A study of peptide-peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry

Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation

Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.

The inorganic polymer, polyphosphate, blocks binding of SARS-CoV-2 spike protein to ACE2 receptor at physiological concentrations

Inorganic polyphosphate (polyP) is a morphogenetically active and metabolic energy-delivering physiological polymer that is released from blood platelets. Here, we show that polyP efficiently inhibits the binding of the envelope spike (S)-protein of the coronavirus SARS-CoV-2, the causative agent of COVID-19, to its host cell receptor ACE2 (angiotensin-converting enzyme 2). To stabilize polyP against the polyP-degrading alkaline phosphatase, the soluble polymer was encapsulated in silica/polyP nanoparticles. Applying a binding assay, soluble Na-polyP (sizes of 40 P_i and of 3 P_i units) as well as silica-nanoparticle-associated polyP significantly inhibit the interaction of the S-protein with ACE2 at a concentration of 1 µg/mL, close to the level present in blood. This inhibition is attributed to an interaction of polyP with a basic amino acid stretch on the surface of the receptor binding domain of S-protein. PolyP retains its activity in a flushing solution, opening a new strategy for the prevention and treatment of SARS-CoV-2 infection in the oropharyngeal cavity. The data suggest that supplementation of polyP might contribute to a strengthening of the human innate immunity system in compromised, thrombocytopenic COVID-19 patients.

On the Preservation of Non-covalent Peptide Assemblies in a Tandem-Trapped Ion Mobility Spectrometer-Mass Spectrometer (TIMS-TIMS-MS)

Ion mobility spectrometry-mass spectrometry (IMS-MS) has demonstrated the ability to characterize structures of weakly-bound peptide assemblies. However, these assemblies can potentially dissociate during the IMS-MS measurement if they undergo energetic ion-neutral collisions. Here, we investigate the ability of tandem-trapped ion mobility spectrometry-mass spectrometry (TIMS-TIMS-MS) to retain weakly-bound peptide assemblies. We assess ion heating and dissociaton in the tandem-TIMS instrument using bradykinin and its assemblies as reference systems. Our data indicate that non-covalent bradykinin assemblies are largely preserved in TIMS-TIMS under carefully selected operating conditions. Importantly, we observe quadruply-charged bradykinin tetramers, which attests to the "softness" of our instrument. Graphical Abstract.

Histidine, the less interactive cousin of arginine

Electrostatic interactions are one of the main factors influencing biomolecular conformation. The formation of noncovalent complexes by electrostatic interactions is governed by certain amino acid residues and post-translational modifications. It has been demonstrated that adjacent arginine forms noncovalent complex with phosphate; however, histidine noncovalent complexes have rarely been investigated. In the present work, we compare the interaction between basic epitopes (NLRRITRVN, SHHGLHSTPD) and diverse acidic and aromatic-rich peptides using both MALDI and ESI Mass spectrometry. We show that adjacent histidines can also form stable noncovalent bonds and that those bonds are probably formed by a salt bridge between the phosphate or the acid residues and the histidines. However, noncovalent complexes with the arginine epitopes form more readily and are stronger than those with histidine-containing epitopes.

An Electrospray Ionization Mass Spectrometry Study on the "In Vacuo" Hetero-Oligomers Formed by the Antimicrobial Peptides, Surfactin and Gramicidin S

It was previously observed that the lipopeptide surfactants in surfactin (Srf) have an antagonistic action towards the highly potent antimicrobial cyclodecapeptide, gramicidin S (GS). This study reports on some of the molecular aspects of the antagonism as investigated through complementary electrospray ionization mass spectrometry techniques. We were able to detect stable 1:1 and 2:1 hetero-oligomers in a mixture of surfactin and gramicidin S. The noncovalent interaction between GS and Srf, with the proposed equilibrium: GS~Srf↔GS+Srf correlated to apparent K _d values of 6-9 μM in gas-phase and 1 μM in aqueous solution. The apparent K _d values decreased with a longer incubation time and indicated a slow oligomerization equilibrium. Furthermore, the low μM K _d^app values of GS~Srf↔GS+Srf fell within the biological concentration range and related to the 2- to 3-fold increase in [GS] needed for bacterial growth inhibition in the presence of Srf. Competition studies indicated that neither Na⁺ nor Ca²⁺ had a major effect on the stability of preformed heterodimers and that GS in fact out-competed Ca²⁺ and Na⁺ from Srf. Traveling wave ion mobility mass spectrometry revealed near symmetrical peaks of the heterodimers correlating to a compact dimer conformation that depend on specific interactions. Collision-induced dissociation studies indicated that the peptide interaction is most probably between one Orn residue in GS and the Asp residue, but not the Glu residue in Srf. We propose that flanking hydrophobic residues in both peptides stabilize the antagonistic and inactive peptide hetero-oligomers and shield the specific polar interactions in an aqueous environment. Graphical Abstract ᅟ.

