Orientation of the pore-forming peptide GALA in POPC vesicles determined by a BODIPY-avidin/biotin binding assay

We determined the orientation of a biotinylated version of the pore-forming peptide GALA (WEAALAEALAEALAEHLAEALAEALEALAA) at pH 5.0 in large unilamellar phosphatidylcholine vesicles, using the enhancement of BODIPY-avidin fluorescence subsequent to its irreversible binding to a biotin moiety. GALA and its variants were biotinylated at the N- or C-terminus. BODIPY-avidin was either added externally or was pre-encapsulated in vesicles to assess the fraction of liposome-bound biotinylated GALA that exposed its labeled terminus to the external or internal side of the bilayer, respectively. Under conditions where most of the membrane-bound peptides were involved in transmembrane aggregates and formed aqueous pores (at a lipid/bound peptide molar ratio of 2500/1), the head-to-tail (N- to C-terminus) orientation of the membrane-inserted peptides was such that 3/4 of the peptides exposed their N-terminus on the inside of the vesicle and their C-terminus on the outside. Under conditions resulting in reduced pore formation (at higher lipid/peptide molar ratios), we observed an increase in the fraction of GALA termini exposed to the outside of the vesicle. These results are consistent with a model (Parente et al., Biochemistry, 29:8720, 1990) that requires a critical number of peptides (M) in an aggregate to form a transbilayer structure. When the peptides form an aggregate of size i, with i < M = 4 to 6, the orientation of the peptides is mostly parallel to the membrane surface, such that both termini of the biotinylated peptide are exposed to external BODIPY-avidin. This BODIPY-avidin/biotin binding assay should be useful to determine the orientation of other membrane-interacting molecules.     

Thermodynamics of the binding of biotin and some analogues by avidin

1. The reaction between avidin and biotin was found to be exothermic, ΔH being −20·3kcal./mole of biotin bound. The corresponding value of ΔH for streptavidin was −23kcal./mole. 2. The heat evolved was independent of the pH (between 5 and 9), of the buffer (borate or ammonia) and of the fractional saturation of the avidin with biotin. 3. The entropy change for the reaction was zero, and it is suggested that the entropy increase to be expected from hydrophobic interactions was counterbalanced by a decrease in entropy accompanying the formation of buried hydrogen bonds. 4. Modification of the potential hydrogen-bonding sites of the imidazolidone ring led to a decreased heat output and a positive entropy of reaction.     

Evaluation of a competitive binding assay for cortisol using horse transcortin

A non-chromatographic competitive binding assay (CBA) using horse transcortin has been employed in the routine measurement of cortisol in plasma, urine and amniotic fluids. Comparing the values with those of a radioimmunoassay (RIA) or a fluorimetric method (FM) an excellent correlation between the three methods both in plasma and urine has been calculated in normal subjects and in patients with various endocrine disorders. In amniotic fluids, however, there were discrepancies between CBA and RIA. Whereas CBA showed no differences, RIA gave significantly higher values in amniotic fluids of female than of male fetuses. Elevated free plasma cortisol levels observed in patients with prostatic cancer after diethyl stilboestrol diphosphate therapy did not correlate with unconjugated urinary cortisol concentration as measured with CBA and FM. In newborns, a relatively high plasma level found 12 hours after birth was followed by a nadir on the 2nd and 3rd day of life and by an increase until levels of adults on the 5th day of life were reached.     

A competitive protein binding assay for allopurinol and oxipurinol

A competitive protein binding assay for allopurinol or oxipurinol has been developed based on the tight binding of these drugs to reduced xanthine oxidase. Free drug is separated from that bound to xanthine oxidase by absorption with dextran-albumin coated charcoal. This assay can detect as little as 0.1 μm allopurinol or oxipurinol in water, serum, plasma, or urine. Competitive analogs such as hypoxanthine, xanthine, and uric acid require concentrations 100- to 1000-fold greater than those of allopurinol or oxipurinol to cause significant interference with the assay. This assay is simple and rapid with the ability to assay 20–30 samples within 2 h. Measurement of oxipurinol levels in clinical samples shows good correlation with published results using more complex analytical techniques.     

Dye-release assay for investigation of antimicrobial peptide activity in a competitive lipid environment

A dye-release method for investigating the effect of a competitive lipid environment on the activity of two membrane-disrupting antimicrobial peptides (AMP), maculatin 1.1 and aurein 1.2, is presented. The results support the general conclusion that AMP have greater affinity for negatively charged membranes, for example bacterial membranes, than for the neutral membrane surface found in eukaryotic cells, but only within a competitive lipid environment. Indeed, in a single-model membrane environment, both peptides were more potent against neutral vesicles than against charged vesicles. The approach was also used to investigate the effect of pre-incubating the peptides in a neutral lipid environment then introducing charged lipid vesicles. Maculatin was shown to migrate from the neutral lipid bilayers, where pores had already formed, to the charged membrane bilayers. This result was also observed for charged-to-charged bilayers but, interestingly, not for neutral-to-neutral lipid interfaces. Aurein was able to migrate from either lipid environment, indicating weaker binding to lipid membranes, and a different molecular mechanism for lysis of lipid bilayers. Competitive lipid environments could be used to assess other critical conditions that modulate the activity of membrane peptides or proteins.     

