Determination of ligand-protein dissociation constants by electrospray mass spectrometry-based diffusion measurements

A novel approach for the quantification of ligand-protein interactions is presented. Electrospray ionization mass spectrometry (ESI-MS) is used to monitor the diffusion behavior of noncovalent ligands in the presence of their protein receptors. These data allow the fraction of free ligand in solution to be determined, such that the corresponding dissociation constants can be calculated. A set of conditions is developed that provides an "allowable range" of concentrations for this type of assay. The method is tested by applying it to two different inhibitor-enzyme systems. The dissociation constants measured for benzamidine-trypsin and for N,N',N' '-triacetylchitotriose-lysozyme are (50 +/- 10) and (6 +/- 1) mM, respectively. Both of these results are in good agreement with previous data from the literature. In contrast to traditional ESI-MS-based methods, the approach used in this work does not rely on the preservation of specific solution-type noncovalent interactions in the gas phase. It is shown that this method allows an accurate determination of dissociation constants, even in cases in which the ion abundance ratio of free to ligand-bound protein in ESI-MS does not reflect the corresponding concentration ratio in solution.     

Transferred nuclear overhauser effect in nuclear magnetic resonance diffusion measurements of ligand-protein binding

The drug discovery process relies on characterizing structure-activity relationships, since specific ligand-target interactions often result in important biological functions. Measuring diffusion coefficients by nuclear magnetic resonance spectroscopy is a useful way to study binding, because changes can be detected when a small ligand interacts with a macromolecular target. Diffusion coefficients can be miscalculated, however, due to magnetization transfer between the receptor and ligand. This transferred nuclear Overhauser effect (trNOE) disrupts the observed signal decay due to diffusion as a function of the experimental diffusion time. Since longer diffusion times also selectively edit free ligand signal, the measured diffusion coefficients become biased toward the fraction of bound ligand. Despite this discrepancy, under these experimental conditions, the trNOE selectively influences the measured signals of binding ligands and can be used to gain insight into ligand-protein interactions. These phenomena have been studied for caffeine and L-tryptophan, which bind to human serum albumin, and the antimalarial agent trimethoprim, which interacts with dihydrofolate reductase. The results provide insight into the nature of ligand-protein binding and are thus useful for elucidating the molecular features of the ligand that interact with the protein.     

Concentration-Dependent Diffusion Coefficients of Binary Gas Mixtures Using a Loschmidt Cell with Holographic Interferometry

An improved experimental setup and data evaluation procedure are presented for a Loschmidt cell combined with interferometry to measure concentration-dependent binary diffusion coefficients. We overcome long-standing discrepancies about the concentration dependence found in the literature. The systematic analysis of the residuals from parameter estimation enabled the improvement of the experimental setup and the identification of relevant fitting parameters. In particular, we found that it is crucial to account for uncertainties (1) in the initial conditions, (2) in the thermal stability of the optical setup, and (3) in camera calibration. The improved experimental setup and data evaluation procedure are validated with diffusion measurements of the system helium–krypton. The concentration dependence of the diffusion coefficient is successfully determined from multiple experiments with gas mixtures of various initial compositions in the half-cells of the Loschmidt cell. The agreement with literature data and the excellent quality of fit allow for high confidence in the results. In Part II of this paper (Wolff et al., in Int J Thermophys, 2018,  https://doi.org/10.1007/s10765-018-2451-7), the improved measurement setup is combined with a refined diffusion model to determine concentration-dependent diffusion coefficients from single measurements of mixing pure gases.     

Fourier analysis to measure diffusion coefficients and resolve mixtures on a continuous electrophoresis chip

We report a method to measure diffusion coefficients of fluorescent solutes in the 10(2)-10(6) Da molecular mass range in a glass-PDMS chip. Upon applying a permanent electric field, the solute is introduced through a narrow channel into a wide analysis chamber where it migrates along the injection axis and diffuses in two dimensions. The diffusion coefficient is extracted after 1D Fourier transform of the resulting stationary concentration pattern. Analysis is straightforward, requiring no numerical integration or velocity field simulation. The diffusion coefficients measured for fluorescein, rhodamine green-labeled oligonucleotides, and YOYO-1-stained dsDNA fragments agree with the literature values and with our own fluorescence correlation spectroscopy measurements. As shown for 151 and 1257 base pair dsDNA mixtures, the present method allows us to rely on diffusion to quantitatively characterize the nature and the composition of binary mixtures. In particular, we implement a DNA hybridization assay to illustrate the efficiency of the proposed protocol for library screening.     

