What happens to hydrophobic interactions during transfer from the solution to the gas phase? The case of electrospray-based soft ionization methods

Noncovalent Host-Guest Complexes of Artemisinin with α-, β-, and γ- Cyclodextrin Examined by Structural Mass Spectrometry Strategies

Cyclodextrins (CDs) are a family of macrocyclic oligosaccharides with amphiphilic properties, which can improve the stability, solubility, and bioavailability of therapeutic compounds. There has been growing interest in the advancement of efficient and reliable analytical methods that assist with elucidating CD host-guest drug complexation. In this study, we investigate the noncovalent ion complexes formed between naturally occurring dextrins (αCD, βCD, γCD, and maltohexaose) with the poorly water-soluble antimalarial drug, artemisinin, using a combination of ion mobility-mass spectrometry (IM-MS), tandem MS/MS, and theoretical modeling approaches. This study aims to determine if the drug can complex within the core dextrin cavity forming an inclusion complex or nonspecifically bind to the periphery of the dextrins. We explore the use of group I alkali earth metal additives to promote the formation of various noncovalent gas-phase ion complexes with different drug/dextrin stoichiometries (1:1, 1:2, 1:3, 1:4, and 2:1). Broad IM-MS collision cross section (CCS) mapping (n > 300) and power-law regression analysis were used to confirm the stoichiometric assignments. The 1:1 drug:αCD and drug:βCD complexes exhibited strong preferences for Li+ and Na+ charge carriers, whereas drug:γCD complexes preferred forming adducts with the larger alkali metals, K⁺, Rb⁺, and Cs⁺. Although the ion-measured CCS increased with cation size for the unbound artemisinin and CDs, the 1:1 drug:dextrin complexes exhibit near-identical CCS values regardless of the cation, suggesting these are inclusion complexes. Tandem MS/MS survival yield curves of the [artemisinin:βCD + X]⁺ ion (X = H, Li, Na, K) showed a decreased stability of the ion complex with increasing cation size. Empirical CCS measurements of the [artemisinin:βCD + Li]⁺ ion correlated with predicted CCS values from the low-energy theoretical structures of the drug incorporated within the βCD cavity, providing further evidence that gas-phase inclusion complexes are formed in these experiments. Taken together, this work demonstrates the utility of combining analytical information from IM-MS, MS/MS, and computational approaches in interpreting the presence of gas-phase inclusion phenomena.

Stabilization of Labile Lysozyme-Ligand Interactions in Native Electrospray Ionization Mass Spectrometry

Flavonoids are polyphenolic secondary metabolites with extensive biological activities and pharmacological effects. Exploring the interactions of flavonoids with proteins may be helpful for understanding their biological processes. Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool to characterize the noncovalent protein-ligand (PL) complexes. However, some protein-flavonoid complexes are labile during electrospray ionization. Here, the labile lysozyme-flavonoid (rutin, icariin, and naringin) complexes were determined by direct ESI-MS without derivation. It has been found that low amounts of N-methylpyrrolidinone and dimethylformamide can protect labile lysozyme-flavonoid complexes away from dissociation during electrospray ionization process. The intact lysozyme-flavonoid complexes were specifically observed in mass spectra, and the measured binding affinities by ESI-MS were matched with the fluorescence data. The effects of additives on the analysis of lysozyme-flavonoid complexes were investigated by ESI-MS, combined with the molecular docking and fluorescence. This strategy was helpful to investigate the labile PL interactions by direct ESI-MS.

Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences

Machine learning with multi-layered artificial neural networks, also known as "deep learning," is effective for making biological predictions. However, model interpretation is challenging, especially for sequential input data used with recurrent neural network architectures. Here, we introduce a framework called "Positional SHAP" (PoSHAP) to interpret models trained from biological sequences by utilizing SHapely Additive exPlanations (SHAP) to generate positional model interpretations. We demonstrate this using three long short-term memory (LSTM) regression models that predict peptide properties, including binding affinity to major histocompatibility complexes (MHC), and collisional cross section (CCS) measured by ion mobility spectrometry. Interpretation of these models with PoSHAP reproduced MHC class I (rhesus macaque Mamu-A1*001 and human A*11:01) peptide binding motifs, reflected known properties of peptide CCS, and provided new insights into interpositional dependencies of amino acid interactions. PoSHAP should have widespread utility for interpreting a variety of models trained from biological sequences.

