The identification of hydrophobic sites on the surface of proteins using absorption difference spectroscopy of bromophenol blue.

Hydrophobic sites on the surface of protein molecules are thought to have important functional roles. The identification of such sites can provide information about the function and mode of interaction with other cellular components. While the fluorescence enhancement of polarity-sensitive dyes has been useful in identifying hydrophobic sites on a number of targets, strong intrinsic quenching of Nile red and ANSA dye fluorescence is observed on binding to a cytochrome c('). Fluorescence quenching is also observed to take place in the presence of a variety of other biologically important molecules which can compromise the quantitative determination of binding constants. Absorption difference spectroscopy is shown not to be sensitive to the presence of fluorescence quenchers but sensitive enough to measure binding constants. The dye BPB is shown to bind to the same hydrophobic sites on proteins as polarity-sensitive fluorescence probes. The absorption spectrum of BPB is also observed to be polarity sensitive. A binding constant of 3x10(6)M(-1) for BPB to BSA has been measured by absorption difference spectroscopy. An empirical correlation is observed between the shape of the absorption difference spectrum of BPB and the polarity of the environment. The results indicate that absorption difference spectroscopy of BPB provides a valuable supplement to fluorescence for determining the presence of hydrophobic sites on the surface of proteins as well as a method for measuring binding constants.

Complex formation between Chromatium vinosum ferric cytochrome c' and bromophenol blue.

An unusual complex has been observed between the common electrophoresis tracer bromophenol blue (BPB) and the cytochrome c' from Chromatium vinosum during polyacrylamide gel electrophoresis. Complex formation results in a shift and increase in the intensity of the visible absorption band of BPB. Differential spectrophotometric titration of BPB with cytochrome c' indicates that one BPB binds to each of the two subunits of cytochrome c' with a binding constant of 4.2(0.5) x 10(5). The absence of a significant effect of ionic strength on the binding constant and the effect of Triton X-100 on the spectrum of BPB suggest that hydrophobic interactions are important to binding. An analysis of the structure of C. vinosum cytochrome c' shows the presence of a surface hydrophobic patch which may participate in the binding interaction. Many of the hydrophobic amino acids in the patch are well conserved by type among all known sequences of cytochrome c' and are found in loop elements of the 3D structure, suggesting a functional basis for conservation. It is proposed that the binding of BPB may mimic a relevant interaction involving the cytochrome c' biological function.

Molecular cloning and sequencing of cytochrome c' from the phototrophic purple sulfur bacterium Chromatium vinosum.

The gene for cytochrome c' from Chromatium vinosum was cloned from a HindIII-SalI digest of genomic DNA. A 1.4 kbp fragment containing the gene was sequenced in both directions using the Sanger dideoxy method. The cytochrome c' gene codes for a 154-residue peptide, of which the last 131 amino acids match the previously determined sequence of the protein. The remaining 23 residues represent a signal sequence that is cleaved from the polypeptide upon translocation to the periplasmic space. An additional open reading frame on the other strand of the fragment codes for a peptide that contains four regions that are homologous to corresponding regions of the cytochrome b-type subunit of several Ni-Fe hydrogenases.

The effect of in utero insulin exposure on tissue iron status in fetal rats.

Newborn infants of diabetic mothers have serum biochemical signs of iron deficiency in cord blood directly related to elevations of cord erythropoietin and Hb concentrations. In sheep, chronic fetal hyperinsulinemia results in fetal hypoxemia, expansion of the red cell mass, and decreased iron concentrations, most likely due to increased iron utilization for Hb synthesis. To determine whether fetal insulin exposure also results in reduced tissue iron concentrations, we measured liver, skeletal muscle, small intestine, heart, and brain iron concentrations in newborn rat pups after s.c. fetal injection of insulin or diluent alone on d 19 of gestation. The fetuses of 11 pregnant rats were exteriorized, injected with 2 U neutral protamine Hagedorn insulin or diluent, replaced in utero, and delivered on d 22. To determine dose dependency, the fetuses of six pregnant rats were injected with 3 U of longer-acting protamine zinc insulin and delivered on d 21. At delivery, the insulin-treated groups had higher birth weights than the placebo-treated group, although plasma insulin concentrations were not different. The 2 U neutral protamine Hagedorn insulin-treated fetuses had significantly lower mean +/- SEM liver iron concentrations than the control fetuses (910 +/- 34 versus 1014 +/- 43 micrograms/g dry tissue weight; p less than 0.05), but had similar skeletal muscle iron concentrations. The 3 U protamine zinc insulin-treated fetuses had significantly lower liver and skeletal muscle iron concentrations compared to control and to 2 U neutral protamine Hagedorn insulin-treated fetuses (p less than 0.05). No differences in small intestine, heart, or brain iron concentrations were seen among groups.(ABSTRACT TRUNCATED AT 250 WORDS)

Ligand binding properties of cytochromes c'.

