Solid-phase assay for determination of binding parameters of ligand-protein complexes with high dissociation rates

The binding parameters, the affinity constant (Ka) and binding capacity (Q), of a protein possessing ligand-protein complexes with a high dissociation rate (Sex Steroid Binding protein from Bufo arenarum) were determined using a solid-phase method. The technique is based upon the adsorption of the steroid-protein complex to DEAE-cellulose. This method was compared with a nonequilibrium method (charcoal adsorption of free ligand), and the latter resulted in underestimation of both binding parameters, Ka and Q. The solid-phase method reported here is appropriate to determine the binding parameters of proteins with high dissociation rates because the results are independent of the complex half-time. The method also possesses advantages compared to other equilibrium assays such as dialysis or steady-state electrophoresis. With minor modifications, it may be useful to characterize different proteins, particularly those possessing ligand-protein complexes with very high dissociation rates.     

Kinetics of actin-myosin binding. Myosin cooperativity and mixed single-headed and two-headed binding

A model is proposed for the kinetics of actin-myosin interaction that allows for the presence of both one- and two-headed myosin fragments, cooperativity between myosin sites, and the molecular weight distribution of actin filaments. The approach employed makes use of the notion of effectivity factors. In the most general case, the system is described by six coupled first-order differential equations. When only single-headed myosin (S1) is present, the model reduces to simpler versions introduced previously.     

Avidin-biotin interactions at vesicle surfaces: adsorption and binding, cross-bridge formation, and lateral interactions.

Densely packed domains of membrane proteins are important structures in cellular processes that involve ligand-receptor binding, receptor-mediated adhesion, and macromolecule aggregation. We have used the biotin-avidin interaction at lipid vesicle surfaces to mimic these processes, including the influence of a surface grafted polymer, polyethyleneglycol (PEG). Single vesicles were manipulated by micropipette in solutions of fluorescently labeled avidin to measure the rate and give an estimate of the amount of avidin binding to a biotinylated vesicle as a function of surface biotin concentration and surface-grafted PEG as PEG-lipid. The rate of avidin adsorption was found to be four times less with 2 mol% PEG750 than for the unmodified surface, and 10 mol% PEG completely inhibited binding of avidin to biotin for a 2-min incubation. Using two micropipettes, an avidin-coated vesicle was presented to a biotinylated vesicle. In this vesicle-vesicle adhesion test, the accumulation of avidin in the contact zone was observed, again by using fluorescent avidin. More importantly, by controlling the vesicle membrane tension, this adhesion test provided a direct measure of the spreading pressure of the biotin-avidin-biotin cross-bridges confined in the contact zone. Assuming ideality, this spreading pressure gives the concentration of avidin cross-bridges in the contact zone. The rate of cross-bridge accumulation was consistent with the diffusion of the lipid-linked "receptors" into the contact zone. Once adherent, the membranes failed in tension before they could be peeled apart. PEG750 did not influence the mechanical equilibrium because it was not compressed in the contact zone, but it did perform an important function by eliminating all nonspecific adhesion. This vesicle-vesicle adhesion experiment, with a lower tension limit of 0.01 dyn/cm, now provides a new and useful method with which to measure the spreading pressures and therefore colligative properties of a range of membrane-bound macromolecules.     

Kinetics of actin-myosin binding. II. Two-variable model and actin gelation

We consider a model of actin-myosin interaction in which the sites belonging to each seven-site regulated actin unit are subdivided into two classes, "internal" and "external." The time evolution of each class of sites is considered separately, leading to a pair of coupled differential equations that may be integrated numerically. We also consider the critical sol-gel transition point for actin filaments crosslinked by two-headed heavy meromyosin (HMM). The possibility of new types of chemical oscillation and pattern formation arising from periodic sol-gel transitions is discussed.     

The function of interdomain interactions in controlling nucleotide exchange rates in transducin

The intramolecular contacts in heterotrimeric G proteins that determine the rates of basal and receptor-stimulated nucleotide exchange are not fully understood. The alpha subunit of heterotrimeric G proteins consists of two domains: a Ras-like domain with structural homology to the monomeric G protein Ras and a helical domain comprised of six alpha-helices. The bound nucleotide lies in a deep cleft between the two domains. Exchange of the bound nucleotide may involve opening of this cleft. Thus interactions between the domains may affect the rate of nucleotide exchange in G proteins. We have tested this hypothesis in the alpha subunit of the rod cell G protein transducin (Galpha(t)). Site-directed mutations were prepared in a series of residues located at the interdomain interface. The proteins were expressed in vitro in a reticulocyte lysate system. The rates of basal and rhodopsin-catalyzed nucleotide exchange were determined using a trypsin digestion assay specifically adapted for kinetic measurements. Charge-altering substitutions of two residues at the interdomain interface, Lys(273) and Lys(276), increased basal nucleotide exchange rates modestly (5-10-fold). However, we found no evidence that interactions spanning the two domains in Galpha(t) significantly affected either basal or rhodopsin-catalyzed nucleotide exchange rates. These results suggest that opening of the interdomain cleft is not an energetic barrier to nucleotide exchange in Galpha(t). Experiments with Galpha(i1) suggest by comparison that the organization and function of the interdomain region differ among various G protein subtypes.     

