. The overall charge of the peptide complex relates to the protonation state of the acidic and basic sites and the oxidation state of the metal ion(s). The CCS gives information of the conformational shape of the peptide complex because it measures the rotational averaged size which relates to the tertiary structure of the complex. The overall charge state of the complex is also a function of pH and affects the peptide’s metal ion binding affinity because the deprotonated basic or acidic sites such as the carboxyl, His, Cys and Tyr are also the potential binding sites for the metal ion. For the analyses, the peptide and metal ion are prepared in aqueous solutions with the pH adjusted by dilute aqueous acetic acid or ammonium hydroxide. This allows for the pH dependence and metal ion selectivity to be determined for the peptide. Furthermore, the m/z and CCS determined by ESI-IM-MS can be used with B3LYP/LanL2DZ molecular modeling to discover the type of metal ion coordination and tertiary structure of the complex. The results shown in this article reveal how ESI-IM-MS can characterize the selective chelating performance of a set of amb peptides and compare them to the copper-binding peptide mb-OB3b.

Protocol

1. Preparation of reagents

Culture Methylosinus trichosporium OB3b, isolate the Cu(I)-free mb-OB3b¹⁸^,²²^,²³, freeze-dry the sample and store at -80 °C until use.
Synthesize the amb peptides (>98% purity for amb₁, amb₂, amb₄; >70% purity for amb₇), freeze-dry the samples, and store them at -80 °C until use.
Purchase >98% purity manganese(II) chloride, cobalt(II) chloride, nickle(II) chloride, copper(II) chloride, copper(II) nitrate, silver(I) nitrate, zinc(II) chloride, iron(III) chloride and lead(II) chloride.
Purchase the poly-DL-alanine polymers used as calibrants for measuring the collision cross sections of the amb species and HPLC grade or higher ammonium hydroxide, glacial acetic acid, and acetonitrile.

2. Preparation of stock solution

Peptide stock solution
1. Weigh accurately, using at least three significant figures, the mass of 10.0–20.0 mg of the mb-OB3b or amb in a 1.7 mL plastic vial.
  NOTE: The weighed mass should yield either 12.5 mM or 1.25 mM, depending on the solubility of the peptide, when 1.00 mL of deionized (DI) water is added.
2. Using a pipet, add 1.00 mL of deionized water (>17.8 MΩ cm) to the weighed peptide sample to yield either the 12.5 mM or 1.25 mM solution. Place cap securely and mix thoroughly with at least 20 inversions.
3. Using a micropipet dispense 50.0 μL aliquots from the peptide sample into individually labelled 1.5 mL vials and store them at -80 °C until use.
Metal ion stock solutions
1. Weigh accurately, using at least three significant figures, the mass of 10.0–30.0 mg of the metal chloride or silver nitrate in a 1.7 mL vial.
  NOTE: The weighed mass should yield 125 mM when 1.00 mL of DI water is added.
2. Add the 1.00 mL of DI water to the weighed metal sample in the 1.7 mL vial to yield the 125 mM solution. Place cap securely and mix thoroughly with at least 20 inversions.
Ammonium hydroxide stock solutions: prepare a 1.0 M acetic acid solution by diluting 57 μL of the 99.5% acetic acid solution with DI water to a final volume of 1.00 mL. Prepare a 1.0 M ammonium hydroxide solution by diluting 90 μL of the 21% ammonium hydroxide solution with DI water to a final volume of 1.00 mL. Make two successive dilutions of each solution by taking 100 μL of the 1.0 M solutions to prepare 0.10 M and 0.010 M acetic acid and ammonium hydroxide solutions.
Poly-DL-alanine stock solution: prepare the poly-DL-alanine (PA) by weighing 1.0 mg of PA and dissolving in 1.0 mL of DI water to give 1,000 ppm. Mix thoroughly. Using a micropipet, dispense 50.0 μL aliquots, and place each into a 1.7 mL vial and store at -80 °C.

