Quantitation of plasmid DNA in aqueous two-phase systems by fluorescence analysis

The development of aqueous two-phase systems for plasmid purification from Escherichia coli cell lysates requires a reliable DNA quantitation method. Plasmid DNA was quantified by fluorescence using PicoGreen nucleic acid stain. Linearity was obtained up to 40 ng plasmid ml^–1. Two polyethyleneglycol (PEG)/salt systems were studied, PEG 600/K₂HPO₄ and PEG 300/K₂HPO₄. The average plasmid recovery was 41% in the bottom phase of the first system and 35% in the top phase of the second system. This method has proved to be simple and reproducible.     

Relative hydrophobicity of organic compounds measured by partitioning in aqueous two-phase systems

Partitioning of a variety of organic compounds, the majority of which represent therapeutic drugs, was examined in an aqueous dextran–polyethylene glycol (Dex–PEG) two-phase system containing 0.15 M NaCl in 0.01 M sodium phosphate buffer at pH 7.3 and in an octanol–buffer (0.15 M NaCl in 0.01 M sodium phosphate buffer, pH 7.3) system. The possibility of introducing compounds to be partitioned in an aqueous two-phase system with dimethyl sulfoxide, and the effect of this solvent on the solute partitioning was explored. Relative hydrophobicity of the compounds was estimated and expressed in equivalent numbers of methylene units. Comparison of the results obtained for several subsets of compounds in the octanol–buffer and in aqueous Dex–PEG two-phase systems clearly demonstrates the advantage of aqueous two-phase partitioning for the hydrophobicity measurements over partitioning in octanol–buffer system.     

Multivalent ligand–receptor binding on supported lipid bilayers

Fluid supported lipid bilayers provide an excellent platform for studying multivalent protein–ligand interactions because the two-dimensional fluidity of the membrane allows for lateral rearrangement of ligands in order to optimize binding. Our laboratory has combined supported lipid bilayer-coated microfluidic platforms with total internal reflection fluorescence microscopy (TIRFM) to obtain equilibrium dissociation constant (K_D) data for these systems. This high throughput, on-chip approach provides highly accurate thermodynamic information about multivalent binding events while requiring only very small sample volumes. Herein, we review some of the most salient findings from these studies. In particular, increasing ligand density on the membrane surface can provide a modest enhancement or attenuation of ligand–receptor binding depending upon whether the surface ligands interact strongly with each other. Such effects, however, lead to little more than one order of magnitude change in the apparent K_D values. On the other hand, the lipophilicity and presentation of lipid bilayer-conjugated ligands can have a much greater impact. Indeed, changing the way a particular ligand is conjugated to the membrane can alter the apparent K_D value by at least three orders of magnitude. Such a result speaks strongly to the role of ligand availability for multivalent ligand–receptor binding.     

Solvatochromic studies in polyethylene glycol–salt aqueous biphasic systems

The polarities of the co-existing phases of a polyethylene glycol (PEG)-2000–K₃PO₄ aqueous biphasic system (ABS) have been examined using Reichardt’s carboxylated pyridinium-N-phenoxybetaine dye as a probe. Using this probe, the polarities of these phases have been compared to those of conventional solvent extraction systems and micellar systems using values obtained from the literature. In general, these extraction systems are comparable in polarity to rather polar solvents. Data on the free energy of transfer of solvents suggests that this may be due to the failure of the probe to account for the real polarity of the salt-rich phase compared to the polymer-rich phase. Examination of the monophasic region of these systems suggests that the reason for this is that the probe is partitioned to a discreet solvent domain dominated by PEG, even though phase separation of the solution is not observed. The use of linear free energy relationships for the characterization of ABS is briefly discussed.     

