Cooperative biotin binding by streptavidin. Electrophoretic behavior and subunit association of streptavidin in the presence of 6 M urea

We describe the cooperativity in the biotin binding of streptavidin. We have developed an electrophoretic method which can separate streptavidin molecules with bound biotin from those without biotin. In 6 M urea, the electrophoretic mobility of streptavidin in polyacrylamide gels becomes significantly faster upon biotin binding. When streptavidin was titrated with biotin, only two major bands were observed on the gel, consisting of streptavidin molecules without bound biotin and those saturated with biotin. The change in mobility is due partly to the negative charge of the bound biotin, but it must reflect conformational changes of the protein molecule associated with biotin binding. Gel filtration chromatography showed that the streptavidin molecule dissociates into two subunit dimers in the presence of 6 M urea. These results suggest that the biotin binding by the streptavidin subunit dimer is cooperative and that some communication must exist between the two subunits.     

Resolvability of free energy changes for oxygen binding and subunit association by human hemoglobin.

Probability distributions of the free energy changes for oxygen binding, subunit association, and quaternary enhancement by human hemoglobin were obtained from Monte Carlo simulations performed on two independent sets of variable protein concentration equilibrium oxygen-binding data. Uncertainties in unliganded and fully liganded dimer to tetramer association free energy changes (0 delta G'2 and 4 delta G'2) were accounted for in the simulations. Distributions of the dimer to tetramer association free energy changes for forming singly and triply liganded tetramers (1 delta G'2 and 3 delta G'2) are well defined and quite symmetric, whereas that for forming doubly liganded tetramers (2 delta G'2) is poorly defined and highly asymmetric. The distribution of the dimer stepwise oxygen-binding free-energy change (delta g'2i) is well defined and quite symmetric as are those of the tetramer stepwise oxygen-binding free-energy changes for binding the first and last oxygens to tetramers (delta g'41 and delta g'44). Distributions of the intermediate tetramer stepwise oxygen-binding free-energy changes (delta g'42 and delta g'43) are poorly defined and highly asymmetric, but are compensatory in that their sum (delta g'4[2 + 3]) is again well defined and nearly symmetric. Distributions of the free energy changes corresponding to the tetramer product Adair oxygen binding constants (delta G'4i) are well defined and quite symmetric for i = 1, 3, 4 but not for i = 2. The distribution of delta g'44 - delta g'2i (the quaternary enhancement free energy change) is relatively narrow, nearly symmetric, and confined to the negative free-energy domain. This suggests that the quaternary enhancement free energy change (a) may be resolved with good confidence from this data and (b) is finite and negative under the conditions of these experiments. Our results also suggest two different four-state combinatorial switch models that provide accurate characterization of hemoglobin's functional behavior.     

Hemoglobins of the tadpole of the bullfrog, Rana catesbeiana. Temperature dependence of oxygen binding and pH dependence of subunit dissociation.

The temperature dependence of the oxygen equilibrium of tadpole hemoglobin has been determined between 0 degrees and 32 degrees for the unfractionated but phosphate-free lysate and between 12 degrees and 32 degrees for each of the four isolated components between pH 6 and 10 in 0.05 M cacodylate, Tris, or glycine buffers containing 0.1 M NaCl and 1 mM EDTA. Under these conditions the Bohr effect (defined as deltalog p50/deltapH) of the unfractionated lysate is positive at low temperatures between pH 6 and 8.5 and is negative above pH 8.5 to 8.8 at any temperature. As the temperature rises the Bohr effect below pH 8.5 changes greatly. In the interval pH 7.0 to 7.5, the magnitude of the Bohr effect decreases from + 0.28 at 0 degrees to zero at about 24 degrees and becomes negative, as in mammalian hemoglobins, above this temperature. Measurements with the isolated components show that the temperature dependence of oxygen binding for Components I and II and for Components III and IV is very similar. For both sets of components the apparent overall enthalpy of oxygenation at pH 7.5 is about -16.4 kcal/mol and -12.6 kcal/mol at pH 9.5. The measured enthalpies include contributions from the active Bohr groups, the buffer ions themselves, the hemoglobin groups contributing buffering, and any pH-dependent, oxygenation-dependent binding of ions such as chloride by the hemoglobin. The apportioning of the total enthalpy among these various processes remains to be determined. Between pH 8 and 10.5 tadpole oxyhemoglobin undergoes a pH-dependent dissociation from tetramer to dimer. The pH dependence of the apparent tetramer-dimer dissociation constant indicates that at pH 9.5 the dissociation of each tetramer is accompanied by the release of approximately 2 protons. In this pH range the oxygen equilibrium measurements indicate that about 0.5 proton is released for each oxygen molecule bound. The results are consistent with the conclusion that one acid group per alphabeta dimer changes its pK from about 10 to 8 or below upon dissociation of the tetramer.     