3. Electrospray-ion mobility-mass spectrometry analysis

Clean the ESI entrance tubing and needle capillary thoroughly with about 500 μL of 0.1 M glacial acetic acid, 0.1 M ammonium hydroxide, and finally DI water.
Thaw a 50.0 μL aliquot of the 1,000 ppm PA stock solution and dilute it with 450 μL of DI water to give a 100 ppm PA. Pipet 100.0 μL of this solution and dilute it to 1.00 mL with 500 μL of DI water and 500 μL of acetonitrile to give 10 ppm PA solution.
Collect the negative and positive ion IM-MS spectra of the 10 ppm PA solution for 10 min each using native ESI-IM-MS conditions as described in the discussion section.
Thaw a 50.0 μL aliquot of the 12.5 mM or 1.25 mM amb stock solution and make successive dilutions with DI water to give a final concentration of 0.125 mM amb. Mix thoroughly each dilution.
Pipet 100.0 μL of the 125 mM metal ion stock solution, place in a 1.7 mL vial and dilute to 1.00 mL with DI water to give 12.5 mM metal ion. Repeat with two more successive dilutions to give a final 0.125 mM metal ion concentration. Mix thoroughly each dilution.
Pipet 200.0 μL of the 0.125 mM amb into a 1.7 mL vial, dilute with 500 μL of DI water, and mix the solution thoroughly.
Adjust the pH of the sample to 3.0 by adding 50 μL of 1.0 M acetic acid solution.
Add 200.0 μL of the 0.125 mM metal ion to the pH-adjusted sample. Add DI water to yield a final volume of 1.00 mL of the sample, mix thoroughly, and allow the sample to equilibrate for 10 min at RT.
Using a blunt nose syringe take 500 μL of the sample and collect the negative and positive ion ES-IM-MS spectra for 5 min each. Use the remaining 500 μL of the sample to record its final pH using a calibrated micro pH electrode.
Repeat steps 3.6–3.9, while modifying step 3.7 to adjust the pH to 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, or 10.0 by adding new volumes of the 0.010 M, 0.10 M, or 1.0 M acetic acid or ammonium hydroxide solutions.
Collect the negative and positive ion ESI-IM-MS spectra of the 10 ppm PA solution for 10 min each.

4. Preparation of the metal ion titration of amb samples

Follow the steps described in steps 3.1–3.5.
Pipet 200.0 μL of the 0.125 mM amb into a 1.7 mL vial, dilute with 500.0 μL of DI water and mix the solution thoroughly.
Adjust the pH of the sample to pH = 9.0 by adding 80 μL of the 0.010 M ammonium hydroxide solution.
Add 28 μL of the 0.125 mM metal ion solution to give 0.14 molar equivalents of the metal ion, add DI water to make the final volume of the sample 1.00 mL, mix thoroughly, and allow the sample to equilibrate for 10 min at RT.
Using a blunt nose syringe take 500 μL of the sample and collect the negative and positive ion ESI-IM-MS spectra for 5 min each. Use the remaining 500 μL of the sample to record its final pH using a calibrated micro pH electrode.
Repeat steps 4.2–4.5, while modifying step 4.3 to add an appropriate volume of the 0.125 mM metal ion solution to give either 0.28, 0.42, 0.56, 0.70, 0.84, 0.98, 1.12, 1.26, or 1.40 molar equivalents.
Collect the negative and positive ion IM-MS spectra of the 10 ppm PA solution for 10 min each.

5. Analysis of ESI-IM-MS pH titration data

From the IM-MS spectra identify which charged species of ambs are present by matching them to their theoretical m/z isotope patterns.
1. Open MassLynx and click on Chromatogram to open the Chromatogram window.
2. Go to the File menu and Open to locate and open the IM-MS data file.
3. Extract the IM-MS spectrum by right-clicking and dragging across the chromatogram and releasing. The spectrum window will open showing the IM-MS spectrum.
4. In the spectrum window, click on Tools and Isotope model. In the isotope modeling window, enter the molecular formula of the amb species, check the Show charged ion box, and enter the charge state. Click OK.
5. Repeat to identify all the species in the IM-MS spectrum and record their m/z isotope range.
For each amb species, separate any coincidental m/z species and extract their arrival time distributions (ATD) using their m/z isotope patterns to identify them.
1. In MassLynx click on DriftScope to open the program. In DriftScope click on File and Open to locate and open the IM-MS data file.
2. Use the mouse and left-click to zoom in on m/z isotope pattern of the amb species.
3. Use the Selection tool and left mouse button to select the isotope pattern. Click the Accept current selection button.
4. To separate any coincidental m/z species use the Selection tool and left mouse button to select the ATD time-aligned with isotope pattern of the amb species. Click the Accept current selection button.
5. To export the ATD, go to File | Export to MassLynx, then select Retain Drift Time and save file in appropriate folder.
Determine the centroid of the ATD and integrate the area under the ATD curve as a measure of the species population.
1. In the Chromatogram window of MassLynx open the saved exported file. Click on Process | Integrate from the menu. Check the ApexTrack Peak Integration box and click OK.
2. Record the centroid ATD (t_A) and the integrated area as shown on the Chromatogram window. Repeat for all saved amb and PA IM-MS data files.
Use the integrated ATD for all extracted amb species of either the positive or negative ions at each titration point to normalize to a relative percentage scale.
1. Enter the identities of the amb species and their integrated ATD at each pH into a spreadsheet.
2. For each pH, use the sum of the integrated ATDs to normalize the individual amb’s ATD to a percentage scale.
3. Plot the percent intensities of each amb species vs. pH in a graph to show how the population of each species varies as a function of pH.

