Effects of metal ion adduction on the gas-phase conformations of protein ions

Structural and mechanistic insights into amyloid-β and α-synuclein fibril formation and polyphenol inhibitor efficacy in phospholipid bilayers

Under certain cellular conditions, functional proteins undergo misfolding, leading to a transition into oligomers which precede the formation of amyloid fibrils. Misfolding proteins are associated with neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. While the importance of lipid membranes in misfolding and disease aetiology is broadly accepted, the influence of lipid membranes during therapeutic design has been largely overlooked. This study utilized a biophysical approach to provide mechanistic insights into the effects of two lipid membrane systems (anionic and zwitterionic) on the inhibition of amyloid-β 40 and α-synuclein amyloid formation at the monomer, oligomer and fibril level. Large unilamellar vesicles (LUVs) were shown to increase fibrillization and largely decrease the effectiveness of two well-known polyphenol fibril inhibitors, (-)-epigallocatechin gallate (EGCG) and resveratrol; however, use of immunoblotting and ion mobility mass spectrometry revealed this occurs through varying mechanisms. Oligomeric populations in particular were differentially affected by LUVs in the presence of resveratrol, an elongation phase inhibitor, compared to EGCG, a nucleation targeted inhibitor. Ion mobility mass spectrometry showed EGCG interacts with or induces more compact forms of monomeric protein typical of off-pathway structures; however, binding is reduced in the presence of LUVs, likely due to partitioning in the membrane environment. Competing effects of the lipids and inhibitor, along with reduced inhibitor binding in the presence of LUVs, provide a mechanistic understanding of decreased inhibitor efficacy in a lipid environment. Together, this study highlights that amyloid inhibitor design may be misguided if effects of lipid membrane composition and architecture are not considered during development.

Charge-dependent modulation of specific and nonspecific protein-metal ion interactions in nanoelectrospray ionization mass spectrometry

RATIONALE

Previous studies found that charge state could affect both specific and nonspecific binding of protein-metal ion interactions in nanoelectrospray ionization mass spectrometry (nESI-MS). However, the two kinds of interactions have been studied individually in spite of the problem that they often coexist in the same system. Thus, it is necessary to study the effects of charge state on specific and nonspecific protein-metal ion interactions in one system to reveal more accurate binding state.

METHODS

The HIV-1 nucleocapsid protein (NCp7(31-55)) which can bind specifically and nonspecifically to Zn²⁺ served as the model to show the charge-dependent protein-metal ion interactions. Hydrogen/deuterium exchange (HDX) and photodissociation (PD) were used to demonstrate that specific binding state was correlated with protein structure. In addition to NCp7(31-55), three other model proteins were used to investigate the reason for the charge-dependent nonspecific binding.

RESULTS

For specific binding, we proposed that protein ions with different charge states had different conformations. The HDX results showed that labile protons in the NCp7(31-55)-Zn complex were exchanged in a charge-state-dependent way. The PD experiments revealed differential fragment yields for different charge states. For nonspecific binding, higher charge states had more Zn²⁺ additions, but less SO₄ ^2- additions. The effects of charge states on nonspecific binding levels were entirely the opposite for Zn²⁺ and SO₄ ^2- . These results could reveal that the nonspecific binding was caused by electrostatic interaction.

CONCLUSIONS

For specific binding, NCp7(31-55) with lower charge states have folding and undenatured structures. The binding states of lower charge states can better reflect more native binding states. For nonspecific binding, when multiple metal ions adduct to proteins, the proteins have more net positive charges, which tend to generate higher charge ions during electrospray.

Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry-Mass Spectrometry

The strong synergy arising from coupling two orthogonal analytical techniques such as ion mobility and mass spectrometry can be used to separate complex mixtures and determine structural information of analytes in the gas phase. A tandem study is performed using two systems with different gases and pressures to ascertain gas-phase conformations of homopolymer ions. Aside from spherical and stretched configurations, intermediate configurations formed by a multiply charged globule and a "bead-on-a-string" appendix are confirmed for polyethylene-glycol (PEG), polycaprolactone (PCL), and polydimethylsiloxane (PDMS). These intermediate configurations are shown to be ubiquitous for all charge states and masses present. For each charge state, configurations evolve in two distinctive patterns: an inverse evolution which occurs as an elementary charge attached to the polymer leaves the larger globule and incorporates itself into the appendage, and a forward evolution which reduces the globule without relinquishing a charge while leaving the appendix relatively constant. Forward evolutions are confirmed to form self-similar family shapes that transcend charge states for all polymers. Identical structural changes occur at the same mass over charge regardless of the system, gas or pressure strongly suggesting that conformations are only contingent on number of charges and chain length, and start arranging once the ion is at least partially ejected from the droplet, supporting a charge extrusion mechanism. Configurational changes are smoother for PDMS which is attributed to the larger steric hindrance caused by protruding pendant groups. This study has implications in the study of the configurational space of more complex homopolymers and heteropolymers. Graphical Abstract.

