Influence of response factors on determining equilibrium association constants of non-covalent complexes by electrospray ionization mass spectrometry

Reliable determinations of protein-ligand interactions by direct ESI-MS measurements. Are we there yet?

The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein-ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein-ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.

Homology-modelled structure of the βB2B3-crystallin heterodimer studied by ion mobility and radical probe MS

Ion mobility MS was employed to study the structure of the βB2B3-crystallin heterodimer following its detection by ESI-TOF MS. The results demonstrate that the heterodimer has a similar cross-section (3 165 Å(2)) and structure to the βB2B2-crystallin homodimer. Several homology-modelled structures for the βB2B3 heterodimer were constructed and assessed in terms of their calculated collision cross-sections and whether the solvent accessibilities of reactive amino acid side chains throughout the βB3 subunit are in accord with measured oxidation levels in radical probe MS protein footprinting experiments. The βB2B3 heterodimer AD model provides the best representation of the heterodimer's structure overall following a consideration of both the ion mobility and radical probe MS data.

Controlled band dispersion for quantitative binding determination and analysis with electrospray ionization-mass spectrometry

This review discusses recent emerging techniques that have been used to couple flow-injection analysis (FIA) and electrospray ionization-mass spectrometry (ESI-MS) for the quantitation of noncovalent binding interactions. Focus is placed predominantly on two such methods. Diffusion-based measurements, developed by Konermann and co-workers, uses controlled-band dispersion prior to ESI-MS to determine diffusion constants and binding constants based on the temporal variation of ligand signal measured in the mass spectrum (an indirect technique). Dynamic titration, developed by Schug and co-workers, is a direct method, where a temporal compositional gradient of a guest molecule is induced in the presence of host in solution to monitor the concentration dependence of complex formation as a function of observed complex ion abundance after ESI-MS. Further discussion places these techniques in the context of a variety of other direct and indirect ESI-MS-based binding determination methods, and highlights advantages, disadvantages, and practical considerations for their proper use to investigate a broad range of macromolecular and small-molecule interaction systems.

Some critical aspects in the determination of binding constants by electrospray ionisation mass spectrometry at the example of arsenic bindings to sulphur-containing biomolecules

The influences of reactant concentrations, solvent type, acid strength, pH conditions and ionic strength on the determination of apparent gas-phase equilibrium constants K using electrospray ionisation mass spectrometry (ESI-MS) were elucidated. As example serves the interaction of the tripeptide glutathione (GSH) with phenylarsine oxide (PAO). It was shown that rising initial concentrations of both reactants were not adequately compensated by increasing signal intensities of the reaction products in the mass spectra. The equilibrium constant for the formation of the phenylarsenic-substituted peptide species decreased from 1.42 x 10(5) +/- 1.81 x 10(4) l micromol(-1) to 1.54 x 10(4) +/- 1.5 x 10(3) l micromol(-1) with rising initial GSH concentrations from 1 to 10 microM at fixed PAO molarity of 50 microM. K values resulting from a series with a fixed GSH molarity of 5 microM and a PAO molarity varied from 10 to 100 microM remained in a narrower range between 4.59 x 10(4) +/- 2.15 x 10(4) l micromol(-1) and 1.07 x 10(4) +/- 4.0 x 10(3) l micromol(-1). In contrast, consumption numbers calculated from the ion intensity ratios of reaction products to the unreacted peptide were not influenced by the initial reactant concentrations. In a water-acetonitrile-acetic acid mixture (48:50:2, v:v), the consumption of 5 micro M GSH increased from 8.3 +/- 1.4% to 39.6 +/- 1.6% with increased molar excess of PAO from 2 to 20, respectively. The GSH consumption was considerably enhanced in a changed solvent system consisting of 25% acetonitrile and 75% 10 mM ammonium formate, pH 5.0 (v:v) up to 80% of the original peptide amount at an only threefold molar arsenic excess.

Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA

The binding sites and consecutive binding constants of alkali metal ions, (M(+) = Na(+), K(+), Rb(+), and Cs(+)), to thrombin-binding aptamer (TBA) DNA were studied by Fourier-transform ion cyclotron resonance spectrometry. TBA-metal complexes were produced by electrospray ionization (ESI) and the ions of interest were mass-selected for further characterization. The structural motif of TBA in an ESI solution was checked by circular dichroism. The metal-binding constants and sites were determined by the titration method and infrared multiphoton dissociation (IRMPD), respectively. The binding constant of potassium is 5-8 times greater than those of other alkali metal ions, and the potassium binding site is different from other metal binding sites. In the 1:1 TBA-metal complex, potassium is coordinated between the bottom G-quartet and two adjacent TT loops of TBA. In the 1:2 TBA-metal complex, the second potassium ion binds at the TGT loop of TBA, which is in line with the antiparallel G-quadruplex structure of TBA. On the other hand, other alkali metal ions bind at the lateral TGT loop in both 1:1 and 1:2 complexes, presumably due to the formation of ion-pair adducts. IRMPD studies of the binding sites in combination with measurements of the consecutive binding constants help elucidate the binding modes of alkali metal ions on DNA aptamer at the molecular level.