Phosphoryl-Containing Chelating Sorbents for Concentrating Actinides

New chelating sorbents with phosphinate, carbamoylmethylphosphinate, and methylenediphosphine dioxide functionalities are synthesized by chemical and noncovalent binding of the ligands to polymer matrices, chloromethylated styrene copolymer and XAD-7 acrylate polymer. The sorption and kinetic characteristics of the sorbents with respect to U(VI), Th(IV), Pu(IV), and Am(III) are studied in nitric acid solutions. The sorbents obtained by noncovalent binding of the ligands to XAD-7 demonstrate better kinetic properties. The sorbents can be used for concentrating actinides from 3–5 M HNO₃ and for their partitioning.     

Stabilization of gas-phase noncovalent macromolecular complexes in electrospray mass spectrometry using aqueous triethylammonium bicarbonate buffer

The use of triethylammonium bicarbonate (TEAB) solution in electrospray mass spectrometry proved to be a very efficient way for studying proteins or noncovalent protein complexes under "nondenaturing" conditions. The low charge states observed in the mass spectra improve the separation of ions arising from macromolecular species of close masses. Moreover, the multiply charged ions generated in a TEAB solution are significantly more stable than those formed under more conventional conditions (for example, with ammonium bicarbonate or acetate solution). The analytical interest of TEAB for the analysis of macromolecular species that can easily dissociate in the gas phase, such as hemoglobin or other macromolecular noncovalent complexes, is demonstrated.     

Electrochemical investigation of Pb2+ binding and transport through a polymerized crystalline colloidal array hydrogel containing benzo-18-crown-6

The transport of Pb2+ through a sensory gel, a polymerized crystalline colloidal array hydrogel with immobilized benzo-18-crown-6, is important for understanding and optimizing the sensor. Square wave voltammetry at a Hg/Au electrode reveals many parameters. The partition coefficient for Pb2+ into a control gel (no crown ether), K(p), is 1.00 +/- 0.018 (errors reported are SEM). The porosity, epsilon, of the gel is 0.90 +/- 0.01. Log K(c) for complexation in the gel is 2.75 +/- 0.014. Log K(c) in aqueous solution for Pb2+ with the ligand 4-acryloylamidobenzo-18-crown-6 is 3.01 +/- 0.010 with dissociation rate k(d) = (8.34 +/- 0.45) x 10(2) s(-1) and association rate k(f) = (8.79 +/- 0.025) x 10(7) M(-1) s(-1). The partition coefficient of the ligand 4-acryloylamidobenzo-18-crown-6 into the control gel, K(p,L) is 2.07 +/- 0.15. The diffusion coefficient of Pb2+ in the control gel is 6.72 x 10(-6) +/- 0.12 cm(2)/s. For the sensor gel, but not control gel, diffusion coefficients are location dependent. The range of diffusion coefficients for Pb2+ in the probed locations was found to be (6.11-12.60) x 10(-7) cm(2)/s for 0.91 mM Pb2+ and (2.84-9.39) x 10(-7) cm(2)/s for 0.35 mM Pb2+. Lead binding in the sensor gel is slightly less avid than in solution. This is attributed, in part, to the demonstrated affinity of the ligand 4-acryloylamidobenzo-18-crown-6 to the gel. Diffusion coefficients determined for the sensor gel were found to be location dependent. This is attributed to heterogeneities in the crown concentration in the gel. Analysis of diffusion coefficients and rate constants show that diffusion and not chemical relaxation will limit the time response of the material.     

Revealing equilibrium and rate constants of weak and fast noncovalent interactions

Rate and equilibrium constants of weak noncovalent molecular interactions are extremely difficult to measure. Here, we introduced a homogeneous approach called equilibrium capillary electrophoresis of equilibrium mixtures (ECEEM) to determine k(on), k(off), and K(d) of weak (K(d) > 1 μM) and fast kinetics (relaxation time, τ < 0.1 s) in quasi-equilibrium for multiple unlabeled ligands simultaneously in one microreactor. Conceptually, an equilibrium mixture (EM) of a ligand (L), target (T), and a complex (C) is prepared. The mixture is introduced into the beginning of a capillary reactor with aspect ratio >1000 filled with T. Afterward, differential mobility of L, T, and C along the reactor is induced by an electric field. The combination of differential mobility of reactants and their interactions leads to a change of the EM peak shape. This change is a function of rate constants, so the rate and equilibrium constants can be directly determined from the analysis of the EM peak shape (width and symmetry) and propagation pattern along the reactor. We proved experimentally the use of ECEEM for multiplex determination of kinetic parameters describing weak (3 mM > K(d) > 80 μM) and fast (0.25 s ≥ τ ≥ 0.9 ms) noncovalent interactions between four small molecule drugs (ibuprofen, S-flurbiprofen, salicylic acid and phenylbutazone) and α- and β-cyclodextrins. The affinity of the drugs was significantly higher for β-cyclodextrin than α-cyclodextrin and mostly determined by the rate constant of complex formation.     