Native mass spectrometry beyond ammonium acetate: effects of nonvolatile salts on protein stability and structure

Structures and stabilities of proteins investigated with native mass spectrometry can be affected by nonvolatile salts, including Tris buffer, in solution.

Cation-Dependent Conformations in 25-Hydroxyvitamin D3-Cation Adducts Measured by Ion Mobility-Mass Spectrometry and Theoretical Modeling

Ion mobility-mass spectrometry is a useful tool in separation of biological isomers, including clinically relevant analytes such as 25-hydroxyvitamin D3 (25OHD3) and its epimer, 3-epi-25-hydroxyvitamin D3 (epi25OHD3). Previous research indicates that these epimers adopt different gas-phase sodiated monomer structures, either the "open" or "closed" conformer, which allow 25OHD3 to be readily resolved in mixtures. In the current work, alternative metal cation adducts are investigated for their relative effects on the ratio of "open" and "closed conformers. Alkali and alkaline earth metal adducts caused changes in the 25OHD3 conformer ratio, where the proportion of the "open" conformer generally increases with the size of the metal cation in a given group. As such, the ratio of the "open" conformer, which is unique to 25OHD3 and absent for its epimer, can be increased from approximately 1:1 for the sodiated monomer to greater than 8:1 for the barium adduct. Molecular modeling and energy calculations agree with the experimental results, indicating that the Gibbs free energy of conversion from the "closed" to the "open" conformation decreased with increasing cation size, correlating with the variation in ratio between the conformers. This work demonstrates the effect of cation adducts on gas-phase conformations of small, flexible molecules and offers an additional strategy for resolution of clinically relevant epimers.

Native electrospray mass spectrometry approaches to probe the interaction between zinc and an anti-angiogenic peptide from histidine-rich glycoprotein

Zinc modulates the biological function of histidine-rich glycoprotein (HRG) through binding to its His-rich region (HRR). The Zn2+-binding properties of a 35 amino-acid biologically-active peptide mimic of the HRR, HRGP330, were investigated using dissociative mass spectrometry approaches in addition to travelling-wave ion mobility mass spectrometry (TWIM-MS). Native mass spectrometry confirmed zinc binding to HRGP330; however, broadening of the 1H NMR resonances upon addition of Zn2+ ions precluded the attainment of structural information. A complementary approach employing TWIM-MS indicated that HRGP330 has a more compact structure in the presence of Zn2+ ions. Top-down MS/MS data supported a metal-binding-induced conformational change, as fewer fragments were observed for Zn2+-bound HRGP330. Zn2+-bound fragments of both N-terminal and C-terminal ends of the peptide were identified from collision-induced dissociation (CID) and electron transfer dissociation/proton transfer reaction (ETD/PTR) experiments, suggesting that multiple binding sites exist within this region of HRG. The combination of mass spectrometry and NMR approaches provides new insight into the highly dynamic interaction between zinc and this His-rich peptide.

Charge-State-Dependent Variation of Signal Intensity Ratio between Unbound Protein and Protein-Ligand Complex in Electrospray Ionization Mass Spectrometry: The Role of Solvent-Accessible Surface Area

Native electrospray ionization mass spectrometry (ESI-MS) is nowadays widely used for the direct and sensitive determination of protein complex stoichiometry and binding affinity constants ( K_a). A common yet poorly understood phenomenon in native ESI-MS is the difference between the charge-state distributions (CSDs) of the bound protein-ligand complex (PL) and unbound protein (P) signals. This phenomenon is typically attributed to experimental artifacts such as nonspecific binding or in-source dissociation and is considered highly undesirable, because the determined K_a values display strong variation with charge state. This situation raises serious concerns regarding the reliability of ESI-MS for the analysis of protein complexes. Here we demonstrate that, contrary to the common belief, the CSD difference between P and PL ions can occur without any loss of complex integrity, simply due to a change in the solvent-accessible surface area (ΔSASA) of the protein upon ligand binding in solution. The experimental CSD shifts for PL and P ions in ESI-MS are explained in relation to the magnitude of ΔSASA for diverse protein-ligand systems using a simple model based on the charged residue mechanism. Our analysis shows that the revealed ΔSASA factor should be considered rather general and be given attention for the correct spectral interpretation of protein complexes.

Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex

Manganese oxidation is an important biogeochemical process that is largely regulated by bacteria through enzymatic reactions. However, the detailed mechanism is poorly understood due to challenges in isolating and characterizing these unknown enzymes. A manganese oxidase, Mnx, from Bacillus sp. PL-12 has been successfully overexpressed in active form as a protein complex with a molecular mass of 211 kDa. We have recently used surface induced dissociation (SID) and ion mobility-mass spectrometry (IM-MS) to release and detect folded subcomplexes for determining subunit connectivity and quaternary structure. The data from the native mass spectrometry experiments led to a plausible structural model of this multicopper oxidase, which has been difficult to study by conventional structural biology methods. It was also revealed that each Mnx subunit binds a variable number of copper ions. Becasue of the heterogeneity of the protein and limited mass resolution, ambiguities in assigning some of the observed peaks remained as a barrier to fully understanding the role of metals and potential unknown ligands in Mnx. In this study, we performed SID in a modified Fourier transform-ion cyclotron resonance (FTICR) mass spectrometer. The high mass accuracy and resolution offered by FTICR unveiled unexpected artificial modifications on the protein that had been previously thought to be iron bound species based on lower resolution spectra. Additionally, isotopically resolved spectra of the released subcomplexes revealed the metal binding stoichiometry at different structural levels. This method holds great potential for in-depth characterization of metalloproteins and protein-ligand complexes. Graphical Abstract ᅟ.

What factors determine the stability of a weak protein-protein interaction in a charged aqueous droplet?

Maintaining the interface of a weak transient protein complex transferred from bulk solution to the gaseous state via evaporating droplets is a critical question in the detection of the complex association (dissociation) constant by using electrospray ionization mass spectrometry (ESI-MS). Here we explore the factors that may affect the stability of a protein-protein interaction (PPI) using atomistic molecular dynamics (MD) modelling of a complex of ubiquitin (Ub) and the ubiquitin-associated domain (UbA) (RCSB PDB code ) and a non-covalent complex of diubiquitin (RCSB PDB code ) in aqueous droplets. A general method is presented to determine the protonation states of the complexes we investigate in particular, and that of a protein in general, under various pH conditions that an evaporating droplet acquires due to its change in size. We find that the combination of high temperature and high charge states of the protein complexes may destabilize the interface by creating new interfaces instead of a direct rupture of the initial stable interface. We provide evidence that highly charged protein complexes are found in droplets that form conical extrusions of the solvent on the surface due to charge-induced instability. This distinct droplet morphology leads to a higher solvent evaporation rate that assists in transferring the complex in the gaseous state without dissociation. The conical solvent protrusions expose on the droplet surface certain amino acids that otherwise would be solvated in a droplet with the protein complex of low charge states. The new vapor-protein interface does not have a direct effect on the stability of the PPI. A common way in experiments to stabilize the protein complexes in droplets is to reduce the protonation state of the proteins. Here we find that weakly bound protein complexes even at high protonation states can be stabilized by the presence of a small number of counterions, without affecting the protonation state of the protein. Our findings may provide guiding principles in ESI-MS experiments to stabilize weak transient PPIs.

Letter: Supermetallization of peptides and proteins with tetravalent metal Th(IV)

Supermetallization is the recently observed phenomenon of the formation of complex ions of peptide-metal in the gas phase when the peptide accepts an unexpectedly large number of metal atoms. It has been found that supermetallization takes place during electrospray ionization when charged droplets are evaporating at relatively high temperature (ca 400°C). In the present paper, we demonstrate supermetallized complexes of small protein ubiquitin and two peptides with Th(IV). We have observed complexes of ubiquitin with up to five thorium atoms, and attaching each Th(IV) requires the removal of four hydrogen atoms. To our knowledge, this is the first demonstration of gas-phase complexes of peptides and proteins with tetravalent metal atoms..