Tryptophanase in aqueous methanol: the solvent effects and a probable mechanism of the hydrophobic control of substrate specificity

To shed light on the mechanism of hydrophobic control in reactions of microbial tryptophanase the direct effect of the solvent hydrophobicity on affinities of amino acid inhibitors was first examined. Values of inhibition constants (K_i) for a variety of amino acids were determined in 37.5% aqueous methanol, and no general correlation between the change of K_i, on passing from water to aqueous methanol, and amino acid hydrophobicity was found. The solvent effects on the separate stages of the external aldimine formation (K_D) and deprotonation to form a quinonoid intermediate (K_q) were determined for the reactions of tryptophanase with 2-oxindolyl- -alanine and -alanine by stopped-flow technique. For 2-oxindolyl- -alanine, which is a close transition-state analogue for the enzyme reaction with natural substrate, the decrease in the affinity in aqueous methanol is associated exclusively with the α-proton abstraction stage but not with the preceding formation of external aldimine. We conclude that the environment of amino acid side chains in the active site cannot be considered to be permanently hydrophobic irrespective of the bound amino acid. We suggest that complexes of tryptophanase with amino acids may exist either in a hydrophobic, presumably “closed”, conformation, where bound amino acids are isolated from the solvent, or in an accesible to solvent, “open”, conformation, depending on the structure of the bound amino acid and stage of the catalytic mechanism. For 2-oxindolyl- -alanine the transfer from an open to a closed conformation probably accompanies deprotonation of the external aldimine. The change of the active site hydrophobicity may provide an efficient way of modulating the relative acid–base properties of the catalytic groups to ensure the movement of protons in the “correct” direction depending on the elementary stage of catalysis.     

Differentiation of EDTA-sensitive from EDTA-insensitive human serum esterases hydrolysing phenylacetate

The aim of this study was to differentiate the EDTA-sensitive from the EDTA-insensitive human serum esterases by evaluating their catalytic constants, K_M and V_m, for the hydrolysis of phenylacetate (PA). Measurements were done at 37°C in 0.1 M Tris/HCl buffer pH 7.4 and 8.4. The K_M,sen and K_M,ins constants were significantly different, 0.97 and 2.7 mM respectively, confirming that two esterases hydrolyse PA. The pH of the medium had no effect on K_M values, and also no effect on V_m,sen while V_m,ins was two fold higher at pH 8.4 than at 7.4 further confirming the existence of two different enzymes. The stability of the esterases in aqueous media was also studied. EDTA-sensitive activity in buffer without CaCl₂ was extremely unstable; the time-course of inactivation followed a two-phase reaction kinetics, indicating that two EDTA-sensitive esterases hydrolyse PA. The EDTA-insensitive activity remained constant in aqueous media under the same experimental conditions.     

Determination of the dissociation constant of valine from acetohydroxy acid synthase by equilibrium partition in an aqueous two-phase system

An aqueous polyethylene glycol/salt two-phase system was used to estimate the dissociation constant, K_dis, of the Escherichia coli isoenzyme AHAS III regulatory subunit, IlvH protein, from the feedback inhibitor valine. The amounts of the bound and free radioactive valine in the system were determined. A Scatchard plot of the data revealed a 1:1 valine–protein binding ratio and K_dis of 133±14 μM. The protein did not bind leucine, and the ilvH protein isolated from a valine resistant mutant showed no valine binding. This method is very simple, rapid and requires only a small amounts of protein compared to the presently used equilibrium dialysis method.     

Bovine serum albumin partitioning in an aqueous two-phase system: Effect of pH and sodium chloride concentration

The partitioning of bovine serum albumin (BSA) in a polyethylene glycol 3350 (8% w/w)–dextran 37 500 (6% w/w)–0.05 M phosphate aqueous two-phase was investigated at different pHs, at varying concentrations of sodium chloride at 20°C. The effect of NaCl concentration on the partition coefficient of BSA was studied for the PEG–dx systems with initial pH values of 4.2, 5.0, 7.0, 9.0, and 9.8. The NaCl concentrations in the phase systems with constant pH value were 0.06, 0.1, 0.2, 0.3, and 0.34 M. It was observed that the BSA partition coefficient decreased at concentrations smaller than 0.2 M NaCl and increased at concentrations greater than 0.2 M NaCl for all systems with initial pHs of 4.2, 5.0, 7.0, 9.0, and 9.8. It was also seen that the partition coefficient of BSA decreased as the pH of the aqueous two-phase systems increased at any NaCl salt concentration studied.     