Rapid characterization of cross-links, mono-adducts, and non-covalent binding of psoralens to deoxyoligonucleotides by LC-UV/ESI-MS and IRMPD mass spectrometry

Upon UV photoactivation, psoralen analogs form covalent mono-adducts and cross-links with DNA at thymine residues. Electrospray ionization mass spectrometric analysis allowed rapid and efficient determination of the reaction percentages of each psoralen analog with DNA duplexes containing different binding sites after exposure to UV irradiation. The distribution of cross-linked products and mono-adducts was monitored by both LC-UV and IRMPD-MS methods with the highest ratio of cross-linked products to mono-adducts obtained for 8-methoxypsoralen (8-MOP), psoralen (P), and 5-methoxypsoralen (5-MOP). Reactions at 5'-TA sites were favored over 5'-AT sites, and duplexes containing two and three binding sites showed extensive binding by the psoralens. 4'-Aminomethyl-4,5',8-trimethylpsoralen (AMP) bound non-selectively via non-covalent interactions and was the only psoralen analog to show significant binding in the absence of UV irradiation. 8-MOP binding displayed the greatest sequence selectivity among the psoralen analogs. The sites of interstrand cross-linking were determined by fragmentation of the duplex/psoralen complexes by infrared multiphoton dissociation (IRMPD), which produced cross-linked product ions containing an intact single strand, the psoralen analog, and either a w(n) or a(n)-B portion of the complementary strand. IRMPD of DNA/AMP complexes after UV irradiation also produced high abundances of the intact single strands with the AMP ligand attached, products indicative of a significant population of mono-adducts.

Noncanonical interactions between serum transferrin and transferrin receptor evaluated with electrospray ionization mass spectrometry

The primary route of iron acquisition in vertebrates is the transferrin receptor (TfR) mediated endocytotic pathway, which provides cellular entry to the metal transporter serum transferrin (Tf). Despite extensive research efforts, complete understanding of Tf-TfR interaction mechanism is still lacking owing to the complexity of this system. Electrospray ionization mass spectrometry (ESI MS) is used in this study to monitor the protein/receptor interaction and demonstrate the ability of metal-free Tf to associate with TfR at neutral pH. A set of Tf variants is used in a series of competition and displacement experiments to bracket TfR affinity of apo-Tf at neutral pH (0.2-0.6 microM). Consistent with current models of endosomal iron release from Tf, acidification of the protein solution results in a dramatic change of binding preferences, with apo-Tf becoming a preferred receptor binder. Contrary to the current models implying that the apo-Tf/TfR complex dissociates almost immediately upon exposure to the neutral environment at the cell surface, our data indicate that this complex remains intact. Iron-loaded Tf displaces apo-Tf from TfR, making it available for the next cycle of iron binding, transport and delivery to tissues. However, apo-Tf may still interfere with the cellular uptake of engineered Tf molecules whose TfR affinity is affected by various modifications (e.g., conjugation to cytotoxic molecules). This work also highlights the great potential of ESI MS as a tool capable of providing precise details of complex protein-receptor interactions under conditions that closely mimic the environment in which these encounters occur in physiological systems.

Nonspecific interactions between proteins and charged biomolecules in electrospray ionization mass spectrometry

An investigation of the nonspecific association of small charged biomolecules and proteins in electrospray ionization mass spectrometry (ES-MS) is described. Aqueous solutions containing pairs of proteins and a small acidic or basic biomolecule that does not interact specifically with either of the proteins were analyzed by ES-MS and the distributions of the biomolecules bound nonspecifically to each pair of proteins compared. For the basic amino acid arginine and the peptide RGVFRR, nonequivalent distributions were measured in positive ion mode, but equivalent distributions were measured in negative ion mode. In the case of uridine 5'-diphosphate, nonequivalent distributions were measured in negative ion mode, but equivalent distributions observed in positive ion mode. The results of dissociation experiments performed on the gaseous ions of the nonspecific complexes suggest that the nonequivalent distributions result from differences in the extent to which the nonspecific complexes undergo in-source dissociation. To test this hypothesis, the distributions of nonspecifically bound basic molecules measured in the presence of imidazole, which protects complexes from in-source dissociation, were compared. In all cases, equivalent distributions were obtained. The results indicate that nonspecific binding of charged molecules to proteins during ES is a statistical process, independent of protein structure and size. However, the kinetic stabilities of the nonspecific interactions are sensitive to the nature of the protein ions. It is concluded that the reference protein method for correcting ES mass spectra for nonspecific ligand-protein binding can be applied to the analysis of ionic ligands, provided that in-source dissociation of the nonspecific interactions is minimized.