ETD and sequential ETD localize the residues involved in D2-A2A heteromerization

ETD²to identify binding site in NCX.

MALDI/post ionization-ion mobility mass spectrometry of noncovalent complexes of dopamine receptors' epitopes

Protein domains involved in receptor heteromer formation are disordered and rich in the amino acids necessary for the formation of noncovalent complexes (NCX). We present mass spectral NCX data from proteins and protein receptors' epitopes obtained by combining ion mobility (IM) and MALDI. We focus on NCX involved in heteromer formation occurring between epitopes of the Dopamine D2 (D2R) and Adenosine A2A receptors (A2AR) as well as D2R and the α2 nicotinic (NR) receptor's subunit. The IM data yield information on the gas phase conformation of the singly charged NCX which are observed either directly from MALDI or as codesorbed neutrals that are subsequently postionized by a time-delayed excimer laser pulse directed onto a portion of the neutral plume created by the MALDI desorption laser. Imaging mass spectrometry of the matrix/epitope dried droplet surface shows that the acidic and basic epitopes and their NCX are found to be spatially collocated within regions as small as 25 × 50 μm(2). Subtle differences in the relative abundance of protonated and cationized NCX and epitopes are measured in spatial regions near the sodium-rich outer border of the droplet.

Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.

Neuronal metabolomics by ion mobility mass spectrometry: cocaine effects on glucose and selected biogenic amine metabolites in the frontal cortex, striatum, and thalamus of the rat

We report results of studies of global and targeted neuronal metabolomes by ambient pressure ion mobility mass spectrometry. The rat frontal cortex, striatum, and thalamus were sampled from control nontreated rats and those treated with acute cocaine or pargyline. Quantitative evaluations were made by standard additions or isotopic dilution. The mass detection limit was ~100 pmol varying with the analyte. Targeted metabolites of dopamine, serotonin, and glucose followed the rank order of distribution expected between the anatomical areas. Data was evaluated by principal component analysis on 764 common metabolites (identified by m/z and reduced mobility). Differences between anatomical areas and treatment groups were observed for 53 % of these metabolites using principal component analysis. Global and targeted metabolic differences were observed between the three anatomical areas with contralateral differences between some areas. Following drug treatments, global and targeted metabolomes were found to shift relative to controls and still maintained anatomical differences. Pargyline reduced 3,4-dihydroxyphenylacetic acid below detection limits, and 5-HIAA varied between anatomical regions. Notable findings were: (1) global metabolomes were different between anatomical areas and were altered by acute cocaine providing a broad but targeted window of discovery for metabolic changes produced by drugs of abuse; (2) quantitative analysis was demonstrated using isotope dilution and standard addition; (3) cocaine changed glucose and biogenic amine metabolism in the anatomical areas tested; and (4) the largest effect of cocaine was on the glycolysis metabolome in the thalamus confirming inferences from previous positron emission tomography studies using 2-deoxyglucose.

Cellular membrane phospholipids act as a depository for quaternary amine containing drugs thus competing with the acetylcholine/nicotinic receptor

We previously demonstrated that ammonium- or guanidinium-phosphate interactions are key to forming noncovalent complexes (NCXs) through salt bridge formation with G-protein coupled receptors (GPCR), which are immersed in the cell membrane's lipids. The present work highlights MALDI ion mobility coupled to orthogonal time-of-flight mass spectrometry (MALDI IM oTOF MS) as a method to determine qualitative and relative quantitative affinity of drugs to form NCXs with targeted GPCRs' epitopes in a model system using, bis-quaternary amine based drugs, α- and β- subunit epitopes of the nicotinic acetylcholine receptor' (nAChR) and phospholipids. Bis-quaternary amines proved to have a strong affinity for all nAChR epitopes and negatively charged phospholipids, even in the presence of the physiological neurotransmitter acetylcholine. Ion mobility baseline separated isobaric phosphatidyl ethanolamine and a matrix cluster, providing an accurate estimate for phospholipid counts. Overall this technique is a powerful method for screening drugs' interactions with targeted lipids and protein respectively containing quaternary amines and guanidinium moieties.

Unraveling the early events of amyloid-β protein (Aβ) aggregation: techniques for the determination of Aβ aggregate size

The aggregation of proteins into insoluble amyloid fibrils coincides with the onset of numerous diseases. An array of techniques is available to study the different stages of the amyloid aggregation process. Recently, emphasis has been placed upon the analysis of oligomeric amyloid species, which have been hypothesized to play a key role in disease progression. This paper reviews techniques utilized to study aggregation of the amyloid-β protein (Aβ) associated with Alzheimer's disease. In particular, the review focuses on techniques that provide information about the size or quantity of oligomeric Aβ species formed during the early stages of aggregation, including native-PAGE, SDS-PAGE, Western blotting, capillary electrophoresis, mass spectrometry, fluorescence correlation spectroscopy, light scattering, size exclusion chromatography, centrifugation, enzyme-linked immunosorbent assay, and dot blotting.

MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.

Liquid phase ion mobility spectrometry

A novel analytical method, called Liquid Phase Ion Mobility Spectrometry (LiPIMS) was demonstrated, where aqueous phase analytes were ionized and introduced into non-aqueous liquids, transported by an external electric field from the point of generation to a collection electrode. Ions were produced from a unique liquid phase ionization process, called Electrodispersion Ionization. Spectra of analyte ions illustrated the potential of LiPIMS as a new separation technique. Experimental data showed that electrodispersion ionization was effective in generating nanoampere level of ion current in hexane and benzene from aqueous samples. By controlling the ionization voltage in relation to the sample flow rate, it was possible to operate the electrodispersion ionization source in both continuous and pulsed ionization modes. Unique LiPIMS spectra of aqueous samples of tetramethylammonium bromide, tetrabutylammonium bromide and bradykinin were presented and their respected liquid phase ion mobility values were determined.

Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source

Comprehensive metabolome analysis using mass spectrometry (MS) often results in a complex mass spectrum and difficult data analysis resulting from the signals of numerous small molecules in the metabolome. In addition, MS alone has difficulty measuring isobars and chiral, conformational and structural isomers. When a matrix-assisted laser desorption ionization (MALDI) source is added, the difficulty and complexity are further increased. Signal interference between analyte signals and matrix ion signals produced by MALDI in the low mass region (<1500 Da) cause detection and/or identification of metabolites difficult by MS alone. However, ion mobility spectrometry (IMS) coupled with MS (IM-MS) provides a rapid analytical tool for measuring subtle structural differences in chemicals. IMS separates gas-phase ions based on their size-to-charge ratio. This study, for the first time, reports the application of MALDI to the measurement of small molecules in a biological matrix by ion mobility-time of flight mass spectrometry (IM-TOFMS) and demonstrates the advantage of ion-signal dispersion in the second dimension. Qualitative comparisons between metabolic profiling of the Escherichia coli metabolome by MALDI-TOFMS, MALDI-IM-TOFMS and electrospray ionization (ESI)-IM-TOFMS are reported. Results demonstrate that mobility separation prior to mass analysis increases peak-capacity through added dimensionality in measurement. Mobility separation also allows detection of metabolites in the matrix-ion dominated low-mass range (m/z < 1500 Da) by separating matrix signals from non-matrix signals in mobility space.

Laser desorption/ionization mass spectrometric analysis of small molecules using fullerene-derivatized silica as energy-absorbing material

In spite of the growing acceptance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the analysis of a wide variety of compounds, including polymers and proteins, its use in analyzing low-molecular-weight molecules (<1000 m/z) is still limited. This is mainly due to the interference of matrix molecules in the low-mass range. Here the derivatized fullerenes covalently bound to silica particles with different pore sizes are applied as thin layer for laser desorption/ionization (LDI) mass spectrometric analysis. Thus, an interference of intrinsic matrix ions can be eliminated or minimized in comparison with the state-of-the-art weak organic acid matrices. The desorption/ionization ability of the developed fullerene-silica materials depends on the applied laser power, sample preparation and pore size of the silica particles. Thus, fullerene-silica serves as an LDI support for mass spectrometric analysis of molecules (<1500 Da). The performance of the fullerene-silica is demonstrated by the mass analysis of variety of small molecules such as carbohydrates, amino acids, peptides, phospholipids and drugs.

Characterizing ion mobility-mass spectrometry conformation space for the analysis of complex biological samples

The conformation space occupied by different classes of biomolecules measured by ion mobility-mass spectrometry (IM-MS) is described for utility in the characterization of complex biological samples. Although the qualitative separation of different classes of biomolecules on the basis of structure or collision cross section is known, there is relatively little quantitative cross-section information available for species apart from peptides. In this report, collision cross sections are measured for a large suite of biologically salient species, including oligonucleotides (n = 96), carbohydrates (n = 192), and lipids (n = 53), which are compared to reported values for peptides (n = 610). In general, signals for each class are highly correlated, and at a given mass, these correlations result in predicted collision cross sections that increase in the order oligonucleotides < carbohydrates < peptides < lipids. The specific correlations are described by logarithmic regressions, which best approximate the theoretical trend of increasing collision cross section as a function of increasing mass. A statistical treatment of the signals observed within each molecular class suggests that the breadth of conformation space occupied by each class increases in the order lipids < oligonucleotides < peptides < carbohydrates. The utility of conformation space analysis in the direct analysis of complex biological samples is described, both in the context of qualitative molecular class identification and in fine structure examination within a class. The latter is demonstrated in IM-MS separations of isobaric oligonucleotides, which are interpreted by molecular dynamics simulations.

Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges

Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H](5-) obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H](5-) ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug.