Universality versus nonuniversality of critical transport properties in liquid mixtures

The critical behavior near consolute points and plait points in mixtures and along lines connecting such points in the phase diagram belongs to the universality class of gas-liquid transitions in pure liquids. We give a survey of the results for the temperature dependence of transport coefficients, thermal conductivity, mass diffusion, and thermal-diffusion ratio, in mixtures within a non-asymptotic renormalization-group theory of critical dynamics. The observable critical behavior in some cases is nonuniversal and may be strongly concentration dependent. This is explained by different crossover temperatures in the singular Onsager coefficient of the order parameter and in the hydrodynamic transport coefficients. At the plait point the value of (ie1363-01) determines the crossover to the asymptotic behavior in the transport coefficients, and its smallness explains the situation in³He-⁴He mixtures. We also consider ionic solutions, where long-range forces may be present. The dynamical universality class in this case is different from that of mixtures with short-range interaction. As well as the classical static behavior for sufficient long-range interaction potentials, the dynamical critical behavior depends on the exponent of the power law for the spatial decrease in this interaction. This offers an additional possibility to determine this exponent by measuring the temperature dependence of the hydrodynamic transport coefficients.     

Quantifying protein-protein interactions within noncovalent complexes using electrospray ionization mass spectrometry

Several electrospray-mass spectrometry (ESI-MS)-based methods are available for determining the constant of association (K(a)) between a protein and a small ligand, but current MS-based strategies are not fully adequate for measuring K(a) of protein-protein interactions accurately. We expanded the application of ESI-MS-based titration to determine the strength of noncovalent interactions between proteins, forming a complex. Taking into account relative response factors (probability of being ionized, transmitted, and detected), we determined K(a) values of an equilibrium between dimers and tetramers at three different pH values (6.8, 3.4, and 8.4). We investigated the association of the lectin concanavalin A, whose dimer-tetramer ratio in the gas phase is affected by solution concentration and by pH. To calculate the constants of association in solution, we also utilized isothermal titration calorimetry (ITC) for a comparison with MS-based titration. At pH 6.8 and pH 8.4, the K(a) values measured by MS and by ITC were in agreement. ITC results allowed us to restrain the response factor to a value close to 4. At pH 3.4, we were able to measure the K(a) only by MS, but not by ITC because of limited sensitivity of calorimetry. Our investigation illustrates the great potential MS for calculating the binding strength of protein-protein interactions within noncovalent complexes. The main advantages of MS over ITC are its sensitivity (i.e., the required amount of sample is >100 times less than the one necessary for ITC), and the possibility to obtain precise information on composition of protein complexes, their stoichiometry, their subunit interactions, and their assembly pathway. Compared to previous investigations, our study shows the strong influence of response factors on determining accurate protein-protein association constants by MS.     

Comparative Assessment of Different Histidine-Tags for Immobilization of Protein onto Surface Plasmon Resonance Sensorchips

Surface plasmon resonance (SPR) is widely used to assess the kinetics and thermodynamics of binding of two molecules. The major challenge is immobilization of one molecule onto the sensorchip for robust detection of binding of the other molecule. We have compared a number of immobilization strategies for noncovalent attachment of an example protein (the substrate binding protein SiaP) by hexa-histidine (His), deca-His, and double-His tags to a nickel-nitrilotriacetic acid (NTA) surface. The stability of immobilization was assessed, and the binding of two low molecular weight ligands, Neu5Ac and 2-keto-3-deoxy-d-glycero-d-galacto-nononic acid (KDN), at different temperatures studied. The hexa-His tagged SiaP washed off from the surface too rapidly for ligand binding to be measured reliably. Systematic variation of chip loading identified conditions under which the deca-His tagged SiaP could generate reliable results. The double-His tagged protein performed as well as covalently attached deca-His tagged protein at 15, 25, and 35 °C. The observed ligand binding kinetics were comparable for all immobilization strategies, and thermodynamic values calculated from SPR are in agreement with solution-based isothermal titration calorimetry measurements. Extended trials suggest that covalent attachment is preferable for screening campaigns, whereas the double-His-tag strategy allows rapid regeneration of the chip, for example, when tight binding compounds are assessed.     