Evaluation of DNA/Ligand interactions by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) has enabled the detection and characterization of DNA/ligand complexes, including evaluation of both relative binding affinities and selectivities of DNA-interactive ligands. The noncovalent complexes that are transferred from the solution to the gas phase retain the signature of the native species, thus allowing the use of MS to screen DNA/ligand complexes, reveal the stoichiometries of the complexes, and provide insight into the nature of the interactions. Ligands that bind to DNA via metal-mediated modes and those that bind to unusual DNA structures, such as quadruplexes, are amenable to ESI. Chemical probe methods applied to DNA/ligand complexes with ESI-MS detection afford information about ligand-binding sites and conformational changes of DNA that occur upon ligand binding.

Determination of equilibrium association constants of ligand-DNA complexes by electrospray mass spectrometry

Electrospray mass spectrometry can be used to detect ligand-DNA noncovalent complexes formed in solution. This chapter describes how to determine equilibrium association constants of the complexes. Particular attention is devoted to describing how to tune an electrospray mass spectrometer using a 12-mer oligodeoxynucleotides duplex in order to perform these experiments. This protocol can then be applied to any nucleic acid structure that can be ionized with electrospray mass spectrometry.

Electrospray ionization mass spectrometry studies of cyclodextrin-carboxylate ion inclusion complexes

Aqueous solutions containing simple model aliphatic and alicyclic carboxylic acids (surrogates 1-4) were studied using negative ion electrospray mass spectrometry (ESI-MS) in the presence and absence of alpha-, beta-, and gamma-cyclodextrin. Molecular ions were detected corresponding to the parent carboxylic acids and complexed forms of the carboxylic acids; the latter corresponding to non-covalent inclusion complexes formed between carboxylic acid and cyclodextrin compounds (e.g., beta-CD, alpha-CD, and gamma-CD). The formation of 1:1 non-covalent inclusion cyclodextrin-carboxylic complexes and non-inclusion forms of the cellobiose-carboxylic acid compounds was also observed.Aqueous solutions of Syncrude-derived mixtures of aliphatic and alicyclic carboxylic acids (i.e. naphthenic acids; NAs) were similarly studied using ESI-MS, as outlined above. Molecular ions corresponding to the formation of CD-NAs inclusion complexes were observed whereas 1:1 non-inclusion forms of the cellobiose-NAs complexes were not detected. The ESI-MS results provide evidence for some measure of inclusion selectivity according to the 'size-fit' of the host and guest molecules (according to carbon number) and the hydrogen deficiency (z-series) of the naphthenic acid compounds. The relative abundances of the molecular ions of the CD-carboxylate anion adducts provide strong support for differing complex stability in aqueous solution. In general, the 1:1 complex stability according to hydrogen deficiency (z-series) of naphthenic acids may be attributed to the nature of the cavity size of the cyclodextrin host compounds and the relative lipophilicity of the guest.

Interactions of sulfur-containing acridine ligands with DNA by ESI-MS

The alkylating proficiency of sulfur-containing mustards may be increased by using an acridine moiety to guide the sulfur mustard to its cellular target. In this study, the interactions of a new series of sulfur-containing acridine ligands, some that also function as alkylating mustards, with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/acridine mixtures. The extent of binding observed for the series of sulfur-containing acridines was similar, presumably because the intercalating acridine moiety was identical. Upon infrared multi-photon dissociation (IRMPD) of the resulting oligonucleotide/sulfur-containing acridine complexes, ejection of the ligand was the dominant pathway for most of the complexes. However, for AS4, an acridine sulfide mustard, and AN1, an acridine nitrogen mustard, strand separation with the ligand remaining on one of the single strands was observed. At higher irradiation times, a variety of sequence ions were observed, some retaining the AS4/AN1 ligand, which was indicative of covalent binding.

Cyclodextrin carriers of positively charged porphyrin sensitizers

The cationic sensitizer 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) forms supramolecular complexes with native, per-methylated, sulfonated and dimethyl-sulfonated cyclodextrins (CDs). Binding interactions were proved by NMR, mass spectra, capillary zone electrophoresis, UV-Vis and fluorescence spectroscopy. The 2D-NMR experiments on native CDs indicate that the interaction of TMPyP with the external CD surface is the dominant binding mode. The high binding affinity of TMPyP towards sulfonated CDs is due to electrostatic interactions. Binding is accompanied by an increase of the TMPyP basicity. Whereas betaCD does not affect the lifetime of the TMPyP triplet states, binding with sulfonated CDs causes the protonation of the TMPyP triplet states even in neutral solution. The diprotonated anionic sensitizer 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPSH(2)(2+)) forms host-guest complexes with native betaCD and gammaCD, similarly as in its non-protonated state. The positive charge of pyrrole nitrogen atoms does not significantly influence the mode of the interaction. In contrast to TMPyP, the lifetimes of the triplet states of bound TPPSH(2)(2+) to native CDs increase.