Solid phase enzyme-linked competitive binding assay for riboflavin

A new solid-phase enzyme-linked assay for riboflavin (vitamin B2) is described. The assay is based on the competition between analyte vitamin molecules and a glucose-6-phosphate dehydrogenase-3-carboxymethylriboflavin conjugate for a limited number of riboflavin-binding protein sites immobilized on Sepharose particles. Significant improvements in conjugate catalytic activity and thus detectability are achieved by optimizing the reaction conditions used to covalently link 3-carboxymethylriboflavin to the enzyme. Optimization experiments include studying the effects of reaction pH and organic solvent composition. Final assay detection limits and the sensitivity of the dose-response curves are dependent on the ratio of conjugate to binding protein sites utilized in an equilibrium assay protocol. Selectivity of the method correlates well with that predicted based on the known association constants of riboflavin-binding protein with flavin analogs. The assay is shown to offer adequate detection limits and selectivity for direct measurement of riboflavin in urine, infant formula, and vitamin capsules.     

A competitive binding assay for fructose 2,6-bisphosphate

A new direct assay method for fructose 2,6-bisphosphate has been developed based on competitive binding of labeled and unlabeled fructose 2,6-P2 to phosphofructokinase. Phosphofructokinase (0.5-1.3 pmol protomer) is incubated with saturating concentrations (5.0-5.5 pmol) of fructose 2,6-[2-32P]P2 and samples containing varying concentrations of fructose 2,6-P2. The resulting stable binary complex is retained on nitrocellulose filters with a binding efficiency of up to 70%. Standard curves obtained with this assay show strict linearity with varying fructose 2,6-P2 in the range of 0.5 to 45 pmol, which exceeds the sensitivity of most of the previously described assay methods. Fructose 2,6-P2, ATP, and high concentrations of phosphate interfere with this assay. However, the extent of this inhibition is negligible since their tissue contents are one-half to one-tenth that examined. This new assay is simple, direct, rapid, and does not require pretreatment of tissue extracts.     

Determination of calmodulin by competitive binding assay

Calmodulin levels in tissue or cellular extracts can be determined by competition with 125I-calmodulin in a filtration-based direct binding assay. The method is rapid, uses readily available stable components, and possesses a selectivity and sensitivity comparable to that observed with immunoassay and phosphodiesterase activation. This assay provides a tool to readily probe changes in calmodulin levels in cells and tissues as a function of pathophysiologic state.     

A reexamination of the chelex competitive calcium binding assay

The chelex competitive calcium binding assay has been examined as a tool for the analysis of the kinetic parameters of calcium binding substances. Scatchard analysis of calcium binding demonstrates that chelex binds calcium with apparent negative cooperativity or with more than one class of calcium binding sites, and therefore, cannot be used to provide accurate estimations of the dissociation constant or total number of binding sites on an unknown ligand. Results presented in this study indicate that the chelex assay can be effectively used for the qualitative detection of calcium binding substances in tissue extracts or biological fluids.     

Flow cytometric competitive binding assay for determination of actinomycin-D concentrations

A single step, separation free competitive binding reaction between the fluorescent antibiotic mithramycin and actinomycin-D for common binding sites on DNA coated 10 microns diameter microspheres is described. The fluorescence of the microspheres is measured with a flowcytometer. In the presence of a constant amount of mithramycin, the microsphere fluorescence is inversely proportional to actinomycin-D concentration.     

Measurement of a progestational and antiandrogenic compound by a competitive protein binding assay

Medrogestone (MDG), viz. 6,17-dimethy1-4,6-pregnadiene-3,20-dione (Colprone®) is a compound with progestational and antiandrogenic properties. A simple method based on competitive protein binding is described for the determination of piasma MDG concentration. The method involves extraction with petroleum ether of a small volume of human plasma (50–200 μ1) containing an internal standard of 3_H-progesterone for the correction of procedural losses. Sample MDG is used to displace ³H-progesterone bound to pregnant quinea pig serum. Free and bound ³H-progesterone are separated by the use of Florisil. The precision, accuracy, reproducibility and specificity of the assay were evaluated and shown to be satisfactory for the measurement of MDG in human male plasma. The concentration of MDG in blood after oral administration was determined in male dogs and humans. The compound was rapidly absorbed; partially micronized MDG produced higher blood levels than the non-micronized compound.     

Enzymatic solid-phase assay for biotin and a biotin-benzodiazepine conjugate

A novel enzymatic ligand binding assay for biotin and its benzodiazepine conjugate is based on their binding to horseradish peroxidase-avidin conjugate (A-P) followed by the uptake of biotin-unsaturated A-P onto polystyrene beads coated with biotin-BSA. The detection limit is 1.3 x 10(-16) mol per tube (300 microL) with a 3.3 x 10(-12) M A-P solution and varies with the conjugate concentration employed. The coefficient of variation for 10 repetitive assays of 10(-15) mol of biotin is 6.22%.     