Kinetics of actin-myosin binding. ATP-ase activity and sol-gel dissipative structures

The simple kinetic model of actin-myosin binding-dissociation process including ATP-ase activity is considered. We demonstrated how one may easily include cooperativity in such a model by using effectivity factors introduced in our previous papers. A possibility of further simplifying the model through quasi-stationary approximation for some variables is considered. Sol-gel dissipative structures and possible biological implications of such structures are discussed.     

Comparing mono- and divalent DNA groove binding cyanine dyes -- binding geometries, dissociation rates, and fluorescence properties

The unsymmetrical cyanine dyes BOXTO-PRO and BOXTO-MEE were derived from the DNA groove binder BOXTO, by adding a positively charged or a non-ionic hydrophilic tail to BOXTO, respectively. The main objective was to obtain more efficient DNA probes, for instance in electrophoresis and microscopy, by slowing down the dissociation of BOXTO from DNA. The interactions with mixed sequence DNA was studied with fluorescence and absorbance spectroscopy, stopped-flow dissociation and gel electrophoresis. Both the derivatives are groove bound as BOXTO, and have similar fluorescence properties when bound to mixed sequence DNA in free solution. BOXTO-PRO exhibits a slower dissociation than BOXTO from DNA, whereas the dissociation rate for BOXTO-MEE is faster and, unexpectedly independent of the ionic strength. During gel electrophoresis both BOXTO-PRO and BOXTO-MEE exhibit a faster dissociation rate than BOXTO. Still, BOXTO-PRO seems to be a good alternative as DNA probe, especially for applications in free solution where the dissociation is slower than for the corresponding intercalator TOPRO-1.     

Selective formation of Sed5p-containing SNARE complexes is mediated by combinatorial binding interactions

Sed5p is the only syntaxin family member required for protein transport through the yeast Golgi and it is known to bind up to nine other soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins in vivo. We describe in vitro binding experiments in which we identify ternary and quaternary Sed5p-containing SNARE complexes. The formation of SNARE complexes among these endoplasmic reticulum- and Golgi-localized proteins requires Sed5p and is syntaxin-selective. In addition, Sed5p-containing SNARE complexes form selectively and this selectivity is mediated by Sed5p-containing intermediates that discriminate among subsequent binding partners. Although many of these SNAREs have overlapping distributions in vivo, the SNAREs that form complexes with Sed5p in vitro reflect their functionally distinct locales. Although SNARE-SNARE interactions are promiscuous and a single SNARE protein is often found in more than one complex, both the biochemical as well as genetic analyses reported here suggest that this is not a result of nonselective direct substitution of one SNARE for another. Rather our data are consistent with the existence of multiple (perhaps parallel) trafficking pathways where Sed5p-containing SNARE complexes play overlapping and/or distinct functional roles.     

Site-specific cyclic nucleotide binding and dissociation of the holoenzyme of cAMP-dependent protein kinase

The photoaffinity reagent 8-azidoadenosine 3':5'-monophosphate (8-N3cAMP) was previously shown to modify a single tyrosine residue on the type II regulatory subunit of cAMP-dependent protein kinase (Kerlavage, A.R., and Taylor, S.S. (1980) J. Biol. Chem, 255, 8483-8488). In the present studies, the binding stoichiometries of type II holoenzyme for cAMP and 8-N3cAMP were determined using Millipore filtration assays in the absence (Assay A) and presence (Assay B) of 2 M NaCl and histone. The binding stoichiometry of holoenzyme for cAMP was 2 mol/mol with Assay A, and 4 mol/mol with assay B. The binding stoichiometry for 8-N3cAMP was 2 mol/mol with Assay B or with Assay A following photolysis of the holoenzyme:8-N3cAMP mixture. In the absence of photolysis, the binding stoichiometry for 8-N3cAMP was 0.4 mol/mol with Assay A. Both 8-N3cAMP and cAMP fully dissociated the holoenzyme. Holoenzyme, labeled with 8-N3[3H]cAMP on a preparative scale, incorporated 1 mol of 8-N3[3H]cAMP/mol of regulatory subunit (RII) monomer. The labeled RII was separated from catalytic subunit, cleaved with cyanogen bromide, and the resultant peptides were separated by high performance liquid chromatography. A single radioactive peptide was observed which had the same NH2 terminal residue and amino acid composition as the peptide obtained when dissociated RII was labeled with 8-N3cAMP.     