The cytochromes c' bind CO, alkylisocyanides and CN- with rate and equilibrium constants which are 10(2)- to 10(6)-fold smaller than other high-spin hemoproteins. The decreased affinity for exogenous ligands is largely associated with steric interactions at the heme coordination site. While CO and alkylisocyanides bind noncooperatively to the dimeric Rhodospirillum molischianum cytochrome c', CO, alkylisocyanides and CN- appear to bind cooperatively to the dimeric Chromatium vinosum cytochrome c' due to a ligand-linked dimer-monomer dissociation equilibrium. The differences between the cytochromes c' are thought to be due to differences in amino acid residues near the heme coordination site and subunit interface.

Cyanide-linked dimer-monomer equilibrium of Chromatium vinosum ferric cytochrome c'.

Cyanide binding to Chromatium vinosum ferricytochrome c' has been studied to further investigate possible allosteric interactions between the subunits of this dimeric protein. Cyanide binding to C. vinosum cytochrome c' appears to be cooperative. However, the cyanide binding reaction is unusual in that the overall affinity of cyanide increases as the concentration of cytochrome c' decreases and that cyanide binding causes the ligated dimer to dissociate to monomers as shown by gel-filtration chromatography. Therefore, the cyanide binding properties of C. vinosum ferricytochrome c' are complicated by a cyanide-linked dimer to monomer dissociation equilibrium of the complexed protein. The dimer to monomer dissociation constant is 20-fold smaller than that for CO linked dissociation constant of ferrocytochrome c'. Furthermore, the pH dependence of both the intrinsic equilibrium binding constant and the dimer to monomer equilibrium dissociation constant was investigated over the pH range of 7.0 to 9.2 to examine the effect of any ionizable groups. The equilibrium constants did not exhibit a significant pH dependence over this pH range.

Kinetics of cyanide binding to Chromatium vinosum ferricytochrome c'.

The kinetics of the reversible binding of cyanide by the ferric cytochrome c' from Chromatium vinosum have been studied over the pH range 6.9-9.6. The reaction is extremely slow at neutral pH compared to the reactions of other high-spin ferric heme proteins with cyanide. The observed bimolecular rate constant at pH 7.0 is 2.25 X 10(-3) M-1 s-1, which is approximately 10(7)-fold slower than that for peroxidases, approximately 10(5)-fold slower than those for hemoglobin and myoglobin, and approximately 10(2)-fold to approximately 10(3)-fold slower than that recently reported for the Glycera dibranchiata hemoglobin, which has anomalously slow cyanide rate constants of 4.91 X 10(-1), 3.02 X 10(-1), and 1.82 M-1 s-1 for components II, III, and IV, respectively [Mintorovitch, J., & Satterlee, J. D. (1988) Biochemistry 27, 8045-8050; Mintorovitch, J., Van Pelt, D., & Satterlee, J. D. (1989) Biochemistry 28, 6099-6104]. The unusual ligand binding property of this cytochrome c' is proposed to be associated with a severely hindered heme coordination site. Cyanide binding is also characterized by a nonlinear cyanide concentration dependence of the observed rate constant at higher pH values, which is interpreted as involving a change in the rate-determining step associated with the formation of an intermediate complex between the cytochrome c' and cyanide prior to coordination. The pH dependence of both the binding constant for the formation of the intermediate complex and the association rate constant for the subsequent coordination to the heme can be attributed to the ionization of HCN, where cyanide ion binding is the predominant process.(ABSTRACT TRUNCATED AT 250 WORDS)

Alkyl and aromatic isocyanide binding to haem complexes.