A sensitive competitive protein binding assay for vitamin D in plasma

A sensitive protein binding assay for vitamin D is described. The vitamin D3 was extracted from plasma with diethyl ether and methylene chloride. The lipid extract was purified in Sephadex LH-20 followed by Lipidex 5000 and finally by high pressure liquid chromatography on a Zorbax Sil column (0.79 x 25 cm) developed in 0.25:99.75 isopropanol: methylene chloride. The vitamin D fraction was collected and quantitated by competitive protein binding assay with a 1/50,000 dilution of sheep plasma in 0.05 M potassium phosphate buffer (pH 7.5) containing 0.01% gelatin. [H3]-25-Hydroxyvitamin D3 was used as a radioactive tracer in the assay. We found that under these conditions, sheep plasma had equal affinity for vitamin D2 and vitamin D3 and could detect as little as 0.1 ng of vitamin D. When rat, cow, or human plasma was substituted for the sheep plasma, the decline in sensitivity to vitamin D2 was fivefold to tenfold. With this assay, we found excellent agreement (r = 0.98) between the results obtained by competitive protein binding analysis and direct U.V. absorbance analysis by high pressure liquid chromatography.     

A competitive binding assay for measurement of heparan sulfate in tissue digests

Glycosaminoglycans complex with constituents of normal human serum, a finding that was exploited to develop a competitive binding assay for these substances. Heparan sulfate was isolated from renal cortex and radiolabeled with tritiated borohydride. The elution pattern of the radiolabeled material on Sephadex G-25, Bio-Gel P-30, and AG- 1X8 resin was identical to that of unlabeled heparan sulfate. The tritiated heparan sulfate formed radiolabeled precipitates when incubated with serum and zinc acetate. Binding was dose dependent and saturable. Heparin, heparan sulfate, and the chondroitin sulfates, but not hyaluronate or keratan sulfate, competed with the radiolabeled heparan sulfate for binding in a dose-dependent manner. The assay is specific for heparin polysaccharides in chondroitinase ABC-treated samples and is sensitive to microgram quantities.     

Simple reproducible competitive radioligand assay for plasma protein binding of aldosterone

A simple reliable and specific binding assay for the estimation of plasma (or serum) aldosterone-binding globulins (ABGs) is described. The method is based on the determination of the aldosterone-binding capacity of diluted plasma (with water 1:5), and relating it to the total aldosterone concentration in the same sample. The method distinguishes between the heat-labile and heat-stable ABG, the binding to the latter being determined following heating of plasma at 60 degrees C for 25 min. The binding to the heat-labile protein is determined by subtraction of the value for the binding to the heat-stable protein from the binding of the nonheated diluted plasma. Free aldosterone is separated from the bound fraction by adsorption of the former to dextran-coated charcoal. Two different concentrations of [3H]-aldosterone are used throughout the assay. Data obtained by incorporating chromatographic separation into the cross-reactivity procedure using several steroids are presented as evidence for the specificity of the method. This chromatography separates plasma ABG from corticosteroid-binding globulin. In 316 male or female controls, ABG capacity was 9.7 +/- 0.38% (SE)-range 2-17. Samples in females were taken during the first 8 days from the onset of menstruation. Higher ABG-binding capacity (p less than 0.001) was found during pregnancy.     

A single-step competitive binding assay for mapping of single DNA molecules

Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification of pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.     

Pardaxin, a fish toxin peptide interaction with a biomimetic phospholipid/polydiacetylene membrane assay

Pardaxin is a fish toxin belonging to the alpha-helical, pore-forming peptide family, used in toxicological and biophysical research to study toxin-cell and -lipid-artificial membranes interactions. We investigated the membrane interaction of two pardaxin analogues using a colorimetric phospholipid/polydiacetylene biomimetic assay. In this assay, polydiacetylene undergoes visible, concentration dependent, blue-red transformation induced through interactions of pardaxins with the vesicle membrane. Pardaxins P4 and P5, are composed of 33 amino acids, but differ in a single amino acid substitution at the carboxy-terminal (G(31) to D(31), respectively) known to decrease the pore forming activity. Addition of pardaxins in the colorimetric assay induced dose-dependent color transitions with different kinetics. The colorimetric analysis could distinguish between different pardaxins-membrane interaction profiles, suggesting bilayer surface association for P4 and vesicle membrane penetration for P5. The colorimetric assay could distinguish between pardaxins membrane interaction profiles although circular dichroism spectra of vesicle-interacting pardaxins did not indicate a significant difference in the secondary structure between these two toxin analogues. The colorimetric platform utilized in the present report represents a useful assay with general applications for studying membrane interactions of peptides in general and pore-forming toxins in particular, and may become an important tool for evaluating quantitative toxin structure-activity relationship.