Mass Spectrometric Evaluation of β-Cyclodextrins as Potential Hosts for Titanocene Dichloride

Bent metallocene dichlorides (Cp₂MCl₂, M = Ti, Mo, Nb, …) have found interest as anti-cancer drugs in order to overcome the drawbacks associated with platinum-based therapeutics. However, they suffer from poor hydrolytic stability at physiological pH. A promising approach to improve their hydrolytic stability is the formation of host-guest complexes with macrocyclic structures, such as cyclodextrins. In this work, we utilized nanoelectrospray ionization tandem mass spectrometry to probe the interaction of titanocene dichloride with β-cyclodextrin. Unlike the non-covalent binding of phenylalanine and oxaliplatin to β-cyclodextrin, the mixture of titanocene and β-cyclodextrin led to signals assigned as [βCD + Cp₂Ti–H]⁺, indicating a covalent character of the interaction. This finding is supported by titanated cyclodextrin fragment ions occurring from collisional activation. Employing di- and trimethylated β-cyclodextrins as hosts enabled the elucidation of the influence of the cyclodextrin hydroxy groups on the interaction with guest structures. Masking of the hydroxy groups was found to impair the covalent interaction and enabling the encapsulation of the guest structure within the hydrophobic cavity of the cyclodextrin. Findings are further supported by breakdown curves obtained by gas-phase dissociation of the various complexes.

Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry

Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.

Study of the noncovalent interactions between phenolic acid and lysozyme by cold spray ionization mass spectrometry (CSI-MS), multi-spectroscopic and molecular docking approaches

Elucidating the recognition mechanisms of the noncovalent interactions between pharmaceutical molecules and proteins is important for understanding drug delivery in vivo, and for the further rapid screening of clinical drug candidates and biomarkers. In this work, a strategy based on cold spray ionization mass spectrometry (CSI-MS), combined with fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR), and molecular docking methods, was developed and applied to the study of the noncovalent interactions between phenolic acid and lysozyme (Lys). Based on the real characterization of noncovalent complex, the detailed binding parameters, as well as the protein conformational changes and specific binding sites could be obtained. CSI-MS and tandem mass spectrometry (MS/MS) technique were used to investigate the phenolic acid-Lys complexes and the structure-affinity relationship, and to assess their structural composition and gas phase stability. The binding affinity was obtained by direct and indirect MS methods. The fluorescence spectra showed that the intrinsic fluorescence quenching of Lys in solution was a static quenching mechanism caused by complex formation, which supported the MS results. The CD and FTIR spectra revealed that phenolic acid changed the secondary structure of Lys and increased the α-helix content, indicating an increase in the tryptophan (W) hydrophobicity near the protein binding site resulting in a conformational alteration of the protein. In addition, molecular docking studies were performed to investigate the binding sites and binding modes of phenolic acid on Lys. This strategy can more comprehensively and truly characterize the noncovalent interactions and can guide further research on the interactions of phenolic acid with other proteins.

Experimental Insights into the Electronic Nature, Spectral Features, and Role of Entropy in Short CH3···CH3 Hydrophobic Interactions

Hydrophobic interactions are often explored in solution-state aggregation of molecules. However, an experimental electron density description about these interactions is still lacking. Here, we report a systematic study on the electronic nature of methyl···methyl hydrophobic interactions in a series of multicomponent crystals of biologically active molecules. Charge density models based on high-resolution X-ray diffraction allow the visualization of subtle details of electron density features in the interaction region. Our study classifies these interactions as atypical group···group interactions in contrast to σ-hole interactions, which are stabilized by the minimized electrostatic repulsion and maximized dispersion forces. For the first time, we quantified the solid-state entropic contribution from the torsional mode of the methyl groups in stabilizing these interactions by thermal motion analysis based on neutron diffraction as well as variable-temperature crystallography. The carbon atoms in methyl···methyl interactions show a unique upfield chemical shift in the ¹³C solid-state NMR signal.

Gas-Phase Fragmentation of Cyclic Oligosaccharides in Tandem Mass Spectrometry

Modern mass spectrometry, including electrospray and MALDI, is applied for analysis and structure elucidation of carbohydrates. Cyclic oligosaccharides isolated from different sources (bacteria and plants) have been known for decades and some of them (cyclodextrins and their derivatives) are widely used in drug design, as food additives, in the construction of nanomaterials, etc. The peculiarities of the first- and second-order mass spectra of cyclic oligosaccharides (natural, synthetic and their derivatives and modifications: cyclodextrins, cycloglucans, cyclofructans, cyclooligoglucosamines, etc.) are discussed in this minireview.