6. Collision cross-sections

Using a spreadsheet, convert the CCSs (Ω) of PA negative²⁵^,²⁶ and positive²⁷ ions measured in He buffer gas²⁸ to corrected CCS (Ω_c) using Equation 1 below, where: z = ion charge; e_c = electron charge (1.602×10^-19 C); m_N₂ = mass of N₂ gas (Da); and m_ion = ion mass.²⁹

Convert the average arrival times (t_A) of the PA calibrants and amb species into drift times (t_D) using Equation 2 below, where: c = the enhanced duty cycle delay coefficient (1.41), and m/z is the mass-to-charge of the peptide ion.

Plot the PA calibrants’ t_D vs. their Ω_c. Then, using a least-squares regression fit of Equation 3 shown below, determine the A' and B values, where: A' is the correction for the temperature, pressure, and electric field parameters; and B compensates for the nonlinear effect of the IM device.

Using these A' and B values and the centroid t_D value from the ATD of the ambs determine their Ω_c using Equation 3 and their Ω using Equation 1. This method provides CCSs for the peptide species with estimated absolute errors of about 2%²⁵^,²⁶^,²⁷.

7. Computational methods

Use the B3LYP/LanL2DZ level of theory, comprising of the Becke 3-parameter hybrid functionals³⁰ and the Dunning basis set³¹ and electron core potentials³²^,³³^,³⁴ to locate geometry-optimized conformers for all possible types of coordinations of the observed m/z amb species³⁵.
NOTE: For details of how to build and submit calculations refer to the GaussView usage in Supplementary File.
Compare the predicted free energy of each of the conformers and calculate their theoretical CCSs using the ion-scaled Lennard-Jones (LJ) method from the Sigma program³⁶.
From the lowest free energy conformers determine which conformer exhibits the LJ CCS which agrees with the IM-MS measured CCS to identify the tertiary structure and type of coordination for the conformers observed in the experiment.

Representative Results

Metal binding of amb₁
The IM-MS study²⁰ of amb₁ (Figure 1A) showed that both copper and zinc ions bound to amb₁ in a pH-dependent manner (Figure 2). However, copper and zinc bound to amb₁ through different reaction mechanisms at different coordination sites. For example, adding Cu(II) to amb₁ resulted in oxidation of amb₁ (amb_1ox) by disulfide bridge formation, and at a pH of >6, the [amb_1ox−3H+Cu(II)]⁻ ion (Figure 2A) was formed. This indicated the deprotonation of two imidazoliums, carboxyl group, and two additional sites that were coordinating Cu(II).

Molecular modeling of the [amb_1ox−3H+Cu(II)]⁻ ion using B3LYP/LanL2DZ determined the lowest energy complex was Cu(II) coordinated via the imidazole δN of His₁ and the deprotonated nitrogens of the backbone amide groups of Cys₂ and Gly₃. However, below a pH of 6, adding Cu(II) to amb₁ formed a m/z isotope pattern that could only be accounted for by Cu(I) binding, forming the [amb_1ox+Cu(I)]⁺ ion (Figure 2B). In contrast, a pH higher than 6 caused the m/z isotope pattern to decrease 1 m/z, accounted for by the positive charged [amb_1ox−H+Cu(II)]⁺ ion. Adding Zn(II) did not oxidize amb₁, and Zn(II) binding was observed at a pH of >6, primarily forming the [amb₁−3H+Zn(II)]⁻ ion (Figure 2C). This indicated the deprotonation of the imidazoliums, thiol, and carboxyl groups. Molecular modeling of the [amb₁−3H+Zn(II)]⁻ ion determined the lowest energy conformers to be either tetrahedral Zn(II) coordination via 2His-2Cys or His-2Cys and the carboxylate of the C-terminus.