Equilibrium constants for the binding of ethyl (EIC), n-butyl (BIC), p-toluenesulphonylmethyl (TMIC) and 2,6-dimethylphenyl isocyanides (DIMPI) to an imidazole-haem complex in toluene and aqueous detergent micelle solutions were determined. In contrast to an earlier study, which indicated that the large affinities of myoglobin for binding DIMPI and 2,6-diethylphenylisocyanide (DEPI) relative to EIC were due to an electronic effect, the present study shows a similarity in binding constants for EIC, BIC, and DIMPI to the imidazole-haem complex in toluene, suggesting no such electronic effect is present. The measured hydrophobic effect (KDIMPI/KEIC = 11) cannot account for the large binding constant reported for DIMPI relative to the binding of EIC to myoglobin. Based on the results of these model studies, the equilibrium binding constant for DIMPI to myoglobin has been re-measured and the standard free energy of binding has been analysed by a more recent method.

Steric and hydrophobic effects in alkyl isocyanide binding to Rhodospirillum molischianum cytochrome c'.

Equilibrium constants for the binding of a series of alkyl isocyanides to ferrous cytochrome c' from Rhodospirillum molischianum have been measured spectrophotometrically. The equilibrium constants range from 3.3 M-1 to 2.6 x 10(2) M-1 and follow the order methyl greater than ethyl less than n-propyl less than tert-butyl less than n-butyl less than amyl less than cyclohexyl less than n-hexyl. The decrease in equilibrium constant from methyl to ethyl isocyanide provides evidence for a steric interaction between the ligand and the protein. The increase in equilibrium constant from ethyl to n-hexyl isocyanide is accounted for by a favorable partitioning of the ligand into a hydrophobic heme coordination site. The effect of steric interactions on the differences in the binding constants has been further evaluated by comparing the alkyl isocyanide and CO binding constants for the ferrous cytochrome c' to those of a sterically unconstrained model heme complex in a detergent micelle. The results indicate that the heme coordination site of the ferrous cytochrome c' is severely sterically hindered, similar to that of the reported crystal structure of Rs. molischianum ferric cytochrome c'.

Binding of cyanide to cytochrome c' from Chromatium vinosum.

Spectroscopic evidence is presented which demonstrates the binding of cyanide to the ferric cytochrome c' from Chromatium vinosum. The cytochrome was shown to bind one equivalent of cyanide with an equilibrium constant of 2.1 X 10(4) at pH 7.0 and 25 degrees C. This finding represents the first observation of the binding of an anionic ligand to the heme iron in a ferric cytochrome c'. These results suggest that the binding site of the ferric Chromatium cytochrome c' may be significantly more accessible than previously indicated.

Cyanate binding to the ferric heme octapeptide from cytochrome c. A model for anion binding to high spin ferric hemoproteins.

Equilibrium constants for the binding of cyanate to the ferric heme c octapeptide in 50% ethylene glycol, 50% aqueous buffer were measured spectrophotometrically. Equilibrium constants measured at several temperatures from -20 degrees C to 0 degrees C exhibited an apparent van't Hoff relationship yielding thermodynamic values of delta Ho = -1.3 X 10(3) +/- 0.9 X 10(3) J/mol (-3.1 X 10(2) +/- 2 X 10(2) cal/mol), delta So = -3 +/- 3 J/K X mol (-0.6 +/- 0.8 cal/K X mol). The equilibrium constant for cyanate binding at 25 degrees C and pH 7.4 is 1.21 which is approximately 2 to 3 orders of magnitude lower than that observed for cyanate binding to methemoglobin and metmyoglobin. Krel, the ratio of the hemoprotein to model heme octapeptide binding constants, for NCO- is smaller than Krel for N3- suggesting that hydrogen bonding between the terminal ligand atoms and the distal histidine in hemoglobin and myoglobin does not contribute to the increased protein ligand stabilization observed for these anions relative to the model. A donor-acceptor interaction between the distal histidine and the electrophilic middle atoms of these bound ligands is proposed.

Cytochromes c' in their reaction with ethyl isocyanide.