Pressure dependence of equilibria and kinetics of Escherichia coli ribosomal subunit association

Equilibria and rates were observed over the ranges 1-1600 atm, 3-10 mM Mg2+, at 60 mM NH4Cl, pH 7.5, 20 degrees C, by light scattering. The main reaction is accurately represented at all conditions by the following phenomenological equations. 30 S + 50 S = 70 S, KA70 = ka/kd = [70 S]/[30 S][50 S] The equilibrium constants obey simple rules: the volume of association, delta VA0, has the constant value 242 +/- 9 ml/mol, independent of pressure, at all Mg2+ concentrations; the derived values of log KA70 at 1 atm increase linearly with log [Mg2+] at a slope of 7.5. In contrast, the rate constants show a clear break at 6 mM Mg2+: below 6 mM, log ka decreases with pressure with a delta Va of 105 +/- 9 ml/mol and increases with log [Mg2+] at a slope of 4.9; above 6 mM, these values are halved; a split can actually be seen at 6 mM Mg2+, near 500 atm. The usual two-step mechanism for second order reactions in solution, which would insert a 70 S' species, either an encounter complex or a true low concentration steady state intermediate, into the above equation can accommodate these results: as [Mg2+] increases, the rate of transformation of 70 S' into 70 S finally predominates over the rate of dissociation of 70 S' into subunits. The bulk of the pressure effects and all of the [Mg2+] dependence arise from the progressive increase in delta GA0 (electrostatic) that occurs when 30, 50, and 70 S particles all lose equivalent fractions of their internal Mg2+ in response to increases in pressure or decreases in [Mg2+].     

Energy coupling between DNA binding and subunit association is responsible for the specificity of DNA-Arc interaction.

The effects of several DNA molecules on the free energy of subunit association of Arc repressor were measured. The association studies under equilibrium conditions were performed by the dissociating perturbation of hydrostatic pressure. The magnitude of stabilization of the subunit interaction was determined by the specificity of the protein-DNA interaction. Operator DNA stabilized the free energy of association by about 2.2 kcal/mol of monomeric unit, whereas poly(dG-dC) stabilized the subunit interaction by only 0.26 kcal. Measurements of the stabilizing free energy at different DNA concentrations revealed a stoichiometry of two dimers per 21 bp for the operator DNA sequence and for the nonspecific DNA poly(dA-dT). However, the maximum stabilization was much larger for operator sequence (delta p = 1,750 bar) as compared for poly(dA-dT) (delta p = 750 bar). The importance of the free-energy linkage for the recognition process was corroborated by its absence in a mutant Arc protein (PL8) that binds to operator and nonspecific DNA sequences with equal, low affinity. We conclude that the coupling accounts for the high specificity of the Arc-operator DNA interaction. We hypothesize a mutual coupling between the protein subunits and the two DNA strands, in which the much higher persistency of the associated form when Arc is bound to operator would stabilize the interactions between the two DNA strands.     

Concentration dependence of protein diffusion.

The concentration dependence of protein self-diffusion constants is described by a free volume diffusion theory which accounts for the effects of local protein concentration fluctuations.     

Morphine dependence in the isolated guinea-pig ileum and its modification by p-chlorophenylalanine.