A study of phospholipids by ion mobility TOFMS

Combining matrix-assisted laser desorption/ionization (MALDI) mass spectrometry with ion mobility (IM) results in the fast sorting of biomolecules in complex mixtures along trend lines. In this two-dimensional (2D) analysis of biological families, lipids, peptides, and nucleotides are separated from each other by differences in their ion mobility drift times in a timescale of hundreds of microseconds. Molecular ions of similar chemical type fall along trend lines when plotted in 2D plots of ion mobility drift time as a function of m/z. In this study, MALDI-IM MS is used to analyze species from all of the major phospholipid classes. Complex samples, including tissue extracts and sections, were probed to demonstrate the effects that radyl chain length, degree of unsaturation, and class/head group have upon an ion's cross section in the gas phase. We illustrate how these changes can be used to identify individual lipid species in complex mixtures, as well as the effects of cationization on ion cross section and ionization efficiency.

How calmodulin interacts with the adenosine A(2A) and the dopamine D(2) receptors

Receptor heteromerization is a mechanism used by G protein-coupled receptors to diversify their properties and function. We previously demonstrated that these interactions occur through salt bridge formation between epitopes of the involved receptors. Recent studies claim that calmodulin (CaM) binds to an Arg-rich epitope located in the amino-terminus of the dopamine D(2) receptor third intracellular loop. This is the same epitope involved in adenosine A(2A)-D(2) receptor heteromerization, through Coulombic interaction between the Arg residues and a phosphorylated serine (pS) located in the medial segment of the C-terminus of the A(2A) receptor. Mass spectrometric analysis indicates that an electrostatic interaction involving the D(2) receptor Arg-rich epitope and several CaM acidic epitopes are mainly responsible for the D(2) receptor-CaM binding. CaM could also form multiple noncovalent complexes by means of electrostatic interactions with an epitope localized in the proximal segment of the C-terminus of the A(2A) receptor. Ca(2+) disrupted the binding of CaM to the D(2) but not to the A(2A) receptor epitope, and CaM disrupted the electrostatic interactions between the D(2) receptor epitope and the more distal A(2A) receptor epitope. A model is introduced with the possible functional implications of A(2A)-D(2)-CaM interactions. These in vitro findings imply a possible regulatory role for CaM in receptor heteromers formation.

Ion mobility-mass spectrometry

This review article compares and contrasts various types of ion mobility-mass spectrometers available today and describes their advantages for application to a wide range of analytes. Ion mobility spectrometry (IMS), when coupled with mass spectrometry, offers value-added data not possible from mass spectra alone. Separation of isomers, isobars, and conformers; reduction of chemical noise; and measurement of ion size are possible with the addition of ion mobility cells to mass spectrometers. In addition, structurally similar ions and ions of the same charge state can be separated into families of ions which appear along a unique mass-mobility correlation line. This review describes the four methods of ion mobility separation currently used with mass spectrometry. They are (1) drift-time ion mobility spectrometry (DTIMS), (2) aspiration ion mobility spectrometry (AIMS), (3) differential-mobility spectrometry (DMS) which is also called field-asymmetric waveform ion mobility spectrometry (FAIMS) and (4) traveling-wave ion mobility spectrometry (TWIMS). DTIMS provides the highest IMS resolving power and is the only IMS method which can directly measure collision cross-sections. AIMS is a low resolution mobility separation method but can monitor ions in a continuous manner. DMS and FAIMS offer continuous-ion monitoring capability as well as orthogonal ion mobility separation in which high-separation selectivity can be achieved. TWIMS is a novel method of IMS with a low resolving power but has good sensitivity and is well intergrated into a commercial mass spectrometer. One hundred and sixty references on ion mobility-mass spectrometry (IMMS) are provided.

Profiling and imaging of tissues by imaging ion mobility-mass spectrometry

Molecular profiling and imaging mass spectrometry (IMS) of tissues can often result in complex spectra that are difficult to interpret without additional information about specific signals. This report describes increasing data dimensionality in IMS by combining two-dimensional separations at each spatial location on the basis of imaging ion mobility-mass spectrometry (IM-MS). Analyte ions are separated on the basis of both ion-neutral collision cross section and m/z, which provides rapid separation of isobaric, but structurally distinct ions. The advantages of imaging using ion mobility prior to MS analysis are demonstrated for profiling of human glioma and selective lipid imaging from rat brain.

Sulfation, the up-and-coming post-translational modification: its role and mechanism in protein-protein interaction

Tyrosine sulfation is a post-translational modification entailing covalent attachment of sulfate to tyrosine residues. It takes place in the trans-Golgi, is necessary for the bioactivity of some proteins, and improves their ability to interact with other proteins. In the present work, we show that a protein containing a sulfated tyrosine with a delocalized negative charge forms a salt bridge with another protein if it has two or more adjacent arginine residues containing positive delocalized charges. These noncovalent complexes are so stable that, when submitted to collision induced dissociation, the peptides forming the complex dissociate. Just one covalent bond fragments, the covalent bond between the tyrosine oxygen and the SO3 sulfur, and is represented by the appearance of a new peak (basic peptide + SO3), suggesting that in some instances covalent bonds will break down before the noncovalent bonds between the arginine guanidinium and SO3 dissociate. The data implies that the dissociation pathway is preferred; however, fragmentation between tyrosine and the sulfate residue is a major pathway.