Mass Spectrometry as a Complementary Approach for Noncovalently Bound Complexes Based on Cyclodextrins

An important and well-designed solution to overcome some of the problems associated with new drugs is provided by the molecular encapsulation of the drugs in the cyclodextrins (CDs) cavity, yielding corresponding inclusion complexes (ICs). These types of non-covalent complexes are of current interest to the pharmaceutical industry, as they improve the solubility, stability and bioavailability of the guest molecules. This review highlights several methods for cyclodextrin ICs preparation and characterization, focusing mostly on the mass spectrometry (MS) studies that have been used for the detection of noncovalent interactions of CDs inclusion complexes and binding selectivity of guest molecules with CDs. Furthermore, the MS investigations of several ICs of the CD with antifungal, antioxidants or fluorescent dyes are presented in greater details, pointing out the difficulties overcome in the analysis of this type of compounds.

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.

Stability of a Transient Protein Complex in a Charged Aqueous Droplet with Variable pH

Electrospray ionization mass spectrometry (ESI-MS) has the potential to become a high-throughput robust experimental method for the detection of protein-protein equilibrium constants. Poorly understood processes that affect the stability of weak noncovalent protein complexes in the intervening droplet environment are a significant factor that precludes the advancement of the method. We use molecular dynamics to study the stability of a ubiquitin and ubiquitin-associated domain complex (RCSB PDB code 2MRO ) in an aqueous droplet with changing size and charge concentration. We present evidence that a weak protein complex changes conformation and may dissociate in shrinking droplets. Then, the droplets containing these dissociated proteins divide. Our findings suggest that in some cases ESI-MS does not measure the correct association constants. The study intends to stimulate research for systematic development of experimental protocols that stabilize weakly bound protein interfaces in droplets.

Ionization characteristics of glycosides by direct analysis in real time quadrupole-time of flight mass spectrometry

Glycosides were ionized via various different reactions including (de)protonation, molecular ion formation, ISD fragmentation, and the formation of adducts.

Native Mass Spectrometry for the Characterization of Structure and Interactions of Membrane Proteins

Over the past years, native mass spectrometry and ion mobility have grown into techniques that are widely applicable to the study of aspects of protein structure. More recently, it has become apparent that this approach provides a very promising avenue for the investigation of integral membrane proteins in lipid or detergent environments.In this chapter, we discuss applications of native mass spectrometry and ion mobility in membrane protein research-what is important to take into consideration when working with membrane proteins, and what the requirements are for sample preparation for native mass spectrometry. Furthermore, we will discuss the types of information provided by the measurements, including the oligomeric state, subunit composition and stoichiometry, interactions with detergents or lipids, conformational transitions, and the binding and structural effect of ligands and drugs.

Understanding carbohydrate-protein interactions using homologous supramolecular chiral Ru(ii)-glyconanoclusters

Multivalent glycodendrimers make promising tools to tackle the basic and translational research in the field of carbohydrate-mediated interactions. Despite advances in glycodendrimers and glycopolymers, the multivalent probes available to date are still far from being ideal biological mimics. This work demonstrates the inherent chirality of glycodendrimers to be one of the promising factors to generate different spatial carbohydrate micro-environments to modulate specific carbohydrate-protein interactions. By exploiting the host-guest strategy, chiral Ru(ii) complexes (Δ and Λ) and mannose capped β-cyclodextrin (β-CD), we generated a library of homologous metallo-glycodendrimers (MGDs) with sizes of 50-70 nm. These nanoclusters can enantioselectively bind to specific C-type lectins and displayed selectivity in cellular uptake. We also discovered their potential clathrin-mediated endocytotic pathway in DC-SIGN and SIGNR3-transfected cell lines. Finally, in vivo biodistribution and sequestration of MGDs was determined to understand the role of chirality mediated spatial arrangement in carbohydrate-mediated interactions.

Probing the common alkali metal affinity of native and variously methylated β-cyclodextrins by combining electrospray-tandem mass spectrometry and molecular modeling

In the study herein, we investigated the solution and gas phase affinity of native and variously methylated β-cyclodextrins (CDs) as hosts towards three common alkali metals as guests namely lithium, sodium and potassium. For this purpose, two complementary approaches have been employed: electrospray-tandem mass spectrometry (ESI-MS/MS) with two energetic regimes: Collision Induced Dissociation (CID) and Higher Collision Dissociation (HCD), respectively, and DFT molecular modeling. These approaches have been achieved by taking into account the interaction of either one or two alkali metals with the host molecules. The results showed a good agreement between experimental and theoretical data. It was demonstrated that increasing the methylation degree strengthened the gas phase affinity towards all studied alkali metals. Furthermore, it was established that the cation selectivity was Na(+) > Li(+) > K(+) and Li(+) > Na(+) > K(+) for the solution and gas phase, respectively.