Diffusion of sucrose in xanthan gum solutions

Molecular diffusion of solutes, like sucrose in the xanthan gum fermentation, is important in order to understand the complex behavior of mass transfer mechanisms during the process. This work was focused to determine the diffusion coefficient of sucrose, a carbon source for xanthan production, using similar sucrose and xanthan concentrations to those occurring in a typical fermentation. The diaphragm cell method was used in experimental determinations. The data showed that diffusion coefficient of sucrose significantly decreases when xanthan gum concentration increases. Theoretical and semiempirical models were used to predict sucrose diffusivity in xanthan solutions. Molecular properties and rheological behavior of the system were considered in the modeling. The models tested fitted well the behavior of experimental data and that reported for oxygen in the same system.List of Symbols A constant in eq. (5) - C _pg cm^–3 polymer concentration - D cm² s^–1 diffusivity - D _ABcm² s^–1 diffusivity of A through liquid solvent - D _APcm² s^–1 diffusivity of A in polymer solution - D _AWcm² s^–1 diffusivity of A in water - D _Pcm² s^–1 diffusivity of polymer in liquid solvent - E _D gradient of the activation energy for diffusion - H _P hydratation factor of the polymer in water (g of bound water/g of polymer) - K dyn sⁿ cm^–2 consistency index - K ₁ constant in eq. (5) - K _P overall binding coefficient [g of bound solute/cm³ of solution]/[g of free solute/cm³ of polymer free solution] - n flow behavior index - M _Bg g mol^–1 molucular weight of liquid solvent - M _Pg g mol^–1 molecular weight of the polymer - M _Sg g mol^–1 Molecular weight of polymer solution (= M _BX_B+M_PX_P) - R cm³ atm g mol^–1 K^–1 ideal gas law constant - T K absolute temperature - V _Bcm³ g mol^–1 molar volume of liquid solvent - V _Pcm³ g mol^–1 molar volume of polymer - V _Scm³ g mol^–1 molar volume of polymer solution - X _B solvent molar fraction - X _P polymer molar fraction - polymer blockage shape factor - _P volume fraction of polymer in polymer solution - g cm^–1 s^–1 viscosity - _ag cm^–1 s^–1 apparent viscosity of the polymer solution - _icm³ g^–1 intrinsic viscosity - ₀ g cm^–1 s^–1 solvent viscosity - _Pg cm^–1 s^–1 polymer solution viscosity - _R relative viscosity (= / ₀) - ₌₀ g cm^–1 s^–1 viscosity of polymer solution obtained at zero shear rate - ₀ g cm^–3 water density     

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

pH is a ubiquitous regulator of biological activity, including protein‐folding, protein‐protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH‐dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi‐site λ‐dynamics (CPHMD^MSλD). In the CPHMD^MSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi‐site λ‐dynamics, and designed novel biasing potentials to ensure that the physical end‐states are predominantly sampled. We show that explicit solvent CPHMD^MSλD simulations model realistic pH‐dependent properties of proteins such as the Hen‐Egg White Lysozyme (HEWL), binding domain of 2‐oxoglutarate dehydrogenase (BBL) and N‐terminal domain of ribosomal protein L9 (NTL9), and the pK_a predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pK_a units. With the recent development of the explicit solvent CPHMD^MSλD framework for nucleic acids, accurate modeling of pH‐dependent properties of both major class of biomolecules—proteins and nucleic acids is now possible. Proteins 2014; 82:1319–1331. © 2013 Wiley Periodicals, Inc.     