Numerical analysis of moisture vapor diffusion in asphalt mixtures using digital images

The presence of moisture in asphalt mixtures is detrimental to their performance, e.g., softening the asphalt binder and weakening the aggregate-binder bond. One of the mechanisms of moisture transport, and the focus of this study, is molecular diffusion. Moisture diffusion occurs in response to a concentration gradient. The objective of this study was to estimate the diffusion coefficient of moisture vapor in asphalt mixtures by using finite element (FE) and finite difference (FD) numerical algorithms that employ digital images to discretize the composite. X-ray computed tomography was used to characterize the microstructure of laboratory-prepared specimens and provide the required three-dimensional digital images, which were segmented into three phases: air voids, a mixture of asphalt binder and the fine aggregate fraction, and coarse aggregates. Individual diffusion coefficients were assigned to each phase and the effective diffusion coefficient for the composite was computed using the numerical algorithms. The outcome was compared against experimental values. The effective diffusion coefficient for the asphalt mixtures obtained using the FD method showed closer agreement with the experimental data, while the FE results overestimated the experimental measurements in all cases.     

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.     

Applications of a catch and release electrospray ionization mass spectrometry assay for carbohydrate library screening

Applications of a catch and release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against target proteins are described. Direct ESI-MS measurements were performed on solutions containing a target protein (a single chain antibody, an antigen binding fragment, or a fragment of a bacterial toxin) and a library of carbohydrates containing multiple specific ligands with affinities in the 10(3) to 10(6) M(-1) range. Ligands with moderate affinity (10(4) to 10(6) M(-1)) were successfully detected from mixtures containing >200 carbohydrates (at concentrations as low as 0.25 μM each). Additionally, the absolute affinities were estimated from the abundance of free and ligand-bound protein ions determined from the ESI mass spectrum. Multiple low affinity ligands (~10(3) M(-1)) were successfully detected in mixtures containing >20 carbohydrates (at concentrations of ~10 μM each). However, identification of specific interactions required the use of the reference protein method to correct the mass spectrum for the occurrence of nonspecific carbohydrate-protein binding during the ESI process. The release of the carbohydrate ligands, as ions, was successfully demonstrated using collision-induced dissociation performed on the deprotonated ions of the protein-carbohydrate complexes. The use of ion mobility separation, performed on deprotonated carbohydrate ions following their release from the complex, allowed for the positive identification of isomeric ligands.     

Determination of diffusion coefficients of glycerol and glucose from starch based thermoplastic compounds on simulated physiological solution

Blends of corn starch with poly(ethylene-vinylalcohol) copolymer (SEVA-C) have been studied and reported as biodegradable. These materials are known to be sensitive to enzymatic action, evidencing a degradation of the starch phase in -amylase assays. However, from the physical-chemical point of view the degradation of the blend is mainly associated with the leaching of glycerol, since other compounds are not released and no carbohydrates were found in the degradation solution. Based on these results, the present work attempts to determinate the respective diffusion coefficients. Four different experiments were performed, using samples with different thicknesses that were immersed in a simulated physiological solution. High performance liquid chromatography (HPLC) was used to separate the sugar derivatives and glycerol from the degradation solutions. The obtained data were fitted to an empirical model to allow the estimation of the diffusion coefficient for glycerol and glucose, based on the analytical solution for Ficks law of diffusion, and a good agreement was found (R² 1). The glycerol leaches quickly out during the first few days of immersion, stabilizing thereafter, presenting greater diffusion coefficients for thicker samples. As the quantity of saccharides in the solution remains almost invariable along the experiments, this work also confirms that the degradation process is difficult without the action of enzymes.     