Direct determination of the primary binding site of cisplatin on cytochrome C by mass spectrometry

Protein-cisplatin interactions lie at the heart of both the effectiveness of cisplatin as a therapeutic agent and side effects associated with cisplatin treatment. Because a greater understanding of the protein-cisplatin interactions at the molecular level can inform the design of cisplatin-like agents for future use, mass spectrometric determination of the binding site of cisplatin on a model protein, cytochrome c, was undertaken in this paper. The monoadduct cytochrome c-Pt(NH(3))(2)(H(2)O) is found to be the primary adduct produced by the cytochrome c-cisplatin interactions under native conditions. To locate the primary binding site of cisplatin, both free cytochrome c and the cytochrome c adducts underwent trypsin digestion, followed by Fourier transform mass spectrometry (FT-MS) to identify unique fragments in the adduct digest. Four such fragments were found in the adduct digest. Tandem mass spectrometry (MS/MS and MS(3) indicates that two fragments are Pt(NH(3))(2)(H(2)O) bound peptides (Gly56-Glu104 and Asn54-Glu104) with one water associated at the peptide bond Lys79-Met80, and the other two fragments are heme containing peptides (acety1-Gly1-Lys53 and acety1-Gly1-Lys55). The product-ion spectra of the four fragments reveal that Met65 is the primary binding site of cisplatin on cytochrome c.

Mass-spectrometric studies of the interactions of selected metalloantibiotics and drugs with deprotonated hexadeoxynucleotide GCATGC

ESI tandem mass spectrometry is employed in a detailed study of the interactions of a hexameric duplex d(5'GCATGC) with three types of ligated first-row transition metal dications M(2+): metallated bleomycins, singly, doubly, and triply ligated metallophenanthrolines and [M(triethylenetetramine)](2+). The singly, doubly, and triply metallated species were found to dissociate by noncovalent separation into two strands with metal ions attached either to one or to both. Relative gas-phase stabilities of the double-stranded oligodeoxynucleotide (ODN)-M(2+) complexes were found to follow the order Mn(II) > Fe(II) > Co(II) > Ni(II) > Zn(II) > Cu(II). Overall, the presence of metal dications is found to increase the gas-phase stability of the duplex against noncovalent dissociation with the exception of one and three copper dications. An analysis of the dissociation pathways and relative gas-phase stabilities of the species that were investigated provided a basis for the assessment of the possible binding modes between duplex oligonucleotides and metallocomplexes.

How to deal with weak interactions in noncovalent complexes analyzed by electrospray mass spectrometry: cyclopeptidic inhibitors of the nuclear receptor coactivator 1-STAT6

Mass spectrometry, and especially electrospray ionization, is now an efficient tool to study noncovalent interactions between proteins and inhibitors. It is used here to study the interaction of some weak inhibitors with the NCoA-1/STAT6 protein with K(D) values in the microM range. High signal intensities corresponding to some nonspecific electrostatic interactions between NCoA-1 and the oppositely charged inhibitors were observed by nanoelectrospray mass spectrometry, due to the use of high ligand concentrations. Diverse strategies have already been developed to deal with nonspecific interactions, such as controlled dissociation in the gas phase, mathematical modeling, or the use of a reference protein to monitor the appearance of nonspecific complexes. We demonstrate here that this last methodology, validated only in the case of neutral sugar-protein interactions, i.e., where dipole-dipole interactions are crucial, is not relevant in the case of strong electrostatic interactions. Thus, we developed a novel strategy based on half-maximal inhibitory concentration (IC(50)) measurements in a competitive assay with readout by nanoelectrospray mass spectrometry. IC(50) values determined by MS were finally converted into dissociation constants that showed very good agreement with values determined in the liquid phase using a fluorescence polarization assay.

Mass spectrometric investigations of alpha- and beta-cyclodextrin complexes with ortho-, meta- and para-coumaric acids by negative mode electrospray ionization

The mass spectrometric characterization of aqueous solutions of alpha- and beta-cyclodextrins (CDs) and o-, m- and p-coumaric acids (CAs) by negative ion electrospray ionization (ESI) indicates that the [CD+CA](-) ions were sourced from the inclusion complex present in solution and from the anion attached to CD molecules formed in the spray processes. The anion adducts formed in the spray process contribute significantly to the signal intensity of an ionized inclusion complex thus overestimating the calculated stability constant (K) of solution-phase complexes by one to two orders of magnitude. The relative intensities of anion adducts in mass spectra depend on the concentration ratio of the anion and the CD in spray droplets, while the relative intensity of the ionized inclusion complex depends on CD and CA concentrations in solutions and the value of K. Ion Mobility Spectrometry Mass Spectrometry [IMS-MS] measurements show that the collision cross-section (Omega) values of the [CD+CA](-) or [(CD)(2+)CA](2-) and [CD+CA](2) (2-) complex ions are 5-6% larger than or equal to CD(-) or [CD](2) (2-), respectively. Therefore, in the gas phase the anion adducts [CD+CA(-)] on cyclodextrin molecules possess the same conformations as the ionized inclusion complexes [CD+CA](-).