The binding of ethyl isocyanide (EIC) to a representative number of cytochromes c' is demonstrated. Spectroscopic and equilibrium constants have been measured and compared for the binding of EIC to cytochromes c' from the photosynthetic bacteria Chromatium vinosum, Rhodopseudomonas palustris, Rhodospirillum rubrum, and Rhodopseudomonas sphaeroides. While the absorption spectra of the EIC complexes resemble those of EIC complexes of other high-spin hemoproteins, the Soret half band widths and extinction coefficients per heme exhibit more than a 2-fold difference with the values of C. vinosum being most similar to those of Rh. sphaeroides and of Rh. palustris similar to those of Rs. rubrum. The cytochromes exhibit binding equilibria consistent with the ligation of one molecule of EIC per heme in contrast to the reported binding of more than one molecule of CO per heme. The binding constants exhibit more than a 1000-fold difference with the values of C. vinosum being closely similar to those of Rh. sphaeroides and of Rh. palustris similar to those of Rs. rubrum. The lack of correlation between EIC and CO binding properties indicates that electronic factors do not determine the difference in EIC binding properties. The observed correlation between the extinction coefficients, half band widths, and equilibrium constants for EIC complex formation provides the first spectroscopic evidence that the differences in binding properties are associated with sterically hindered ligation to the heme. Although the differences in binding properties provide evidence of steric hindrance, the EIC binding constants for particular cytochromes c' indicate that the distal heme binding site is more accessible than previously indicated.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of solvent on the absorption maxima of five-coordinate heme complexes and carbon monoxide-heme complexes as models for the differential spectral properties of hemoglobins and myoglobins.

Absorption spectra were recorded for 5- and 6-coordinate model ferrous heme complexes of hindered and unhindered ligands in aqueous, and detergent solutions. Heme complexes exhibited differences in absorption maxima up to 6 nm which were correlated with the polarity of the heme environment. Increasing polarity of the solvent resulted in a general blue shift of absorption maxima of both deoxy- and (carbon monoxy)heme complexes. The differences in absorption maxima of heme complexes with different heme environments are offered as a possible explanation for some of the differences in absorption maxima among hemoproteins such as hemoglobin, myoglobin, and leghemoglobin.

Fluoride binding to the cytochrome c ferric heme octapeptide. A model for anion binding to the active site of high spin ferric heme proteins.

The temperature dependence of the magnetic susceptibility of the ferric hemeoctapeptide from cytochrome c was measured in the presence and absence of fluoride ion to study the fluoride binding equilibrium of the hemeoctapeptide. The shift in the 1H NMR signal of sodium 4,4-dimethyl-4-silapentanesulfonate caused by the hemeoctapeptide was measured from -11 to 80 degrees C in a D2O/ethylene glycol solution. Magnetic susceptibilities obtained from the shifts were used to calculate the binding constant at each temperature. The equilibrium constant is 0.95 M-1 at 25 degrees C. Thermodynamic values determined from a plot of ln K versus 1/T are delta H0 = 19,700 J/mol (4,700 cal/mol) and delta S0 = 66.1 J/K mol (15.8 entropy units). The equilibrium and thermodynamic values are compared with those for fluoride binding to hemeproteins and with values for azide and cyanide binding to the hemeoctapeptide and hemoproteins. The differential binding data are used to assess the proposed bonded and nonbonded interactions between the distal histidine and the protein on the axial anionic ligand affinity. The results suggest that bonded interactions between the distal histidine and the ligand may contribute considerable stabilization to the hemoprotein-ligand complex.

Cyanide binding to the cytochrome c ferric heme octapeptide. A model for anion binding to the active site of high spin ferric heme proteins.

Equilibrium constants for the binding of cyanide to the ferric heme c octapeptide in 20% ethylene glycol, 50% buffer were measured spectrophotometrically. The equilibrium constant for cyanide binding at 20 degrees C and pH 7.4 is 3.47 X 10(7), which is approximately 15-fold lower than that observed for cyanide binding to methemoglobin or metmyoglobin. Equilibrium constants at several temperatures exhibited an apparent van't Hoff relationship, yielding thermodynamic values of delta H degrees = -79,000 J/mol (-18,900 cal/mol) and delta S degrees = J/degrees K mol (-30.1 e.u.). Comparison of the ratio of equilibrium constants for cyanide ligation to methemoglobin the heme octapeptide with the ratio of equilibrium constants for azide ligation to methemoglobin and the heme octapeptide suggests that cyanide binding to the methemoproteins is much smaller than expected by comparison to azide binding. The differences in the ratios, the thermodynamic values, and the preferred binding geometries suggest that CN- ligation, like CO ligation, is sterically hindered. A comparison of these ratios to similar ratios for CO, O2, and NO binding suggests that the Fe-CN bond angle is less subject to distortion than the Fe-CO bond and/or additional binding interactions contribute to N3- but not to CN-binding to the protein.