Dimerization constants of water-soluble porphyrins in aqueous alkali

Spectrophotometric analysis of changes in absorption spectra on dilution of different 2,4-disubstituted derivatives of deuteroporphyrin yielded dimerization constants (K_D) for each porphyrin in aqueous alkali. The K_D values appear to be related to the hydrophobic/hydrophilic interactions of the system such that K_D for proto- > meso- > deutero- > hemato- > coproporphyrin. The effects of alcohol, temperature, and ionic strength on the K_D were examined. A simple approach to the graphic analysis of the dilution curves is presented for use when absorbance readings at A₁₀₀ and A₀ cannot be reliably determined, and the use of soluble porphyrins as model systems for studying hydrophobic/hydrophilic interactions in aqueous media is discussed.     

Transport of malic acid in Leuconostoc oenos strains defective in malolactic fermentation: a model to evaluate the kinetic parameters

Two Leuconostoc oenos mutant strains unable to metabolize malic acid were differentiated by [U-¹⁴C]-labelled L-malate transport assays into a malolactic-enzyme-deficient mutant and a malate-transport-defective mutant. A mathematical analysis of the data from L-malic acid uptake at three pH values (5.2, 4.5, and 3.2) in the malolactic-enzyme-deficient strains suggest two simultaneous uptake mechanisms, presumably a carrier-mediated transport and a passive diffusion for the anionic and the undissociated forms of the acid, respectively. The apparent affinity constant (K _m t) and the maximal rate (V _m t) values for L-malate active transport were, 12 mM and 43 mol L-malate·mg^–1·s^–1, respectively. Active transport was constitutive and strongly inhibited by protonophores and by ATPase inhibitors. L-Lactic acid appeared to inhibit L-malic acid transport, suggesting an L-lactate/L-malate exchange. At pH values of 4.5 or above, the passive diffusion of L-malic acid was negligible. However, at pH 3.2, the mean pH of wine, the permeability of the cells to the undissociated acid by simple diffusion could represent more than 50% of total L-malic acid uptake, with a diffusion constant (K _D) of 0.1 s^–1. Correspondence to: C. Divies     

Effect of CPC,Brij-35, and SDBS Surfactants on the Adsorption and Movement of Carbofuran in Indian Soils

Laboratory studies were conducted to determine adsorption and movement of carbofuran in aqueous surfactant-free and surfactant [(cationic, cetyl pyridinium chloride (CPC), non-ionic, polyoxyethylene lauryl ether (Brij-35) and anionic, sodium dodecyl benezene sulphonate (SDBS)] solutions of different critical micellar concentrations (1/2 × CMC, 1.0 × CMC, and 2 × CMC) in four different Indian soils using batch shake and soil thin layer chromatography (soil TLC) techniques. The measured equilibrium adsorption isotherms were in agreement with the Freundlich equation. Higher adsorption of carbofuran in both systems was observed on FRI silt loam (FSL) soil followed by Alampur silt loam (ASL), Kalai loam (KL), and Bhoran sandy loam (BSL) soils, as anticipated from Freundlich constant K_F and distribution coefficient K_D, in surfactant-free systems and K_F* and K_D* in surfactant-soil-water systems. The adsorption of carbofuran in surfactant-soil-water systems followed the order cationic > anionic > non-ionic at all CMCs studied. The R_f values obtained from soil TLC studies confirmed the above order of adsorption. The K_D and K_D* values were used to evaluate remediation efficiency (K_D*/K_D) of surfactants. Non-ionic surfactant, Brij-35, and anionic surfactant, SDBS, are favorable for remediating soil contaminated with carbofuran as K_D*/K_D ratio is less than 1.     