Differentiation of Disaccharide Isomers by Temperature-Dependent In-Source Decay (TDISD) and DART-Q-TOF MS/MS

Helium direct analysis in real time (He-DART) mass spectrometry (MS) of some compounds, polysaccharides, for example, usually tends to be challenging because of the occurrence of prominent in-source decay (ISD), which was considered as an undesired side reaction, as it complicated the resulting mass spectra. Our approach is to take advantage of an efficient and practical method termed the temperature-dependent ISD (TDISD) technique combined with fragmentation of the dehydrated dimers using DART Q-TOF tandem mass spectrometry for differentiation of disaccharide isomers. In this study, cross-ring cleavages and non-ovalent complexes were detected in the spectra of the saccharides. It was observed that the gas heater temperature had a significant effect on the absence or presence of signal in DART spectra. At high gas temperature, ions in high mass region began to appear. Based on the types of cross-ring cleavages and noncovalent complexes, disaccharide isomers with different linkage positions can be differentiated in both positive and negative ion modes at a lower DART gas temperature. Additionally, anomeric configurations were assigned on the basis of the relative abundance ratio of m/z 198:342 obtained by the comparison of the positive ion mode tandem mass spectrum of an α isomer dimer generated at higher DART gas temperature and that of the corresponding β one. In general, this method is easy, fast, effective, and robust for identifying disaccharide isomers.

Molecular basis for structural heterogeneity of an intrinsically disordered protein bound to a partner by combined ESI-IM-MS and modeling

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered N(TAIL) domain and the phosphoprotein X domain (P(XD)) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire N(TAIL) domain bound to P(XD) at atomic resolution.

How do non-covalent complexes dissociate in droplets? A case study of the desolvation of dsDNA from a charged aqueous nanodrop

We present the desolvation mechanism of a double-stranded oligodeoxynucleotide (dsDNA) from an aqueous nanodrop studied by using atomistic molecular dynamics methods.

Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins

Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.

Application of the Exactive Plus EMR for automated protein-ligand screening by non-covalent mass spectrometry

RATIONALE

Non-covalent mass spectrometry (MS) offers considerable potential for protein-ligand screening in drug discovery programmes. However, there are some limitations with the time-of-flight (TOF) instrumentation typically employed that restrict the application of non-covalent MS in industrial laboratories.

METHODS

An Exactive Plus EMR mass spectrometer was investigated for its ability to characterise non-covalent protein-small molecule interactions. Nano-electrospray ionisation (nanoESI) infusion was achieved with a TriVersa NanoMate. The transport multipole and ion lens voltages, dissociation energies and pressure in the Orbitrap™ were optimised. Native MS was performed, with ligand titrations to judge retention of protein-ligand interactions, serial dilutions of native proteins as an indication of sensitivity, and a heterogeneous protein analysed for spectral resolution.

RESULTS

Interactions between native proteins and ligands are preserved during analysis on the Exactive Plus EMR, with the binding affinities determined in good agreement with expected values. High spectral resolution allows baseline separation of adduct ions, which should improve the accuracy and limit of detection for measuring ligand interactions. Data are also presented showing baseline resolution of glycoforms of a highly glycosylated protein, allowing binding of a fragment molecule to be detected.

CONCLUSIONS

The high sensitivity and spectral resolution achievable with the Orbitrap technology confer significant advantages over TOF mass spectrometers, and offer a solution to current limitations regarding throughput, data analysis and sample requirements. A further benefit of improved spectral resolution is the possibility of using heterogeneous protein samples such as glycoproteins for fragment screening. This would significantly expand the scope of applicability of non-covalent MS in the pharmaceutical and other industries.

Inclusion complexes of ionic liquids and cyclodextrins: are they formed in the gas phase?

The interaction of imidazolium-based ionic liquids with α- and β-cyclodextrins was investigated by electrospray ionization mass spectrometry with variable collision induced dissociation energy and quantum chemical gas-phase calculations. The center-of-mass energy at which 50% of a precursor ion decomposes (Ecm,1/2) was determined for the isolated [cyclodextrin + cation](+) or [cyclodextrin + anion](-) adduct ions of imidazolium-based ionic liquids with different alkyl chain lengths combined with a large set of anions, such as chloride, bromide, bis(trifluoromethylsulfonyl)imide, tetrafluoroborate, hexafluorophosphate, trifluoromethanesulfonate, methanesulfonate, dicyanamide, and hydrogensulfate. Moreover, both symmetric and asymmetric imidazolium cationic cores were evaluated. The relative interaction energies in the adduct ions were interpreted in terms of the influence of cation/anion structures and their inherent properties, such as hydrophobicity and hydrogen bond accepting ability, in the complexation process with the cyclodextrins. The trends observed in the mass spectral data together with quantum-chemical calculations suggest that in the gas phase, cations and anions will preferentially interact with the lower or upper rim of the cyclodextrin, respectively, as opposed to what has been reported in condensed phase where the formation of an inclusion complex between ionic liquid and cyclodextrin is assumed.