Multiple Cu(I) binding of amb₂
The redox reactions between Cu(II) and amb₂ (Figure 1B) resulted in Cu(I) binding. This was studied in more detail using IM-MS, UV-Vis spectrophotometry, and B3LYP molecular modeling³⁷. The main products of the Cu(II) titration of amb₂ at a pH of 5 were amb₂ oxidation (through disulfide bridge formation) and the unoxidized amb₂ species coordinating three Cu(I) ions.

A search using the B3LYP/LanL2DZ method located two low-energy complexes contending for the 3Cu(I) coordinated species. The first was the complex shown in Figure 3A, where the 3Cu(I) ions were coordinated via the bridging thiolate groups³⁸ of Cys₂ and Cys₆ (of His₁) as well as δN₁ and δN₅ (of His₅). The second complex (3c) has a salt bridge between the protonated His₁ side group and C-terminal carboxylate group. These results suggest that at a pH of 3.0–6.0, the principal amb₂+3Cu(I) complex is the salt-bridged structure, which can be successfully transferred from solution to gas-phase with only minimal structural rearrangement.

The theoretical LJ CCS of 209 ± 6 Å², calculated using the Sigma program³⁶ for complex 3c, agreed with the IM-MS measured CCS, indicating that 3c represents [amb₂−2H+3Cu(I)]⁺ conformation at pH 3.0-6.0. However, at a pH of >6, this complex was not observed by IM-MS, probably because further deprotonation of His₁ (pK_a= 6.0) results in an overall neutral complex. Once the imidazoleum group of His₁ is deprotonated, 3Cu(I) coordination may convert to the bridging thiolate groups of Cys₂ and Cys₆ as well as δN₁ and δN₅ of His₁ and His₅, respectively (3a).

The pH dependence of amb₄ Cu(I/II)-binding and redox activity
The IM-MS and B3LYP techniques have been used to investigate the Cu(II) and pH titrations of amb₄ (Figure 1C) and identified monomer, dimer, trimer, and tetramer complexes of amb₄ containing up to three Cu(I) ions or two Cu(II) ions for each monomer subunit³⁹. The complexes also contained various numbers of disulfide bridges, and these products were produced whether or not the Cu(II) reactions with amb₄ were conducted in anaerobic or aerobic aqueous solutions.

Using the IM-MS technique, it was shown that these individual species could be separated and quantified even if they had overlapping isotope patterns because of differences in their arrival times (Figure 4). The identification and quantification of these closely related species is a task that no other instrumental or analytical technique can achieve. These IM-MS studies provide considerable insight into the pH-dependent redox reactions and exactly identified the numbers of inter- or intra-molecular disulfide bridges, number of Cu(I) or Cu(II) ions, and number of deprotonation sites in each of the complexes (Figure 5).

Moreover, measuring the complexes CCS also allowed the determination of each of the individual species conformational size, which was used with an extensive B3LYP/LanL2DZ search to locate conformers with structures that agreed with both the correct molecular stoichiometry and CCS measured by IM-MS. Through this method, the Cu(I/II) coordination of the various complexes were identified. The reactions between Cu(II) and amb₄ included the formation of dimers, trimers, and tetramers coordinating either Cu(I) or Cu(II), depending on the pH of the solution.

For example, in solutions that were mildly acidic (pH = 3.0–6.0), they primarily bound Cu(I) ions and were unoxidized, while in solutions that were slightly basic (pH = 8.0–11.0), they primarily bound Cu(II) ions and were oxidized by all the Cys forming disulfide bonds (Figure 6). The B3LYP/LanL2DZ determined that the Cu(I) ions were linear and bridged by the thiolate and imidazole groups, while the Cu(II) ions were chelated via distorted T-shaped or square planar geometries by an imidazole as well as the deprotonated backbone nitrogens of amide groups.