Localization of noncovalent complexes in MALDI-preparations by CLSM

The unambiguous detection of noncovalent complexes (NCCs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still a far cry from being routine. For protein NCCs such as their quaternary structure it has been reported that signals of the intact complex are only obtained for the first or at most the first few laser exposures of a given sample area. This observation was called the first-shot phenomenon. In the present study, this first-shot phenomenon has been investigated for the hexameric protein complex allophycocyanine (APC) by two independent methods, MALDI-MS with a (nearly) pH-neutral matrix 6-aza-2-thiothymine (6-ATT) and by imaging the fluorescence of the complex in APC-6-ATT preparations by confocal laser scan microscopy (CLSM). The intact APC heterohexamer loses its visible fluorescence upon dissociation into its subunits. Both methods consistently show that intact APC complexes are precipitated at the matrix crystal surface, but dissociate upon incorporation into the matrix crystals.

Phosphate stabilization of intermolecular interactions

Receptor heteromerization is an important phenomenon that results from the interaction of epitopes on two receptors. Previous studies have suggested the possibility of Dopamine D2-NMDA receptors' interaction. We believe that the interaction is through an acidic epitope of the NMDA NR1 subunit (KVNSEEEEEDA) and a basic epitope of the D2 third intracellular loop (VLRRRRKRVN), which was shown to also interact with the Adenosine A2A receptor. In previous work, we highlighted the role of certain amino acid residues, mainly two or more adjacent arginine on one peptide and two or more adjacent glutamate, or aspartate, or a phosphorylated residue on the other in the formation of noncovalent complexes (NCX) between epitopes. In the present work, we use the phosphorylated (KVNSpEEEEEDA), nonphosphorylated (KVNSEEEEEDA) and modified (KVNpSAAAAAAA) forms of the NMDA epitope that possibly interact with the D2 epitope to investigate the gas-phase stability of the NCXs as a function of the nominal energy given to the NCX ion as it enters the collision cell. In addition to theoretical calculations, the experimental data was used to calculate the stability of each electrostatic complex versus that of the dimer of KVNSpEEEEEDA. Our results demonstrate the importance of the phosphate group in stabilizing molecular interactions and that appreciably higher collision energies are required to completely dissociate any of the three different NCX ions that are formed through electrostatic interaction in comparison to the energy required to dissociate the KVNpSEEEEEDA dimer ion, which is mainly kept together by hydrogen bonding. This study emphasizes ionic bonds stability and their importance to protein structure as their potent electrostatic attractions can in the gas-phase surpass the strength of covalent bonds.

Study of the fragmentation patterns of the phosphate-arginine noncovalent bond

Our previous work has highlighted the role of certain amino acid residues, mainly two or more adjacent arginine on one peptide and two or more adjacent glutamate, or aspartate, or a phosphorylated residue on the other in the formation of noncovalent complexes (NCX) between peptides. In the present study, we employ ESI-MS to investigate the gas-phase stability and dissociation pathways of the NCX of a basic peptide VLRRRRKRVN, an epitope from the third intracellular loop of the dopamine D(2) receptor, with the phosphopetide SVSTDpTpSAE, an epitope from the cannabinoid CB1 carboxyl terminus. ESI-MS/MS analysis of the NCX between VLRRRRKRVN and SVSTDpTpSAE suggests two dissociation pathways for the NCX. The major pathway is the disruption of the electrostatic interactions between the Arg residues and the phosphate groups, while an alternative pathway is also recorded, in which the complex is dissociated along the covalent bond between the oxygen from either Thr or Ser and HPO(3). To verify the alternative pathway, we have used an ion trap instrument to conduct MS(3) analysis on the product ions of both dissociation pathways.

Amazing stability of the arginine-phosphate electrostatic interaction

Electrostatic interactions between a basic epitope containing adjacent arginine residues and an acidic epitope containing a phosphorylated serine are involved in receptor heteromerization. In the present study, we demonstrate that this arginine-phosphate electrostatic interaction possesses a "covalent-like" stability. Hence, these bonds can withstand fragmentation by mass spectrometric collision-induced dissociation at energies similar to those that fragment covalent bonds and they demonstrate an extremely low dissociation constant by plasmon resonance. The present work also highlights the importance of phosphorylation-dephosphorylation events in the modulation of this electrostatic attraction. Phosphorylation of the acidic epitope, a casein kinase one consensus site, makes it available to interact with the basic epitope. On the other hand, phosphorylation of serine and/or threonine residues adjacent to the basic epitope, a protein kinase A consensus site, slows down the attraction between the epitopes. Although analyzed here in the frame of receptor heteromerization, the arginine-phosphate electrostatic interaction most likely represents a general mechanism in protein-protein interactions.