Solid phase monofunctionalization of gold nanoparticles using ionic exchange resin as polymer support

A solid phase modification method using anionic exchange resin as polymer support was developed for the synthesis of monofunctional gold nanoparticles. Based on a "catch and release" mechanism to control the number of functional groups attached to the nanoparticle surface, bifunctional thiol ligands with a carboxylic acid end group were first immobilized at a controlled density on anionic exchange resin through electrostatic interactions. Gold nanoparticles were then immobilized to the anionic exchange resin by a one-to-one place exchange reaction between resin-bound thiol ligands and butanethiol-protected gold nanoparticles in solution. After cleaving off from the resin under mild conditions, gold nanoparticles with a single carboxyl group attached to the surface were obtained as the major product. Experimental conditions such as the solvents used for ligand loading and solid phase place exchange reaction, and the loading density of the ligands, were found to play a critical role towards the successful synthesis of monofunctional nanoparticles. Overall, the noncovalent bond-based ligand immobilization technique reported here greatly simplified the process of solid phase monofunctionalization of nanoparticles compared to a previously reported covalent bond-based ligand immobilization technique.     

"Multicolor" electrochemical labeling of DNA hybridization probes with osmium tetroxide complexes

Labeling of oligonucleotide reporter probes (RP) with electroactive markers has frequently been utilized in electrochemical detection of DNA hybridization. Osmium tetroxide complexes with tertiary amines (Os,L) bind covalently to pyrimidine (predominantly thymine) bases in DNA, forming stable, electrochemically active adducts. We propose a technique of electrochemical "multicolor" DNA coding based on RP labeling with Os,L markers involving different nitrogenous ligands (such as 2,2' -bipyridine, 1,10-phenanthroline derivatives or N,N,N',N'-tetramethylethylenediamine). At carbon electrodes the Os,L-labeled RPs produce specific signals, with the potentials of these differing depending on the ligand type. When using Os,L markers providing sufficiently large differences in their peak potentials, parallel analysis of multiple target DNA sequences can easily be performed via DNA hybridization at magnetic beads followed by voltammetric detection at carbon electrodes. Os,L labeling of oligonucleotide probes comprising a segment complementary to target DNA and an oligo(T) tail (to be modified with the osmium complex) does not require any organic chemistry facilities and can be achieved in any molecular biological laboratory. We also for the first time show that this technology can be used for labeling of oligonucleotide probes hybridizing with target DNAs that contain both purine and pyrimidine bases.     

Statistical analysis of concrete transport properties

Results of a statistical analysis of transport properties measurements carried out on a number of concrete mixtures are presented. Migration and drying experiments were performed to evaluate the ionic diffusion coefficients and permeability of concrete mixtures. Seven concrete mixtures were tested. The mixtures were either batched under laboratory conditions or sampled from construction sites. For each mixture, approximately eighty concrete samples from a single batch were tested. Ionic diffusion coefficients were calculated by analyzing the evolution of the electrical current passing through concrete samples during the migration tests. Calculations took into account the volume of permeable pores of the materials and the pore solution chemistry. Permeability was calculated from mass loss measured during drying tests. The study indicates that the coefficient of variation of ionic diffusion coefficients is 11.1 % on average, with a maximum of 23.5 %, and that the coefficient of variation of permeability is 20.6 % on average, with a maximum of 37.3 %.     

Quantifying ligand binding to large protein complexes using electrospray ionization mass spectrometry

An electrospray ionization mass spectrometry (ESI-MS) method for quantifying protein-ligand complexes that cannot be directly detected by ESI-MS is described. The proxy protein ESI-MS method combines direct ESI-MS binding measurements with competitive protein-ligand binding. To implement the method, a proxy protein (P(proxy)), which interacts specifically with the ligand of interest with known affinity and can be detected directly by ESI-MS, is used to quantitatively monitor the extent of ligand binding to the protein of interest. A mathematical framework for establishing the association constant (K(a)) for protein-ligand binding by the proxy protein ESI-MS method, implemented with a P(proxy) containing a single ligand binding site, is given. A modified form of the proxy protein ESI-MS method, which accounts for real-time changes in ligand concentration, is also described. The reliability of these methods is demonstrated for the interactions between the 180 kDa wildtype homotrimeric tailspike protein of the bacteriophage P22 and its endorhamnosidase point mutant (D392N) with its ligands comprising two and three O-antigen repeats from Salmonella enterica serovar Typhimurium: octasaccharide ([α-Gal-(1→2)-[α-Abe-(1→3)]-α-Man-(1→4)-α-Rha](2)) and dodecasaccharide ([α-Gal-(1→2)-[α-Abe-(1→3)]-α-Man-(1→4)-α-Rha](3)). A 27 kDa single chain antibody, which binds to both ligands, served as P(proxy). The results of binding measurements performed at 10 and 25 °C are in excellent agreement with K(a) values measured previously using a fluorescence quenching assay.