Experiments were performed to quantitatively determine morphine physical dependence in the isolated guinea-pig ileum and to assess the influence of p-chlorophenylalanine (PCPA) on its development. Ileum segments taken from animals treated with 10 s.c. injections of 100 mg/kg of morphine, given at intervals of 8 hr without interruption, responded with intense, prolonged, dose-dependent contractions to the $\text{in}$$\text{vitro}$ administration of naloxone, although contractions guinea-pigs also responded to naloxone, although contractions were smaller and of short duration. The sensitivity to naloxone on segments isolated from morphinized animals was compared to that of controls. Ilea from morphine-treated guinea-pigs were 8 to 32 times more sensitive to naloxone, as determined by a shift in the naloxone concentration-response curve to the left. There was also a three-fold increase in the maximum response. This phenomenon was taken as evidence of narcotic dependence. PCPA, given before morphine administration, at doses producing only a slight (11%) decrease in intestinal serotonin (5-HT) levels, partially reduced the sensitivity of the morphine-treated ileum to naloxone. However, high doses of PCPA, decreasing intestinal 5-HT by 40%, enhanced the abstinence-like effects of naloxone in the morphine pretreated ileum. PCPA by itself changed the responsiveness of the non-morphinized ileum to naloxone. The direction and magnitude of the change produced by PCPA alone was roughly equivalent to that produced by the serotonin depletor in the morphinized ileum. This finding indicates that PCPA has no effect upon the development of physical dependence in the isolated ileum. It remains to be determined whether or not the increased sensitivity to naloxone induced by high doses of PCPA has something in common with the changes in responsiveness to the antagonist induced by narcotics.     

Effect of covalent modification on the binding of cholera toxin B subunit to ileal brush border surfaces.

A competitive binding assay has been developed to determine how modifications to the B subunit of cholera toxin affect the binding affinity of the subunit for an ileal brush border membrane surface. The Ricinus communis120 agglutinin (RCA120) specifically binds to terminal beta-D-galactosyl residues such as those found in oligosaccharide side chains of glycoproteins and ganglioside GM1. Conditions were designed to produce binding competition between the B subunit of cholera toxin and the RCA120 agglutinin. Displacement of RCA120 from brush border surfaces was proportional to the concentration of B subunit added. This assay was used to study the effect of modification of B subunit on competitive binding affinity for the ileal brush border surface. The B subunit of cholera toxin was modified by coupling an average of five sulfhydryl groups to each B subunit molecule and by reaction of the SH-modified B subunit with liposomes containing a surface maleimide group attached to phosphatidylethanolamine. SH-modified B subunit was approximately 200-fold more effective than native B subunit in displacing lectin from brush border surfaces in the competitive binding assay. The enhanced binding activity was retained on covalent attachment of the modified B subunit to the liposome surface. We conclude that the B subunit of cholera toxin may be a useful targeting agent for directing liposomes to cell surfaces that contain a ganglioside GM1 ligand.     

Synthesis of labelled PNA oligomers by a post-synthetic modification approach

The preparation of t-butoxycarbonyl (Boc)-protected O(4)-(o-nitrophenyl) thymine peptide nucleic acid (PNA) monomer is described. This PNA monomer was incorporated into PNA oligomer sequences. The post-synthetic modification of the oligomers to yield fluorescently-labelled PNA oligomers was studied before and after the removal of the protecting groups. In both cases, the desired fluorescently-labelled PNA oligomer was obtained in good yields.     

Concentration of viruses in beef extract by flocculation with ammonium sulfate.

A total of 42 clinical and environmental isolates of Vibrio vulnificus were examined for plasmid carriage. Of these, only five (12%) harbored plasmids, which were of various molecular weights. In contrast, 20 of 32 (62.5%) unidentified lactose-fermenting Vibrio spp. were found to possess plasmids with masses of 2.1 to 150 megadaltons. In these isolates, multiple plasmids were common, with an average of 2.25 plasmids per plasmid-containing strain. Attempts to demonstrate a correlation with the plasmids identified in the various Vibrio spp. and a variety of phenotypic traits, production of several enzymes potentially involved in virulence, cytotoxicity for Chinese hamster ovary cells, and mouse lethality were unsuccessful. A correlation was observed, however, between the presence of a 6.5-megadalton plasmid and resistance to pteridine 0/129. It was concluded that V. vulnificus, unlike most other Vibrio spp., shows a general lack of these extrachromosomal elements.