Matrix Implanted Laser Desorption Ionization (MILDI) Combined with Ion Mobility-Mass Spectrometry for Bio-Surface Analysis

The implantation of low velocity massive gold cluster ions allows homogeneous incorporation of a metallic matrix into the near-surface region of rat brain tissues. Subsequent analysis by laser desorption ionization mass spectrometry yields spectra exhibiting molecular ion peaks in the mass range up to 35 kDa similar to those observed by matrix-assisted LDI. Matrix-implanted LDI when combined with ion-mobility preseparation promises to be a useful technique for molecular imaging of biotissues with a laser microprobe.

Lipid/peptide/nucleotide separation with MALDI-ion mobility-TOF MS

Matrix-assisted laser desorption/ionization when combined with ion mobility-orthogonal time-of-flight mass spectrometry is a viable technique for fast separation and analysis of biomolecules in complex mixtures. Isobaric lipid, peptide, and oligonucleotide ions are preseparated before mass analysis by differences of up to 30% in mobility drift time. Ions of similar chemical type fall along well-defined "trend lines" (with deviations of approximately 3%) when plotted in two-dimensional representations of ion mobility as a function of m/z. Discussion of fundamental and technical limitations of the technique point to its potential for being most useful when applied to systems such as bodily fluids and intact tissue, where an alternative chemical or chromatographic preseparation step prior to mass analysis is either impractical or undesirable.

Correlation of Mass Spectrometry Identified Bacterial Biomarkers from a Fielded Pyrolysis-Gas Chromatography-Ion Mobility Spectrometry Biodetector with the Microbiological Gram Stain Classification Scheme

A pyrolysis-gas chromatography-ion mobility spectrometry (Py-GC-IMS) briefcase system has been shown to detect and classify deliberately released bioaerosols in outdoor field scenarios. The bioaerosols included Gram-positive and Gram-negative bacteria, MS-2 coliphage virus, and ovalbumin protein species. However, the origin and structural identities of the pyrolysate peaks in the GC-IMS data space, their microbiological information content, and taxonomic importance with respect to biodetection have not been determined. The present work interrogates the identities of the peaks by inserting a time-of-flight mass spectrometry system in parallel with the IMS detector through a Tee connection in the GC module. Biological substances producing ion mobility peaks from the pyrolysis of microorganisms were identified by their GC retention time, matching of their electron ionization mass spectra with authentic standards, and the National Institutes for Standards and Technology mass spectral database. Strong signals from 2-pyridinecarboxamide were identified in Bacillus samples including Bacillus anthracis, and its origin was traced to the cell wall peptidoglycan macromolecule. 3-Hydroxymyristic acid is a component of lipopolysaccharides in the cell walls of Gram-negative organisms. The Gram-negative Escherichia coli organism showed significant amounts of 3-hydroxymyristic acid derivatives and degradation products in Py-GC-MS analyses. Some of the fatty acid derivatives were observed in very low abundance in the ion mobility spectra, and the higher boiling lipid species were absent. Evidence is presented that the Py-GC-ambient temperature and pressure-IMS system generates and detects bacterial biochemical information that can serve as components of a biological classification scheme directly correlated to the Gram stain reaction in microorganism taxonomy.

MALDI Matrices for Biomolecular Analysis Based on Functionalized Carbon Nanomaterials

When used in small molar ratios of matrix to analyte, derivatized fullerenes and single wall nanotubes are shown to be efficient matrices for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The mixing of an acidic functionalized fullerene with a solution of bioanalyte, depositing a dried droplet, and irradiating with a pulsed nitrogen laser yields protonated or cationized molecular ions. Derivatized fullerenes could offer several advantages over conventional MALDI matrices: a high analyte ionization efficiency, a small molar ratios (less than 1) of matrix/analyte, and a broader optical absorption spectrum, which should obviate specific wavelength lasers for MALDI acquisitions. The major disadvantage to the use of fullerenes is the isobaric interference between matrix and analyte ions; however, it is overcome by using MALDI-ion mobility time-of-flight (IM-oTOF) mass spectrometry to preseparate carbon cluster ions from bioanalyte ions prior to TOF mass analysis. However, an alternative to the dried droplet preparation of fullerene MALDI samples is the aerosolization of matrix-analyte solutions (or slurries) followed by impacting the aerosol onto a stainless surface. We also demonstrate that the fullerene matrices can be used to acquire spectra from rat brain tissue.