Analysis of continuous fermentation processes in aqueous two-phase systems

Simulations of continuous ethanol or acetonobutylic fermentations in aqueous two-phase systems show that at high substrate feed concentrations it is possible to obtain solvent productivities about 25–40% higher than in conventional systems with cell recycle if the biomass bleed rate is kept about one tenth of the value of D.List of Symbols a Volumetric fraction of dextran rich phase - B h^–1 Bleed rate - D h^–1 Dilution rate - P kg m^–3 Product concentration - PD kg m^–3 h^–1 Productivity - S kg m^–3 Substrate - X kg m^–3 Biomass - Partition coefficient     

Modelling alterations in the partition coefficient in in vitro biological systems using headspace gas chromatography

Headspace gas chromatography was used to determine the physiological media–air partition coefficient (K) of four volatile organic solvents of industrial importance. The experimental conditions were those likely to be used in in vitro metabolic and toxicological studies on volatile compounds. The addition of solvent to the liquid phase from a stock solution in ethanol, or the presence of organic material at concentrations normally seen in in vitro studies, did not significantly alter the K value. Binary solvent addition resulted in a dose-dependent decrease in K for each solvent that was also influenced by the solvent solubility and the constituents of the liquid matrix. The aromatic solvents exerted the greatest effect and showed the greatest change in K value.     

Reversible addition of bisulfite buffer to the cytidine ring system

The rate constants for the reversible addition of protons and sulfite to the 5,6 double bond of cytidine and 3-methylcytidine have been spectrophotometrically measured under conditions (25°C, μ = 1.0 ) where the deamination of 5,6-dihydrocytidine-6-sulfonate is minimal. Both the addition and the elimination of sulfite from the ring system are subject to general catalysis of proton transfer. For the reaction in either direction, plots of the pseudo-firstorder rate constants against increasing buffer concentration are biphasic and indicative of at least a two-step reaction pathway with both steps being subject to general acid-base catalysis. Kinetic hydrogen-deuterium isotope effects were measured for both buffer-catalyzed steps of sulfite elimination from 3-methyl-5,6-dihydrocytidine-6-sulfonate and sulfite addition to 3-methylcytidine. Both H₂O and D₂O were used as solvent. For both the addition and the elimination of SO₃²⁻ values of k₂^H/k₂^D were 6.3–7.1 and 2.3–2.6 at low and high imidazole buffer concentration, respectively. The large isotope effects values in the range of 6–7 can be attributed to rate-determining proton transfer to carbon-5 of the cytidine ring system. The smaller values are more likely caused by proton transfer to a electronegative atom such as the oxygen on carbon-2 of the cytidine ring. The equilibrium constants for bisulfite buffer addition to 3-methylcytidine and cytidine at 25°C, μ = 1.0 , pH 7.2, are 10.2 and 1.3 ⁻¹, respectively.     

Normal acid behavior for C(α)-proton transfer from a thiazolium lon

Rate constants for C(α)-proton transfer from racemic 2-(1-hydroxyethyl)-3,4-dimethylthi-oazolium ion catalyzed by lyoxide ion and various oxygen-containing and amine buffers were determined by iodination at 25°C and ionic strength 1.0 in H₂O. Thermodynamically unfavorable C(α)-proton transfer to oxygen-containing and amine bases shows general base catalysis with a Brønsted β value of ≥0.92 for bases of pK_a^′ ≤ 15; this indicates that the thermodynamically favorable protonation reaction in the reverse direction has a Brønsted α value ≤0.08, which is consistent with diffusion-controlled reprotonation of the C(α)-enamine by most acids. General base catalysis is detectable because there is an 85-fold negative deviation from the Brønsted correlation by hydroxide ion. Primary kinetic isotope effects of (k_H/k_D)_obsd = 1.0 for thermodynamically unfavorable proton transfer to buffer bases and hydroxide ion (ΔpK_a ≤ −6) and a secondary solvent isotope effect of k_DO⁻/k_HO⁻ = 2.3 for C(α)-proton transfer are consistent with a very late, enamine-like transition state and rate-limiting diffusional separation of buffer acids from the C(α)-enamine in the rate-limiting step, as expected for a “normal” acid. The second-order rate constants for catalysis by buffer bases were used to calculate a pK_a^′ of 21.8 for the C(α)-proton assuming a rate constant of 3 × 10^{9 −1} s⁻¹ for the diffusion-controlled reprotonation of the C(α)-enamine by buffer acids in the reverse direction. It is concluded (i) that C(α)-proton removal occurs at the maximum possible rate for a given equilibrium constant, and (ii) that C(α)-enamines can have a significant lifetime in aqueous solution and on thiamin diphosphate-dependent enzymes.     