Mg2+-paracrystal formation of tropomyosin as a condensation phenomenon. Effects of pH, salt, temperature, and troponin binding.

Tropomyosin (Tm) paracrystal formation induced by Mg2+ was studied by monitoring increases in light scattering. Paracrystals formed above a critical Tm concentration with lag phases in the time courses at pH 7.5 and 6.0, indicating that condensation polymerization processes are involved. The kinetic data at pH 7.5 reasonably fit a model in which nucleation and elongation are taken into account. The rate and extent of light scattering increased at low [Mg2+] and decreased at high [Mg2+] with a maximum at [Mg2+] = 15 mM, indicating different effects of Mg2+ in the two [Mg2+] ranges. The paracrystals were destabilized by increasing the salt concentration and decreasing the temperature. Mg2+ produces paracrystals at pH 6.0 and pH 7.5 by different kinetic mechanisms. Different Tm intermolecular interactions at the two pH values were indicated by studies of the excimer fluorescence of pyrene-labeled Tm and by effects of salt and temperature on the kinetics. At pH 6.0 Tm more readily formed paracrystals with decreased electrostatic effects. Effects of troponin on Mg2+-paracrystal formation of Tm at the two pH values correlated with the known differences in paracrystal structure when troponin is bound to Tm.     

The effect of temperature on nucleotide pool formation in Tetrahymena pyriformis

Warming of exponentially growing T. pyriformis to 34°C results in severe inhibition of nucleotide pool formation. The utilization of the pool for stable RNA synthesis is poorly affected at the high temperature. It thus appears that the synthesis and processing of ribosomal RNA precursors are not primarily impaired at 34°C.     

Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study

Detailed residue-wise interactions involved in the binding of myosin to actin in the rigor conformation without nucleotides have been examined using molecular dynamics simulations of the chicken skeletal myosin head complexed with two actin monomers, based on the cryo-microscopic model of Holmes et al. (Nature 2003;425:423-427). The overall interaction is largely electrostatic in nature, because of the charged residues in the four loops surrounding the central primary binding site. The 50k/20k loop, disordered in crystal structures and in simulations of free myosin in solution, was found to be in a conformation stabilized with 1 - 2 internal salt bridges. The cardiomyopathy loop forms 2 - 3 interprotein salt bridges with actin monomers upon binding, whereas its Arg405 residue, the mutation site associated with the hypertrophic cardiomyopathy, forms a strong salt bridge with Glu605 in the neighboring helix away from actin in the actin-bound myosin. The myopathy loop of the R405Q mutant maintains a high degree of two-strand beta-sheet character when bound to actin with the corresponding salt bridges broken.     

The dissociation of b-TSH. The effect of sodium dodecyl sulfate, pH, urea and temperature.

In the present study SDS polyacrylamide gel electrophoresis was used to reinvestigate the conditions under which b-TSH dissociates into its constituent subunits. The effects of SDS, itself, urea, acid pH and temperature were assessed by the decrease in the amount of undissociated TSH and the increase in the dissociated components as revealed by SDS gel electrophoresis. In SDS alone 25--30% dissociation occurred. Pre-treatment with increasing concentrations of urea up to 7.1 M increased the degree of dissociation to 70% after h at room temperature. Maximum dissociation was achieved by treatment at pH 2.5 and 37 degree C for 1 h. In 1 M propionic acid approximately 10% of the TSH was still undissociated after 18 h at 25 degree C.     

Accelerated dissociation of estrogen receptor--ligand complexes by estradiol. Evidence for negative cooperativity of binding

The rate of dissociation of 17β-[³H]estradiol that had been previously equilibrated to a low degree of saturation of immature rat uterine cytoplasmic estrogen receptor was shown to increase over 40-fold in the presence of additional ligand. This effect was specific for either labeled or unlabeled estradiol, was observed under conditions in which the rebinding of dissociated ligand was shown not to occur, was distinguishable from the activation of cytoplasmic receptor, and was dependent upon the degree of saturation of the receptor by ligand. It occurred under conditions in which the receptor population was apparently uniform and stable and utilized an assay method that is particularly sensitive to low concentrations of cytosol protein. Once saturation of the receptor attained 15% of the available ligand binding sites, further increases of the dissociation rate of receptor-ligand complex could not be produced by the inclusion of additional estradiol. It was shown that exchange of ligand molecules in given binding sites was unlikely. Rather, support was given to the hypothesis that interactions were occurring between separate binding sites in the receptor population. The decrease of the apparent affinity of receptor for ligand when the fractional saturation of receptor increases has been defined as negative cooperativity. It is proposed that this phenomenon may be significant in the regulation of the response of target cells to estrogens.     