Combining mass spectrometry and pull-down techniques for the study of receptor heteromerization. Direct epitope-epitope electrostatic interactions between adenosine A2A and dopamine D2 receptors

Previous results from FRET and BRET experiments and computational analysis (docking simulations) have suggested that a portion of the third intracellular loop (I3) of the human dopamine D2 receptor (D2R) and the C-tail from the human adenosine A2A receptor (A2AR) are involved in A2AR-D2R heteromerization. The results of the present studies, using pull-down and mass spectrometry experiments, suggest that A2AR-D2R heteromerization depends on an electrostatic interaction between an Arg-rich epitope from the I3 of the D2R (217RRRRKR222) and two adjacent Asp residues (DD401-402) or a phosphorylated Ser (S374) residue in the C-tail of the A2AR. A GST-fusion protein containing the C-terminal domain of the A2AR (GST-A2ACT) was able to pull down the whole D2R solubilized from D2R-tranfected HEK-293 cells. Second, a peptide corresponding to the Arg-rich I3 region of the D2R (215VLRRRRKRVN224) and bound to Sepharose was able to pull down both GST-A2ACT and the whole A2AR solubilized from A2AR-tranfected HEK-293 cells. Finally, mass spectometry and pull-down data showed that the Arg-rich D2R epitope binds to two different epitopes from the C-terminal part of the A2AR, containing the two adjacent Asp residues or the phosphorylated Ser residue (388HELKGVCPEPPGLDDPLAQDGAVGS412 and 370SAQEpSQGNT378). The present results are the first example of epitope-epitope electrostatic interaction underlying receptor heteromerization, a new, expanding area of protein-protein interactions.

Adenosine A2A-dopamine D2 receptor–receptor heteromers. Targets for neuro-psychiatric disorders

Emerging evidence shows that G protein-coupled receptors can form homo- and heteromers. These include adenosine A(2A) receptor-dopamine D(2) receptor heteromers, which are most probably localized in the dendritic spines of the striatopallidal GABAergic neurons, where they are in a position to modulate glutamatergic neurotransmission. The discovery of A(2A) receptor-dopamine D(2) receptor heteromers gives a frame for the well-known antagonistic interaction between both receptors, which is the bases for a new therapeutic approach for neuro-psychiatric disorders, such as Parkinson's disease and schizoprenia. The present review deals mainly with the biochemical and molecular aspects of A(2A) receptor-dopamine D(2) receptor interactions. Recent results at the molecular level show that A(2A) receptor-dopamine D(2) receptor heteromers represent the first example of epitope-epitope electrostatic interaction underlying receptor heteromerization. Most probably A(2A) receptor-D(2) receptor heteromerization is not static, but subject to a dynamic regulation, related to the phosphorylation dependence of the A(2A) receptor epitope and to the ability of the D(2) receptor epitope to bind different partners. Finding out the mechanisms involved in this dynamic regulation can have important implications for the treatment of basal ganglia disorders, schizophrenia and drug addiction.

The Mighty Arginine, the Stable Quaternary Amines, the Powerful Aromatics, and the Aggressive Phosphate: Their Role in the Noncovalent Minuet

In the age of proteomics, the role of certain amino acid residues and some post-translational modifications in noncovalent complex formation are gaining in importance, as the understanding of interactions between biological molecules, is at the heart of the structure function relationship puzzle. In this work, mass spectrometry is used to highlight ammonium- or guanidinium-aromatic interactions through Cation-pi bonds and ammonium- or guanidinium-phosphate interactions through salt bridge formation. Such interactions are crucial factors in certain ligand-receptor interactions and receptor-receptor interactions. In addition, the ability of phosphorylated residues and phosphorylated lipids to form noncovalent complexes with guanidinium and quaternary ammonium (mostly through Coulombic interactions) is demonstrated, and could explain the stability of certain membrane embedded protein, or a possible role for phosphorylation in protein-protein interactions. Dougherty's work demonstrates cation-pi interactions in intra-protein interactions and folding, the present work explores inter-peptide interactions, i.e., the formation of noncovalent complexes between peptides' epitopes containing adjacent aromatic residues and ones containing adjacent Arg as a model to better understand the role of cation-pi complexes in protein-protein interaction. Complexes of peptides containing aromatic residues with quaternary amines as well as the interaction of aromatic compounds, with the guanidinium group of Arg are also investigated. Considering that an inordinate number of therapeutic compounds contain aromatic rings and quaternary amines, the above-described interactions could possibly be of great importance in better understanding their mechanism of action.

Detection of specific noncovalent interaction of peptide with DNA by MALDI-TOF

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to obtain spectra of peptide-DNA complexes formed by basic domain (BD15) of c-Fos protein and DNA AP-1 site (5'-TGAGTCA-3'). The noncovalent interaction between single stranded DNA and BD15 was observed and confirmed to be an ionic one between the negatively charged sugar-phosphate backbone of DNA and positively charged side chains of Arg- and lys-rich peptides as demonstrated by Vertes and coworkers and Woods and coworkers. But the specific noncovalent interaction between DNA AP-1 site and the dimer of BD15 was firstly detected in this paper. Various different sequence DNAs were studied and it was found that this interaction is a sequence-specific one, and AP-1 site was essential for this interaction. This specific interaction depends on the matrix. It was only observed in the ATT matrix and not in the other two matrixes (CHCA and DHBA).

Structure of bacterial lipopolysaccharides

Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in "smooth-type" lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.