IM-MS analysis of mb-OB3b
The IM-MS studies¹⁹^,⁴⁰ of mb-OB3b (Figure 1D) showed that in the gas-phase, Cu(I)-free mb-OB3b exists as three negatively charged species: [mb-OB3b–H]^–, [mb-OB3b–2H]^2–, and [mb-OB3b–3H]^3–, consistent with expected solution-phase behavior. Individual metal ion titrations were performed¹⁹ to determine the metal ion selectivity of mb-OB3b. Figure 7 shows the results of the selected metal ion titrations and shows that the apparent binding selectivity of mb-OB3b can be categorized as three major groups: 1) Cu(I) and Ag(I); 2) Ni(II), Zn(II) and Co(II); and 3) Pb(II), Fe(II), and Mn(II). This order of binding selectivity was shown to be in general agreement with that found by fluorescence quenching experiments¹⁹ and isothermal titration calorimetry¹⁸.

Comparison of mb-OB3b and amb₇ metal binding selectivity
The apparent binding selectivity of mb-OB3b was compared to the binding selectivity of amb₇ at a pH of 7. The amb₇ was designed with the same amino acid sequence as mb-OB3b, but with the two enethiol oxazolone groups replaced with two His-Cys groups. The amb₇ (Figure 1E) has a single disulfide bond between Cys₆ and Cys₁₂. The results of the formation of negative charged complexes (Figure 8) showed that amb₇ preferred binding selectivity for Ni(II) and Zn(II) (60%), followed by Co(II) and Pb(II) (40%). Furthermore, there was about 20% Cu(II) binding. There was either trace or no amb₇ binding of Ag(I), Mn(II), or Fe(II). This compared to mb-OB3b’s preferred binding selectivity of over 90% for Cu(I) and Ag(I) binding.

Figure 1: Primary structures of the alternative methanobactin (amb) and methanobactin (mb-OB3b) peptides. (A) Acetyl-His₁-Cys₂-Gly₃-Pro₄-His₅-Cys₆ (amb₁); (B) acetyl-His₁-Cys₂-Tyr₃-Pro₄-His₅-Cys₆ (amb₂); (C) acetyl-His₁-Cys₂-Gly₃-Ser₄-Tyr₅-Pro₆-His₇-Cys₈-Ser₉ (amb₄); (D) 1-(N-[mercapto-(5-oxo-2-(3-methylbutanoyl)oxazol-(Z)-4-ylidene)methyl]-Gly₁–Ser₂–Cys₃–Tyr₄)-pyrrolidin-2-yl-(mercapto-[5-oxo-oxazol-(Z)-4-ylidene]methyl)–Ser₅–Cys₆–Met₇ (mb-OB3b); and (E) acetyl-Leu₁-His₂-Cys₃-Gly₄-Ser₅-Cys₆-Tyr₇-Pro₈-His₉-Cys₁₀-Ser₁₁-Cys₁₂-Met₁₃ (amb₇). Shading shows the: 2His-2Cys or enethiol-oxazolone binding sites (); proline or pyrrolidine hinges (); acetyl or methylbutanol group N-terminus (); and tyrosine, which can stabilize metal ion coordination via a second solvation shell π–cation interaction (). Please click here to view a larger version of this figure.

Figure 2: Mean relative intensities of the alternative methanobactin (amb₁) acetyl-His₁-Cys₂-Gly₃-Pro₄-His₅-Cys₆ and metal-bound complex (amb₁+X) (where X = Cu or Zn). Observations were made during negative and positive ion mass spectrometry analyses of 1:1 molar ratio solution of amb:XCl₂ over the pH range of 3.0–11.0. Error bars show standard deviations of the means of both the relative intensity and pH from three replicate pH titration experiments. The 1:1 molar solution of amb:CuCl₂ resulted in the oxidation of amb (amb_ox) with Cys₂ and Cys₆, forming a disulfide bridge. (A) Negative ion analysis of amb:CuCl₂ showing [amb_ox−H]⁻ and [amb_ox−3H+Cu(II)]⁻. (B) Positive ion analysis of amb:CuCl₂ showing [amb_ox]⁺ and [amb_ox+Cu(I/II)]⁺; the oxidation state of Cu in the complex was pH-dependent, being [amb_ox+Cu(I)]⁺; below a pH of 8 and [amb_ox−H+Cu(II)]⁺; above a pH of 8. (C) Negative ion analysis of amb:ZnCl₂ showing [amb]ⁿ⁻ and [amb+Zn(II)]ⁿ⁻. (D) Positive ion analysis of amb:ZnCl₂ showing [amb]ⁿ⁺ and [amb+Zn(II)]ⁿ⁺. This figure has been adapted from a previous publication²⁰. Please click here to view a larger version of this figure.