Quantifying protein-ligand binding constants using electrospray ionization mass spectrometry: a systematic binding affinity study of a series of hydrophobically modified trypsin inhibitors

NanoESI-MS is used for determining binding strengths of trypsin in complex with two different series of five congeneric inhibitors, whose binding affinity in solution depends on the size of the P3 substituent. The ligands of the first series contain a 4-amidinobenzylamide as P1 residue, and form a tight complex with trypsin. The inhibitors of the second series have a 2-aminomethyl-5-chloro-benzylamide as P1 group, and represent a model system for weak binders. The five different inhibitors of each group are based on the same scaffold and differ only in the length of the hydrophobic side chain of their P3 residue, which modulates the interactions in the S3/4 binding pocket of trypsin. The dissociation constants (K(D)) for high affinity ligands investigated by nanoESI-MS ranges from 15 nM to 450 nM and decreases with larger hydrophobic P3 side chains. Collision-induced dissociation (CID) experiments of five trypsin and benzamidine-based complexes show a correlation between trends in K(D) and gas-phase stability. For the second inhibitor series we could show that the effect of imidazole, a small stabilizing additive, can avoid the dissociation of the complex ions and as a result increases the relative abundance of weakly bound complexes. Here the K(D) values ranging from 2.9 to 17.6 μM, some 1-2 orders of magnitude lower than the first series. For both ligand series, the dissociation constants (K(D)) measured via nanoESI-MS were compared with kinetic inhibition constants (K(i)) in solution.

Solution and gas-phase H/D exchange of protein-small-molecule complexes: Cex and its inhibitors

The properties of noncovalent complexes of the enzyme exo-1,4-β-D-glycanase ("Cex") with three aza-sugar inhibitors, deoxynojirimycin (X(2)DNJ), isofagomine lactam (X(2)IL), and isofagomine (X(2)IF), have been studied with solution and gas-phase hydrogen deuterium exchange (H/Dx) and measurements of collision cross sections of gas-phase ions. In solution, complexes have lower H/Dx levels than free Cex because binding the inhibitors blocks some sites from H/Dx and reduces fluctuations of the protein. In mass spectra of complexes, abundant Cex ions are seen, which mostly are formed by dissociation of complexes in the ion sampling interface. Both complex ions and Cex ions formed from a solution containing complexes have lower cross sections than Cex ions from a solution of Cex alone. This suggests the Cex ions formed by dissociation "remember" their solution conformations. For a given charge, ions of the complexes have greater gas-phase H/Dx levels than ions of Cex. Unlike cross sections, H/Dx levels of the complexes do not correlate with the relative gas-phase binding strengths measured by MS/MS. Cex ions from solutions with or without inhibitors, which have different cross sections, show the same H/Dx level after 15 s, indicating the ions may fold or unfold on the seconds time scale of the H/Dx experiment. Thus, cross sections show that complexes have more compact conformations than free protein ions on the time scale of ca. 1 ms. The gas-phase H/Dx measurements show that at least some complexes retain different conformations from the Cex ions on a time scale of seconds.

Alkali metal cation-induced destabilization of gas-phase protein-ligand complexes: consequences and prevention

Electrospray ionization, now a well established technique for studying noncovalent protein-ligand interactions, is prone to production of alkali metal adducts. Here it is shown that this adduction significantly destabilizes the interactions between two model proteins and their ligands and that destabilization correlates with cation size. For both the [FKBP·FK506] and [lysozyme·NAG(n)] systems, dissociation of the metalated complex occurs at markedly lower collision energies than their purely protonated equivalents. Dependency upon size of the metal(+) demonstrates the importance of electrostatic charge density during the dissociation process. Differences in the gas phase basicities (GBapp) of the multiply charged protein ions and proton and sodium affinities of the ligands explain the observed charge partitioning during dissociation of the complexes. Ion mobility-mass spectrometry measurements demonstrate that metal cation adduction does not induce a significant increase in unfolding of the polypeptides, indicating that this is not the principal mechanism responsible for destabilization. Destabilizing effects can be largely reduced by exposing the electrospray to solvent (e.g., acetonitrile) vapor, a method that acts to reduce the amount of adduct formation as well as decrease the charge states of the resulting ions. This approach leads to more accurate determination of apparent K(D)s in the presence of trace alkali metals.