Effect of adduct formation with molecular nitrogen on the measured collisional cross sections of transition metal-1,10-phenanthroline complexes in traveling wave ion-mobility spectrometry: N2 is not always an "inert" buffer gas

The number of separations and analyses of molecular species using traveling wave ion-mobility spectrometry-mass spectrometry (TWIMS-MS) is increasing, including those extending the technique to analytes containing metal atoms. A critical aspect of such applications of TWIMS-MS is the validity of the collisional cross sections (CCSs) measured and whether they can be accurately calibrated against other ion-mobility spectrometry (IMS) techniques. Many metal containing species have potential reactivity toward molecular nitrogen, which is present in high concentration in the typical Synapt-G2 TWIMS cell. Here, we analyze the effect of nitrogen on the drift time of a series of cationic 1,10-phenanthroline complexes of the late transition metals, [(phen)M](+), (M = Ni, Pd, Pt, Cu, Ag, Au, Zn, Cd, and Hg) in order to understand potential deviations from expected drift time behaviors. These metal complexes were chosen for their metal open-coordination site and lack of rotameric species. The target species were generated via electrospray ionization (ESI), analyzed using TWIMS in N2 drift gas, and the observed drift time trends compared. Theoretically derived CCSs for all species (via both the projection approximation and trajectory method) were also compared. The results show that, indeed, for metal containing species in this size regime, reaction with molecular nitrogen has a dramatic effect on measured drift times and must not be ignored when comparing and interpreting TWIMS arrival time distributions. Density-functional theory (DFT) calculations are employed to analyze the periodic differences due to the metal's interaction with nitrogen (and background water) in detail.

Effects of cations on protein and peptide charging in electrospray ionization from aqueous solutions

The effects of eight different cations with ionic radii between 69 and 337 pm on the charging of peptides and proteins with electrospray ionization from aqueous acetate salt solutions are reported. Significant adduction occurs for all cations except NH4(+), and the average protein charge is lower when formed from solutions containing salts compared with solutions without salts added. Circular dichroism and ion mobility results show the protein conformations are different in pure water compared with salt solutions, which likely affects the extent of charging. The average charge of protein and peptide ions formed from solutions with Li(+) and Cs(+), which have Gibbs solvation free energies (GSFEs) that differ by 225 kJ/mol, is similar. Lower charge states are typically formed from solutions with tetramethylammonium and tetraethylammonium that have lower GSFE values. Loss of the larger cations that have the lowest GSFEs is facile when adducted protein ions are collisionally activated, resulting in the formation of lower analyte charge states. This reaction pathway provides a route to produce abundant singly protonated protein ions under native mass spectrometry conditions. The average protein and peptide charge with NH4(+) is nearly the same as that with Rb(+) and K(+), cations with similar GSFE and ionic radii. This indicates that proton transfer from NH4(+) to proteins plays an insignificant role in the extent of protein charging in native mass spectrometry.

Cation-induced stabilization of protein complexes in the gas phase: mechanistic insights from hemoglobin dissociation studies

Collision-induced dissociation (CID) of electrosprayed protein complexes usually involves asymmetric charge partitioning, where a single unfolded chain gets ejected that carries a disproportionately large fraction of charge. Using hemoglobin (Hb) tetramers as model system, we confirm earlier reports that bound metal ions can stabilize protein complexes under CID conditions. We examine the mechanism underlying this effect. Nonvolatile salts cause extensive adduct formation. Significant stabilization was observed for Mg(2+) and Ca(2+), whereas K(+), Rb(+), and Cs(+) had no effect. Precursor ion selection was used to examine Hb subpopulations with well-defined metal binding levels. K(+), Rb(+), and Cs(+)-adducted tetramers eject monomers that carry roughly one-quarter of the metal ions that were bound to the precursor. This demonstrates that charge migration during CID is exclusively due to proton transfer, not metal ion transfer. Also, replacement of highly mobile charge carriers (protons) with less mobile species (metal ions) does not exert a stabilizing influence under the conditions used here. Interestingly, Hb carrying stabilizing ions (Mg(2+) and Ca(2+)) generates monomeric CID products that are metal depleted. This effect is attributed to a combination of two factors: (1) Me(2+) binding stabilizes Hb via formation of chelation bridges (e.g., R-COO(-) Me(2+) (-)OOC-R); the more Me(2+) a subunit contains the more stable it is. (2) More than ~90% of the tetramers contain at least one subunit with a below-average number of Me(2+). The prevalence of monomeric CID products with depleted Me(2+) levels is caused by the tendency of these low metal-containing subunits to undergo preferential unfolding/ejection.