Figure 3: Proposed structures of [amb₂+3Cu(I)]⁺ using lowest energy and geometry-optimized structures located from the B3LYP/LanL2DZ level of theory. (A) 3 Cu(I) coordination via δN₁δN₅ of His₁ and His₅ and thiolate bridging thiolate groups of Cys₂ and Cys₆ with a theoretical cross-section of 217 ± 6 Å². (B) Illustration of the δN₁δN₅ and thiolate bridging coordination. (C) Salt bridged structure showing the 3 Cu(I) coordination via carboxylate terminal (Cys₆), δN₅, and thiolate bridging with a theoretical cross section of 209 ± 6 Å². (D) Illustration of the carboxylate terminal, δN₅, and thiolate bridging coordination. Bonding distances A, B, C, D, E, and F are shown in the unit of Å. This figure has been adapted from a previous publication³⁷. Please click here to view a larger version of this figure.

Figure 4: IM-MS analysis of products of the 1:1 mixture of amb₄:Cu(II) at pH = 4.4. (A) Extracted isotope patterns for the [amb₄−2H+3Cu(I)]⁺, [diamb₄−4H+6Cu(I)]²⁺, [triamb₄−6H+9Cu(I)]³⁺ and [tetraamb₄−8H+12Cu(I)]⁴⁺ species. (B) Integration of the extracted arrival times of [amb₄−2H+3Cu(I)]⁺, [diamb₄−4H+6Cu(I)]²⁺, [triamb₄−6H+9Cu(I)]³⁺ and [tetraamb₄−8H+12Cu(I)]⁴⁺ were used to calculate their relative intensities. To calculate the percent relative intensities, the summation of the integrated area for all extracted species for each titration point was used to normalize to the percent scale. Please click here to view a larger version of this figure.

Figure 5: Changing isotope pattern for singly Cu(I/II) bound amb₄ observed during the pH titration of molar equivalents of Cu(II):amb₄ at pH = 4.04, 6.02, and 9.98. At pH = 4.04, the experimental result primarily matches the isotope model for [amb₄+Cu(I)]⁺. At pH = 6.02, there is a shift of -2 m/z, signifying the formation of the disulfide bridge (shown as oxidation of amb_4ox) and agreement with the isotope pattern for [amb_4ox+Cu(I)]⁺. At pH = 9.98, there is a further shift of -1 m/z, signifying Cu(II) binding and the removal of a proton to maintain the +1 charge state, which then matches the isotope pattern for [amb_4ox−H+Cu(II)]⁺. Please click here to view a larger version of this figure.

Figure 6: Changing relative intensities of identities of the Cu(I/II) complexes of the monomer, dimer, and trimer of amb₄ over pH range of 3.0–11.0. (A) Monomer with one Cu(I/II) ion, (B) dimer with 2 Cu(I/II) ions, and (C) trimer with 3 Cu(I/II) ions. The captions note how many disulfide bonds were present in the complex. This figure has been adapted from a previous publication³⁹. Please click here to view a larger version of this figure.

Figure 7: Percentage of formation of the Cu(I), Ag(I), Zn(II), Ni(II), Co(II), Mn(II), Pb(II), or Fe(II) complexes of methanobactin. Observed during the individual metal ion titrations of methanobactin. It should be noted that Cu(I) binding resulted from the addition of Cu(II) and Fe(II) binding from the addition of Fe(III). This figure has been adapted from a previous publication¹⁹. Please click here to view a larger version of this figure.

Figure 8: Comparison of the percentage of Cu(I/II), Ag(I), Zn(II), Ni(II), Co(II), Mn(II), Pb(II), or Fe(II) chelation by mb-OB3b and amb₇ at pH = 7. The comparison is for the formation of negatively charged ions. Please click here to view a larger version of this figure.

Supplementary File. GaussView usage. Please click here to download this file.

Discussion

Critical steps: conserving solution-phase behaviors for examination via ESI-IM-MS
Native ESI instrumental settings must be used that conserve the peptides stoichiometry, charge state, and conformational structure. For native conditions, the conditions in the ESI source such as the cone voltages, temperatures, and gas flows have to be optimized. Also, the pressures and voltages in the source, trap, ion mobility, and transfer traveling waves (especially the DC trap bias that controls injection voltage into the IM cell) must be checked for their influences on charge-state and ion mobility distributions.