Determination of binding constants by affinity capillary electrophoresis, electrospray ionization mass spectrometry and phase-distribution methods

Many methods for determining intermolecular interactions have been described in the literature in the past several decades. Chief among them are methods based on spectroscopic changes, particularly those based on absorption or nuclear magnetic resonance (NMR) [especially proton NMR ((1)H NMR)]. Recently, there have been put forward several new methods that are particularly adaptable, use very small quantities of material, and do not place severe requirements on the spectroscopic properties of the binding partners. This review covers new developments in affinity capillary electrophoresis, electrospray ionization mass spectrometry (ESI-MS) and phasetransfer methods.

Monitoring ligand modulation of protein-protein interactions by mass spectrometry: estrogen receptor alpha-SRC1

Many drugs and chemicals exert their biological effect by modulating protein-protein interactions. In vitro approaches to characterize these mechanisms are often based on indirect measurements (e.g., fluorescence). Here, we used mass spectrometry (MS) to directly monitor the effect of small-molecule ligands on the binding of a coactivator peptide (SRC1) by the human estrogen receptor alpha ligand binding domain (hERalpha LBD). Nanoelectrospray mass spectrometry (nanoESI-MS) and high-mass matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with chemical cross-linking were employed to follow these processes. The chemical cross-linking protocol used prior to high-mass MALDI analysis allows detection of intact noncovalent complexes. The binding of intact hERalpha LBD homodimer with two coactivator peptides was detected with nanoESI-MS and high-mass MALDI-MS only in the presence of an agonist ligand. Furthermore, high-mass MALDI-MS revealed an increase of the homodimer abundance after incubating the receptor with a ligand, independent of the ligand character (i.e., agonist, antagonist). The binding characteristics of the compounds tested by MS correlate very well with their biological activity reported by cell-based assays. High-mass MALDI appears to be an efficient and simple tool for directly monitoring ligand regulation mechanisms involved in protein-protein interactions. Furthermore, the combination of both MS methods allows identifying and characterizing endocrine-disrupting compounds or new drug compounds in an efficient way.

Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches

Mass spectrometry (MS) plays a central role in studies on protein structure and dynamics. This review highlights some of the recent developments in this area, with focus on applications involving the use of electrospray ionization (ESI) MS. Although this technique involves the transformation of analytes into highly nonphysiological species (desolvated gas-phase ions in the vacuum), ESI-MS can provide detailed insights into the solution-phase behavior of proteins. Notably, the ionization process itself occurs in a structurally sensitive manner. An increased degree of solution-phase unfolding is correlated with a higher level of protonation. Also, ESI allows the transfer of intact noncovalent complexes into the gas phase, thereby yielding information on binding partners, stoichiometries, and even affinities. A particular focus of this article is the use of hydrogen/deuterium exchange (HDX) methods and hydroxyl radical (.OH) labeling for monitoring dynamic and structural aspect of solution-phase proteins. Conceptual similarities and differences between the two methods are discussed. We describe a simple method for the computational simulation of protein HDX patterns, a tool that can be helpful for the interpretation of isotope exchange data recorded under mixed EX1/EX2 conditions. Important aspects of .OH labeling include a striking dependence on protein concentration, and the tendency of commonly used solvent additives to act as highly effective radical scavengers. If not properly controlled, both of these factors may lead to experimental artifacts.

Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators

Binding of three macrocyclic bis-intercalators, derivatives of acridine and naphthalene, and two acyclic model compounds to mismatch-containing and matched duplex oligodeoxynucleotides was analyzed by thermal denaturation experiments, electrospray ionization mass spectrometry studies (ESI-MS) and fluorescent intercalator displacement (FID) titrations. The macrocyclic bis-intercalators bind to duplexes containing mismatched thymine bases with high selectivity over the fully matched ones, whereas the acyclic model compounds are much less selective and strongly bind to the matched DNA. Moreover, the results from thermal denaturation experiments are in very good agreement with the binding affinities obtained by ESI-MS and FID measurements. The FID results also demonstrate that the macrocyclic naphthalene derivative BisNP preferentially binds to pyrimidine–pyrimidine mismatches compared to all other possible base mismatches. This ligand also efficiently competes with a DNA enzyme (M.TaqI) for binding to a duplex with a TT-mismatch, as shown by competitive fluorescence titrations. Altogether, our results demonstrate that macrocyclic distance-constrained bis-intercalators are efficient and selective mismatch-binding ligands that can interfere with mismatch-binding enzymes.