Fragmentation studies of noncovalent sugar-sugar complexes by infrared atmospheric pressure MALDI

An investigation of sugar-sugar noncovalent complex fragmentation was conducted using a 2.94 microm Er:YAG laser for infrared (IR) atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI) on an ion trap mass spectrometer (ITMS). This approach allowed the analysis of weak noncovalent complexes between a variety of biologically relevant oligosaccharides. The strength of interaction varied with different sugar structures, potentially due to varying strength of hydrogen bonding networks. In some cases, fragmentation of intramolecular sugar bonds preceded breakdown of the noncovalent complex. This result appeared primarily when complexes contained sugars with at least one sialic acid. Globotrios dimers also showed intramolecular fragmentation in preference to breakdown of the noncovalent dimer. This technique will allow further study of sugar-sugar interactions known to play a role in cellular interactions.

Interaction of chlorisondamine with the neuronal nicotinic acetylcholine receptor

An epitope was found on the alpha2-nicotinic isoform of the neuronal nicotinic acetylcholine receptor that would likely form salt bridges with quaternary ammonium compounds and a cation-pi interaction with the pi-cloud of an aromatic ring. Chlorisondamine, a nicotinic antagonist, exerts a long-lasting, if not permanent, blockade of the ion channel gated by acetylcholine. Blocking of the ion channel prevents nicotine from exerting its rewarding effect on the CNS. Chlorisondamine contains two quaternary ammonium groups and a tetrachloroisoindoline ring. We propose that chlorisondamine interacts with an epitope on the alpha2 isoform of the rat neuronal nicotinic receptor (residues 388-402, GEREETEEEEEEEDE), where one or both of the quaternary ammonium groups of chlorisondamine form a salt bridge with dither a glutamic acid side chain or a phosphate group, whereas the tetrachlorobenzene portion of the tetrachloroisoindoline ring interacts with the guanidinium group of arginine in a cation-pi association: In this work, a new way of probing the interaction of a receptor epitope (alpha2) with organic molecules (chlorisondamine and hexachlorobenzene) was undertaken using matrix assisted laser desorption/ionization mass spectrometry.

Investigation of sample preparation and instrumental parameters in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of noncovalent peptide/peptide complexes

The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to the direct detection and investigation of noncovalent solution-phase complexes is far from being routine and some principal problems and questions still exist. Therefore, this study systematically investigates several main problems, namely, the effect of sample preparation and some instrument-related parameters on the stability of the noncovalent complexes as well as the formation of nonspecific cluster ions in the case of the MALDI-MS analysis of specific peptide/peptide complexes. The complexes formed between biologically active fragments of human gastrin I, which contain the sequence motif EEEEE, and different peptides, which contain the interacting sequence motifs RR and RKR, were chosen as examples. A broad variety of MALDI matrices and sample preparation protocols were screened systematically and evaluated. The two 'less acidic' matrices 2,4,6-trihydroxyacetophenone and 6-aza-2-thiothymine, in combination with carefully selected solvents and additives, turned out to allow the reproducible detection of the solution-phase peptide/peptide complexes with good intensity, whereas the classical MALDI matrices could not be applied with the same success. Because both matrices also tend to induce the formation of nonspecific cluster ions, control experiments using nonbinding peptides were performed to definitely prove the specificity of the detected complexes. In contrast to the sensitivity of the peptide/peptide complexes to solution-phase conditions, the gas-phase stability during desorption/ionization was found to be extraordinary high. Neither the application of high laser fluence nor switching from continuous to delayed extraction mode as well as variation of the delay time up to 520 ns had considerable effect on the relative intensities of the specific peptide/peptide complexes.

Rapid screening of aqueous chemical warfare agent degradation products: ambient pressure ion mobility mass spectrometry

The use of electrospray ionization ambient pressure ion mobility spectrometry with an orthogonal reflector time-of-flight mass spectrometer to analyze chemical warfare (CW) degradation products from aqueous environmental samples has been demonstrated. Certified reference materials of analytical standards for the detection of Schedule 1, 2, or 3 toxic chemicals or their precursors as defined by the chemical warfare convention treaty verification were used in this study. A combination of six G/V-type nerve and four S-type vesicant related CW agent degradation products were separated with baseline resolution by this instrumental technique. Analytical figures of merit for each CW degradation product were determined. In some cases, reduced mobility constants (K0) have been reported for the first time. linear response ranges for the selected CW degradation products were found to be generally approximately 2 orders of magnitude, where the overall dynamic response ranges were found to extend to 4 orders of magnitude. Limits of detection for five of the nine chemical products tested were found to be less than 1 ppm. To demonstrate the potential of this instrumental method with complex mixtures, four CW degradation products were separated and detected from a spiked Palouse River water sample in less than 1 min. Finally, a homologous series of n-alkylamines were used as baseline reference standards, producing a mobility/mass trend line to which the CW degradation products could be compared. Comparison of these products in this manner is expected to reduce the number of false positive/negative responses.