Different arachidonate and palmitate binding capacities of the human red cell membrane

Human red cell membrane bindings of arachidonate and palmitate at pH 7.3 are investigated at temperatures between 0 and 38°C by equilibrating ghosts with the long-chain fatty acids bound to bovine serum albumin in molar ratios (v) within the physiological range (<1.7). Linearized relations of ghost uptakes and fatty acid monomer concentrations in buffer provide estimates of the binding capacities and corresponding equilibrium dissociation constants (K _dm ). The temperature-independent arachidonate binding capacity, 5.5 ± 0.5 nmol g^–1 packed ghosts, is approximately fivefold smaller than that of palmitate, 26.6 ± 2.0 nmol g^–1. While K _dm of arachidonate binding 5.1 ± 0.5 nm is temperature independent, K _dm of palmitate increases with temperature from 3.7 nm at 0°C to 12.7 nm at 38°C.The large difference in binding capacities suggests the presence of at least two different fatty acid binding domains in human red cell membranes.     

Molecular interactions of hormonal steroids: the participation of the 17 side chain of corticosteroids in the formation of complexes with Co (II.). II

The c₂₀-c₂₁ α-ketol system of the 176 side chain of deoxycorti-costerone is in equilibrium with its c₂₀-c₂₁ enediol. The apparent dissociation constant of this enol was determined by a photometric method using crystal violet indicator; p K_a¹ = 10.65 ± 044. Formation constants of the (1:1) deoxycorticosterone-cobalt (II) complex were determined by solvent extraction and in mixed solvent systems. The complex formation constant K_f in an aqueous medium was found by graphical extrapolation to be 2.5–3.0 × 10⁻¹ 1. mole⁻¹     

Impact of hapten presentation on antibody binding at lipid membrane interfaces

We report the effects of ligand presentation on the binding of aqueous proteins to solid supported lipid bilayers. Specifically, we show that the equilibrium dissociation constant can be strongly affected by ligand lipophilicity and linker length/structure. The apparent equilibrium dissociation constants (K_D) were compared for two model systems, biotin/anti-biotin and 2,4-dinitrophenyl (DNP)/anti-DNP, in bulk solution and at model membrane surfaces. The binding constants in solution were obtained from fluorescence anisotropy measurements. The surface binding constants were determined by microfluidic techniques in conjunction with total internal reflection fluorescence microscopy. The results showed that the bulk solution equilibrium dissociation constants for anti-biotin and anti-DNP were almost identical, K_D(bulk) = 1.7 ± 0.2 nM vs. 2.9 ± 0.1 nM. By contrast, the dissociation constant for anti-biotin antibody was three orders of magnitude tighter than for anti-DNP at a lipid membrane interface, K_D = 3.6 ± 1.1 nM vs. 2.0 ± 0.2 μM. We postulate that the pronounced difference in surface binding constants for these two similar antibodies is due to differences in the ligands’ relative lipophilicity, i.e., the more hydrophobic DNP molecules had a stronger interaction with the lipid bilayers, rendering them less available to incoming anti-DNP antibodies compared with the biotin/anti-biotin system. However, when membrane-bound biotin ligands were well screened by a poly(ethylene glycol) (PEG) polymer brush, the K_D value for the anti-biotin antibody could also be weakened by three orders of magnitude, 2.4 ± 1.1 μM. On the other hand, the dissociation constant for anti-DNP antibodies at a lipid interface could be significantly enhanced when DNP haptens were tethered to the end of very long hydrophilic PEG lipopolymers (K_D = 21 ± 10 nM) rather than presented on short lipid-conjugated tethers. These results demonstrate that ligand presentation strongly influences protein interactions with membrane-bound ligands.