The following are the typical operating conditions that were used in this work. The aqueous peptide samples were injected using a blunt nose 1.0 mL syringe using a 10 μL min⁻¹ flow rate, 2.0 kV capillary voltage for positive ions (+) or −1.8 kV for negative ions (-), 130 °C source temperature, 250 °C desolvation, 20 V sampling cone, and 4.0 V extraction cone. The IM section was operated with 6.0 V entrance voltage to the trap cell with an argon pressure of 2.25 x 10⁻² mbar using a 1.5 mL/min flow rate. The voltage for injecting ions (trap DC bias) into the IM cell was set at 12 V to avoid dissociation of ions as they initially collided with the nitrogen buffer gas. The IM cell separated ions based on their charge and collision cross-section and utilized a 0.52 mbar nitrogen pressure and 20.0 mL min⁻¹ flow rate. The IM was operated with ramped 12.0–20.0 V (+) or 8.0–30.0 V (−) travelling wave heights and ramped 800–1,500 m s⁻¹ (+) or 250–1,000 m s⁻¹ (−) velocities for every sweep through the cell of the IM travelling wave. The transfer cell was operated with the same argon pressure as the trap cell and guided the IM resolved ions to the orthogonal time-of-flight mass-to-charge analyzer. The ion mobility-mass spectra were acquired by synchronizing the gated release of ions into the IM cell with the time-of-flight mass-to-charge analyzer.

Using native ESI conditions, solution-phase properties such as the charge state and conformational state are conserved during the IM-MS analyses. For example, the charge states of mb-OB3b and ambs observed during IM-MS analyses²⁰^,³⁷ were closely related to the charge states expected in the solution phase⁴⁰. The mb-OB3b peptide is tetraprotic and forms only negatively charged ions during IM-MS analysis⁴⁰, whether Cu(I)-bound or Cu(I)-free, because it contains the C-terminus (pKa < 1.7), two enethiol oxazolone groups (pKa = 5.0 and 9.7), and Tyr group (pKa = 11.0)⁴². The ambs in their fully protonated form will have an overall charge of +2 because of the C-terminus (pKa ≈ 2), two His (pKa = 6.0), two Cys (pKa = 8.3), and Tyr (pKa = 11.0) sites¹⁹^,⁴¹. Thus, they generally form positively charged ions at a pH of <6 and negatively charged ions at a pH of >6.

The ambs also showed clear pH-dependent Cu(I/II) binding behavior and redox activity in which Cu(I)-binding at a low pH transitioned to Cu(II) binding at a higher pH. The Cu(I/II) reactions included forming the oxidized amb species (amb_ox) that contained disulfide bonds and various multimers and multiple Cu(I/II) binding (Figure 5 and Figure 6). These redox reactions are time-dependent and it was shown that the longer the time interval (up to 210 min) between sample preparation and IM-MS analyses the more oxidized products were observed³⁷. Therefore, careful consideration of reaction time dependence on the observation of products is also required.

Limitations: IM-MS and theoretical collision cross-sections identify which type of coordination each metal ion prefers
To help interpret the IM-MS m/z and CCS data, an extensive search was conducted using the B3LYP/LanL2DZ level of theory. Geometry-optimized conformers with different coordination sites were compared between their predicted free energy and agreement with the CCS measured by IM-MS. Molecular modeling of these peptides and their complexes is limited by the type of electronic structure calculations that can be applied to these relatively large systems. Other methods that have been studied or recommended include work by Truhlar et al.⁴³, who found that M05-2X was the best DFT functional and PM7 and MNDO/d were good NDDO semi-empirical methods for Zn(II)-containing compounds⁴⁴. These peptides have a large conformational space and thorough investigation to locate the lowest energy conformers must include comparing the various metal chelating sites, various cis- and trans-peptide bonds, salt-bridges, hydrogen bonding, and π-cation interaction between the aromatic Tyr side group and metal cation.

Significance with respect to existing methods: Cu(I/II) and other selected metal ion binding compared between mb-OB3b and ambs
X-ray crystallography and NMR spectroscopy are the most common techniques used for determining the atomic resolution of peptides tertiary structure. However, X-ray crystallography studies of metallopeptides are scarce due to problems with the crystallization of these complexes⁴⁵. NMR is also not suitable for the interpretation of a sample where closely related individual oligopeptide species are present⁴⁶. Therefore, IM-MS and DFT molecular modelling are alternative techniques for studying peptide reactions especially those that result from complex redox and Cu(I/II)-binding reactions²⁰^,³⁷^,⁴⁰^,⁴⁷. The strength of IM-MS is that it can resolve each of the products and identify their molecular composition by simultaneously measuring their m/z and arrival times that relate to the stoichiometry, protonation state, and conformational structure.