Activation thermodynamics of the binding of carbon monoxide to horseradish peroxidase. Role of pressure, temperature and solvent

The kinetics at 423 nm of the binding of carbon monoxide to ferrous horseradish peroxidase were studied as a function of three parameters: pressure (1-1200 bar), temperature (34 to -20 degrees C) and solvent (water, 40% ethylene glycol, 50% methanol) using a high-pressure stopped-flow apparatus. By using transition state theory the thermodynamic quantities delta V, delta S and delta H were determined under these different experimental conditions and were found to be greatly modulated by the physico-chemical parameters of the media. The results suggest that the macroscopic thermodynamic response is mainly controlled by the solvent. By adjusting two variables (among T, P, solvent), it is possible either to amplify or to cancel out the effect of the third.     

Effect of solvent, pressure and temperature on reaction rates of the multiheme hydroxylamine oxidoreductase. Evidence for conformational change

Hydroxylamine oxidoreductase (HAO) of the ammonia-oxidizing bacterium Nitrosomonas catalyzes the oxidation: NH2OH + H2O----HNO2 + 2e- + 2 H+. The heme-like chromophore P460 is part of a site which binds substrate, extracts electrons and then passes them to the many c hemes of the enzyme. Reduction of the c hemes by hydroxylamine is biphasic with apparent first-order rate constants k1 and k2. CO binds to ferrous P460 with apparent first-order rate constants, k1,CO. In this work we have measured the binding of CO to ferrous P460 of hydroxylamine oxidoreductase and the reduction by substrate of some of the 24 c hemes of the ferric enzyme. These reactions have been studied in water and 40% ethylene glycol, at temperatures ranging from -15 degrees C to 20.7 degrees C and at hydrostatic pressures ranging over 0.1-80 MPa. From the measurements, thermodynamic parameters delta V+ (activation volume), delta G+, delta H+, and delta S+ have been calculated. CO binding. Binding of CO to ferrous P460 was similar to the binding of CO to ferrous horseradish peroxidase. The change of solvent had only a limited effect on delta V+ (-30 ml.mol-1), delta G+, delta H+ or delta S+ and did not cause an inflection in the Arrhenius plot or downward displacement of the linear relationship between ln k1,CO and P at a critical temperature. Binding was exothermic at high temperatures. The response of the binding of CO to solvent, temperature and pressure suggested that the CO binding site had little access to solvent and was not susceptible to change in protein conformation. Fast phase of reduction of c hemes. Changing the solvent from water to 40% ethylene glycol resulted in a decrease from 90% to 50% in the relative number of c hemes reduced during the fast phase, an increase in activation volume from -3.6 ml.mol-1 to 57 ml.mol-1 and changes in other thermodynamic parameters. The activation volume increased with decreasing temperature. The Arrhenius plot had a downward inflection at about 0 degrees C and, in water or ethylene glycol, the linear dependence of ln k1 on P was displaced downwards as the temperature changed from 3.5 degrees C to -15 degrees C. Slow phase of reduction of c hemes. Changing the solvent from water to 40% ethylene glycol resulted in an increase in the relative number of c hemes reduced during the slow phase from 10% to 50%. The activation volume, which was not measurable in water because of the low absorbance change, was -30 ml.mol-1 in ethylene glycol. The activation volume increased with increasing temperature.(ABSTRACT TRUNCATED AT 400 WORDS)     

Determination of rate constants for nucleotide dissociation from Na,K-ATPase.

A method for determining individual rate constants for nucleotide binding to and dissociation from membrane bound pig kidney Na,K-ATPase is presented. The method involves determination of the rate of relaxation when Na,K-ATPase in the presence of eosin is mixed with ADP or ATP in a stopped-flow fluorescence apparatus. It is shown that the nucleotide dependence of this rate of relaxation--taken together with measured equilibrium binding values for eosin and ADP--makes possible a reasonably reliable determination of the rate constant for dissociation of nucleotide, i.e., determination of the rate constant k-1 in the following model (where E denotes Na,K-ATPase): [formula: see text] All experiments are carried out at about 4 degrees C in a buffer containing 200 mM sucrose, 10 mM EDTA, 25 mM Tris and 73 mM NaCl (pH 7.4). Values obtained for the rate constants for dissociation are about 6 s-1 for ADP and 2-3 s-1 for ATP.