Chemical stability and reactivity of deprotonated oligonucleotides (DNA) in the gas phase: protonation and solvation with hydrogen bromide

Selected deprotonated oligodeoxynucleotides generated by electrospray ionization were exposed to a variety of neutral molecules in the gas phase at room temperature in flowing helium gas at 0.35 Torr. Single-stranded [AGTCTG-nH]n- and single- and double-stranded [GCATGC-nH]n- anions were found to be remarkably unreactive with strong oxidants (O3, O2, N2O) and potential intercalators (benzene, pyridine, toluene, and quinoxaline). Hydration also was observed to be inefficient. However, [AGTCTG-nH]n- anions with n=2, 3, 4, and 5 were seen to be sequentially protonated and/or hydrobrominated with HBr (but not damaged) and displayed an interesting "end effect" against protonation. Measurements are provided for the rate coefficients of reaction and the efficiencies of protonation. These experimental results point toward the exciting prospect of measuring the intrinsic chemistry of other bare DNA-like anions, including double-stranded oligonucleotide anions in the gas phase at room temperature.

Binding constant determination of high-affinity protein-ligand complexes by electrospray ionization mass spectrometry and ligand competition

We describe an approach for the determination of binding constants for protein-ligand complexes with electrospray ionization mass spectrometry, based on the observation of unbound ligands competing for binding to a protein target. For the first time, dissociation constants lower than picomolar could be determined with good accuracy by electrospray ionization mass spectrometry. The presented methodology relies only on the determination of signal intensity ratios for free ligands in the low mass region. Therefore, all the advantages of measuring low masses with mass spectrometry, such as high resolution are preserved. By using a reference ligand with known binding affinity, the affinity of a second ligand can be determined. Since no noncovalently bound species are observed, assumptions about response factors are not necessary. The method is validated with ligands binding to avidin and applied to ligands binding to p38 mitogen-activated protein kinase.

Ion internal energy distributions validate the charge residue model for small molecule ion formation by spray methods

This paper reports a detailed study of the internal energy distribution of ions formed by four electrospray ionization (ESI)-related ionization methods, with particular emphasis on electrosonic spray ionization (ESSI). Substituted benzylpyridinium ions were used as thermometer ions to probe the internal energy distribution. The influence of different instrumental parameters was studied. Cone and skimmer voltages as well as the collision energy were found to strongly affect the ion internal energy distribution, whereas the distance between the emitter and the inlet of the mass spectrometer, the nebulizing gas pressure or the flow rate showed no influence. The internal energy distribution obtained with an ESSI source was compared with those obtained for electrospray (ESI), nanoelectrospray (nanoESI) and sonic spray ionization (SSI) on the same mass spectrometer with the same instrumental parameters. No clear differences were observed. As the charge residue model is the only ion formation mechanism possible for SSI, we conclude that benzylpyridinium ions are formed by the pathway suggested by this model.

Method of measuring oligonucleotide-metal affinities: interactions of the thrombin binding aptamer with K+ and Sr2+

We report a new, mass spectrometry-based method for measuring affinity constants for specific metal ion binding to DNA, particularly for quadruplex DNA. This method, which is applicable to other systems, utilizes the gas-phase signal fractions, as determined by mass spectrometry, from the bound and unbound species as input into a mathematical model that determines various parameters, one of which is the binding affinity constant. The system used to develop and test the model was the thrombin-binding aptamer, an appropriate quadruplex structure that binds both K+ and Sr2+ cations. Using this method, we measured the binding constants of potassium and strontium cations with the quadruplex structure to be 5000 and 240 nM, respectively. We then applied the method to measure the change in enthalpy of the binding of strontium cations to the thrombin binding aptamer. The DeltaH for this interaction is -71 kJ/mol (-17 kcal/mol). The binding constant measurements are consistent with earlier measurements on the same system, and the measured change in enthalpy is in excellent agreement with previous work.

Which electrospray-based ionization method best reflects protein-ligand interactions found in solution? a comparison of ESI, nanoESI, and ESSI for the determination of dissociation constants with mass spectrometry

We present a comparison of three different electrospray-based ionization techniques for the investigation of noncovalent complexes with mass spectrometry. The features and characteristics of standard electrospray ionization (ESI), chip-based nanoESI, and electrosonic spray ionization (ESSI) mounted onto a hybrid quadrupole time-of-flight mass spectrometer were compared in their performance to determine the dissociation constant (KD) of the model system hen egg white lysozyme (HEWL) binding to N,N',N''-triacetylchitotriose (NAG3). The best KD value compared with solution data were found for ESSI, 19.4 +/- 3.6 microM. Then, we determined the KDs of the two nucleotide binding sites of adenylate kinase (AK), where we obtained KDs of 2.2 +/- 0.8 microM for the first and 19.5 +/- 8.0 microM for the second binding site using ESSI. We found a weak charge state dependence of the KD for both protein-ligand systems, where for all ionization techniques the KD value decreases with increasing charge state. We demonstrate that ESSI is very gentle and insensitive to instrumental parameters, and the KD obtained is in good agreement with solution phase results from the literature. In addition, we tried to determine the KD for the lymphocyte-specific kinase LCK binding to a kinase inhibitor using nanoESI due to the very low amount of sample available. In this case, we found KD values with a strong charge state dependence, which were in no case close to literature values for solution phase.

Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry

The binding of a series of benzoxazole analogs with different amide- and ester-linked side chains to duplex DNA in the absence and presence of divalent metal cations is examined. All ligands were found to form complexes with Ni2+, Cu2+, and Zn2+, with 2:1 ligand/metal cation binding stoichiometries dominating for ligands containing shorter side chains (2, 6, 7, and 8), while 1:1 complexes were the most abundant for ligands with long side chains (9, 10, and 11). Ligand binding with duplex DNA in the absence of metal cations was assessed, and the long side-chain ligands were found to form low abundance complexes with 1:1 ligand/DNA binding stoichiometries. The ligands with the shorter side chains only formed DNA complexes in the presence of metal cations, most notably for 7 and 8 binding to DNA in the presence of Cu2+. The binding of long side-chain ligands was enhanced by Cu2+ and to a lesser degree by Ni2+ and Zn2+. The cytotoxicities of all of the ligands against the A549 lung cancer and MCF7 breast cancer cell lines were also examined. The ligands exhibiting the most dramatic metal-enhanced DNA binding also demonstrated the greatest cytotoxic activity. Both 7 and 8 were found to be the most cytotoxic against the A549 lung cancer cell line and 8 demonstrated moderate cytotoxicity against MCF7 breast cancer cells. Metal ions also enhanced the DNA binding of the ligands with the long side chains, especially for 9, which also exhibited the highest level of cytotoxicity of the long side-chain compounds.

Method for identifying nonspecific protein-protein interactions in nanoelectrospray ionization mass spectrometry

The nonspecific self-association of proteins in nanoflow electrospray ionization mass spectrometry (nanoES-MS), and the influence of experimental conditions thereon, are investigated using the protein ubiquitin (Ubq) as a model system. Extents of nonspecific protein association generally increase with protein concentration and, interestingly, with decreasing ES spray potential. The extent of self-association is also sensitive to the duration of the accumulation event in an external rf hexapole. Notably, the relative abundance of metal (Na+ and K+) adducts generally increases with the size of nonspecific Ubq multimer. This result suggests that the gaseous ions of monomeric and nonspecific multimeric Ubq have, on average, different ES droplet histories, with monomer ions originating earlier in the ES process than the nonspecific multimeric complexes. This finding forms the basis for a new method for distinguishing between specific and nonspecific protein complexes in ES-MS. A reporter molecule (Mrep), which does not bind specifically to the proteins and protein complexes of interest, is added to the ES solution at high concentration. The distribution of Mrep bound nonspecifically to gaseous ions of the proteins and protein complexes, as determined from the ES mass spectrum, is used to determine whether a given protein complex originates in solution or whether it forms from nonspecific binding during the ES process. The method is demonstrated in cases where the ions of protein complexes detected by nanoES-MS originate exclusively from nonspecific association, exclusively from specific interactions in solution, or from both specific and nonspecific interactions.

On-line dynamic titration: determination of dissociation constants for noncovalent complexes using Gaussian concentration profiles by electrospray ionization mass spectrometry

A new method for determination of dissociation constants (Kd) using on-line titration by electrospray ionization mass spectrometry is presented. Unlike in common titration experiments, where a set of discrete solutions with a fixed concentration of host and increasing concentration of guest is measured, here a continuous Gaussian concentration profile of guest, formed by band-broadening dispersion during passage through a long tubing, is utilized. An equation allowing access to dissociation constant values from experimental data fit to a 1:1 binding model was derived and incorporated into an in-house-written computer program for automated data processing. The new method is demonstrated for noncovalent complexes of cinchona alkaloid carbamate chiral selectors with N-dinitrobenzoylleucine enantiomers and a series of cyclodextrins with sulfonated azo dyes.

Ligand binding mode to duplex and triplex DNA assessed by combining electrospray tandem mass spectrometry and molecular modeling

In this paper, we report the analysis of seven benzopyridoindole and benzopyridoquinoxaline drugs binding to different duplex DNA and triple helical DNA, using an approach combining electrospray ionization mass spectrometry (ESI-MS), tandem mass spectrometry (MS/MS), and molecular modeling. The ligands were ranked according to the collision energy (CE(50)) necessary to dissociate 50% of the complex with the duplex or the triplex in tandem MS. To determine the probable ligand binding site and binding mode, molecular modeling was used to calculate relative ligand binding energies in different binding sites and binding modes. For duplex DNA binding, the ligand-DNA interaction energies are roughly correlated with the experimental CE(50), with the two benzopyridoindole ligands more tightly bound than the benzopyridoquinoxaline ligands. There is, however, no marked AT versus GC base preference in binding, as supported both by the ESI-MS and the calculated ligand binding energies. Product ion spectra of the complexes with triplex DNA show only loss of neutral ligand for the benzopyridoquinoxalines, and loss of the third strand for the benzopyridoindoles, the ligand remaining on the duplex part. This indicates a higher binding energy of the benzopyridoindoles, and also shows that the ligands interact with the triplex via the duplex. The ranking of the ligand interaction energies compared with the CE(50) values obtained by MS/MS on the complexes with the triplex clearly indicates that the ligands intercalate via the minor groove of the Watson-Crick duplex. Regarding triplex versus duplex selectivity, our experiments have demonstrated that the most selective drugs for triplex share the same heteroaromatic core.

Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry

Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding.

Investigation on the interaction of tetrachloride fluorescein–bovine serum albumin-β-cyclodextrin and the determination of protein by flow injection analysis

In this paper, a simple and sensitive flow injection analysis (FIA) for the determination of protein with spectroscopic probe was developed. This method was based on the investigation of the interaction of tetrachloride fluorescein (2,4,5,7-tetrachloro-3,6-fluorandiol)-bovine serum albumin (BSA), the coupling reaction of protein with tetrachloride fluorescein (TCFS) which was used as a spectroscopic probe in the presence of beta-cyclodextrin (beta-CD). The interaction mechanism and the main factors affecting the determination were investigated in details. Under the optimum conditions, the linear range and detection limit were 0.0-28.0 microg mL(-1) and 0.76 microg mL(-1), respectively. The proposed method has been used to determine albumin in serum albumin with satisfactory results.

Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS

The 24-mer DNA aptamer of Harada and Frankel (Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Estrogen receptor-ligand complexes measured by chip-based nanoelectrospray mass spectrometry: an approach for the screening of endocrine disruptors

In the present report, a method based on chip-based nanoelectrospray mass spectrometry (nanoESI-MS) is described to detect noncovalent ligand binding to the human estrogen receptor alpha ligand-binding domain (hERalpha LBD). This system represents an important environmental interest, because a wide variety of molecules, known as endocrine disruptors, can bind to the estrogen receptor (ER) and induce adverse health effects in wildlife and humans. Using proper experimental conditions, the nanoESI-MS approach allowed for the detection of specific ligand interactions with hERalpha LBD. The relative gas-phase stability of selected hERalpha LBD-ligand complexes did not mirror the binding affinity in solution, a result that demonstrates the prominent role of hydrophobic contacts for stabilizing ER-ligand complexes in solution. The best approach to evaluate relative solution-binding affinity by nanoESI-MS was to perform competitive binding experiments with 17beta-estradiol (E2) used as a reference ligand. Among the ligands tested, the relative binding affinity for hERalpha LBD measured by nanoESI-MS was 4-hydroxtamoxifen approximately diethylstilbestrol > E2 >> genistein >> bisphenol A, consistent with the order of the binding affinities in solution. The limited reproducibility of the bound to free protein ratio measured by nanoESI-MS for this system only allowed the binding constants (K(d)) to be estimated (low nanomolar range for E2). The specificity of nanoESI-MS combined with its speed (1 min/ligand), low sample consumption (90 pmol protein/ligand), and its sensitivity for ligand (30 ng/mL) demonstrates that this technique is a promising method for screening suspected endocrine disrupting compounds and to qualitatively evaluate their binding affinity.

Nonspecific protein-carbohydrate complexes produced by nanoelectrospray ionization. Factors influencing their formation and stability

Factors influencing the formation of nonspecific protein-carbohydrate complexes during the nanoelectrospray (nanoES) process have been investigated. Protonated and deprotonated nonspecific complexes of ubiquitin (Ubq) and protonated complexes of carbonic anhydrase (CA) with carbohydrates, ranging in size from mono- to tetrasaccharide, were produced by nanoES and detected with a Fourier transform ion cyclotron resonance mass spectrometer. Both the fraction of protein engaged in nonspecific binding with the carbohydrates and the number of carbohydrates bound to the protein increase with increasing carbohydrate concentration. At a given concentration of protein and carbohydrate, nonspecific binding is favored for small (mono- and disaccharide) or hydrophilic carbohydrates over larger or more hydrophobic molecules, which tend to form gaseous monomer or cluster ions by nanoES. However, the extent of nonspecific binding is insensitive to the structure of the protein, with similar distributions of nonspecific complexes observed for both CA and Ubq. Nonspecific association is also insensitive to the charge state of the complex. A comparable degree of binding is observed for complexes in their protonated and deprotonated forms. Furthermore, the number of bound ligands can exceed significantly the charge state of the complex. Thermal dissociation experiments performed on the gaseous nonspecific complexes reveal that their kinetic stability is sensitive to both the structure of the carbohydrate (i.e., mono- < di- < tri- < tetrasaccharide) and the protein (Ubq < CA) and to the charge state, although no simple relationship between stability and charge state was identified. Taken together, the results of this study suggest that neutral protein-carbohydrate interactions (e.g., hydrogen bonds) contribute significantly and, perhaps, predominantly to the formation and stabilization of the nonspecific complexes. A strategy to minimize the formation of the nonspecific complexes, which is based on the enhancement of gaseous carbohydrate ion formation through the addition of metal salts (e.g., CaCl2) to the nanoES solution, is demonstrated.