For example, the mb-OB3b will chelate a variety of metal ions, and its selectivity towards each ion was displayed by the IM-MS metal ion titrations (Figure 7). The results showed the mb-OB3b preference for binding Cu(I) and Ag(I), while comparing the results at a pH of 7 with amb₇. Figure 8 shows amb₇ preferentially chelates Zn(II) and Ni(II). In general, the amb studies showed that replacing the two enethiol-oxazolones with 2His-2Cys did not exclude Cu(I/II)-binding, but it resulted in multiple Cu(I)-binding via linear-bridging coordination (Figure 3) as opposed to the mononuclear Cu(I) binding of mb-OB3b’s tetrahedral coordination⁴⁸. Cu(II) reduction was also mediated by thiol oxidation and disulfide bridge formation in contrast to the existing disulfide bridge in apo-mb-OB3b and the high reduction potential for copper-loaded mb-OB3b, which supports the strong preference for Cu(I)⁴⁹.

Future applications
Further IM-MS studies of amb peptides are underway, in which their primary sequence is modified by replacing the His or Cys with Gly or Asp, while the Tyr residue is replaced with either Gly or Phe. These studies are also being conducted in 10.0 mM ammonium acetate, with the pH modified with ammonium hydroxide (for pH = 7, 8, and 9) to keep the total ionic strength constant for each sample. These results will be published shortly.

Disclosures

The authors have nothing to disclose.

Acknowledgements

This material is based upon work supported by the National Science Foundation under 1764436, NSF instrument support (MRI-0821247), Welch Foundation (T-0014), and computing resources from the Department of Energy (TX-W-20090427-0004-50) and L3 Communications. We thank the Bower’s group of University of California – Santa Barbara for sharing the Sigma program and Ayobami Ilesanmi for demonstrating the technique in the video.

Materials

acetonitrile HPLC-grade	Fisher Scientific (www.Fishersci.com)	A998SK-4
ammonium hydroxide (trace metal grade)	Fisher Scientific (www.Fishersci.com)	A512-P500
cobalt(II) chloride hexahydrate 99.99%	Sigma-Aldrich (www.sigmaaldrich.com)	255599-5G
copper(II) chloride 99.999%	Sigma-Aldrich (www.sigmaaldrich.com)	203149-10G
copper(II) nitrate hydrate 99.99%	Sigma-Aldrich (www.sigmaaldrich.com)	229636-5G
designed amb1,2,3,4,5,6,7 peptides	Neo BioLab (neobiolab.com)		designed peptides were synthized by order
designed amb5B,C,D,E,F peptides	PepmicCo (www.pepmic.com)		designed peptides were synthized by order
Driftscope 2.1 software program	Waters (www.waters.com)		software analysis program
Freeze-dried, purified, Cu(I)-free mb-OB3b			cultured and isolated in the lab of Dr. DongWon Choi (Biology Department, Texas A&M-Commerce)
glacial acetic acid (Optima grade)	Fisher Scientific (www.Fishersci.com)	A465-250
Iron(III) Chloride Anhydrous 98%+	Alfa Aesar (www.alfa.com)	12357-09
lead(II) nitrate ACS grade	Avantor (www.avantormaterials.com)	128545-50G
manganese(II) chloride tetrahydrate 99.99%	Sigma-Aldrich (www.sigmaaldrich.com)	203734-5G
MassLynx 4.1	Waters (www.waters.com)		software analysis program
nickel chloride hexahydrate 99.99%	Sigma-Aldrich (www.sigmaaldrich.com)	203866-5G
poly-DL-alanine	Sigma-Aldrich (www.sigmaaldrich.com)	P9003-25MG
silver nitrate 99.9%+	Alfa Aesar (www.alfa.com)	11414-06
Waters Synapt G1 HDMS	Waters (www.waters.com)		quadrupole – ion mobility- time-of-flight mass spectrometer
zinc chloride anhydrous	Alfa Aesar (www.alfa.com)	A16281

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Yousef, E. N., Sesham, R., McCabe, J. W., Vangala, R., Angel, L. A. Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides. J. Vis. Exp. (151), e60102, doi:10.3791/60102 (2019).