Nitric oxide and carbon monoxide equilibria of horse myoglobin and (N-methylimidazole)protoheme. Evidence for steric interaction with the distal residues.

The Soret absorption maxima and extinction coefficients of the CO and NO complexes of horse myoglobin and (NMeIm)protoheme (NMeIm = 1-methylimidazole) have been determined. The partition coefficient N, equal to the ratio P1/2 (CO)/P1/2(NO), has been determined spectrophotometrically for horse myoglobin and (NMeIm)protoheme. P1/2-(NO) values calculated from the partition coefficients are 5.7 x 10(7) mmHg for (NMeIm)protheme and 1.1 x 10(6) mmHg for horse myoglobin. The ratio of P1/2(NO) values for protein and model is 1.9 which is similar to a value of 1.6 reported for the ratio of P1/2(O2) values. These values may be compared to a ratio of 15 for CO binding to protein and model complexes. This different ratio for CO provides further evidence for steric interaction of the bound CO with the protein based on a consideration of the preferred nonlinear geometry of Fe-NO and Fe-O2 and the linear geometry of Fe-CO.

Azide binding to the cytochrome c ferric heme octapeptide. A model for anion binding to the active site of high spin ferric heme proteins.

Equilibrium constants for the binding of azide to the ferric heme c octapeptide in 50% ethylene glycol 50% buffer were measured spectrophotometrically. The equilibrium constant for azide binding at 20 degrees C and pH* 7.4 is 29.2, which is approximately 3 to 4 orders of magnitude lower than that observed for azide binding to various ferric hemeproteins. The equilibrium constant was indepent of pH* in the range from 7 to 8. Equilibrium constants at several temperatures exhibited an apparent van't Hoff relationship yielding thermodynamic values of delta H0 = -26,100 J/mol (-6240 cal/mol) and delta S0 = -61.5 J/0K mol (-14.7 e.u.). Comparison of these values to the values for the heme proteins enables one to explain the differences in equiliberium constants in terms of differences in the polarity of the heme environments. The results are consistent with the concept that the oxygen affinity of heme complexes increases with the polarity of the heme environment. The data also suggest that an increase in the polarity of the heme environment should result in a corresponding increase in the susceptibility of ferrous heme dioxygen complexes toward oxidation by the dioxygen.

The redox properties and heme environment of cytochrome c-551.5 from Desulfuromonas acetoxidans.

The environment of the three heme groups in cytochrome c-551.5 from Desulfuromonas acetoxidans was investigated by the technique of solvent perturbation difference spectroscopy. The hemeoctapeptide from cytochrome c plus added imidazole was used as a model compound for the fully exposed chromophore. The average heme exposure in both the ferric and ferrous cytochromes c-551.5 was found to be considerably greater than that previously observed for the monoheme mitochondrial cytochrome c and Prosthecochloris cytochrome c-555. Differences in the average heme exposure for ferric and ferrous cytochromes c-551.5 suggested that a change in oxidation state is accompanied by a change in conformation. A spectrophotometric redox titration of the protein yielded a sigmoidal plot of the potential versus the logarithm of the ratio of oxidized to reduced heme. The resolved plot indicated that two hemes were characterized by a E'o of -177 mV and the third E'o of -102 mV. Each of the resolved steps had an n value of 1 indicating that cytochrome c-551.5 transfers electrons singly.

Comparative solvent perturbation of horse heart cytochrome c and Rhodospirillum rubrum cytochrome c2.

The extent of exposure of heme to solvent in horse heart cytochrome c and Rhodospirillum rubrum c2 was investigated to determine whether a correlation exists between the properties of these oxidation-reduction proteins and their heme environments. Solvent perturbation absorption difference spectra were measured using ethylene glycol, glycerol, and sucrose at concentrations between 0 and 30%. Cytochrome c appears to exhibit a somewhat greater extent of heme exposure than cytochrome c2 for both the oxidized and reduced states. These results suggest that the lower oxidation-reduction potential of cytochrome c may in part be due to a greater extent of exposure of the heme. The oxidized state of both proteins appears to exhibit a greater exposure than that of the reduced state which is consistent with a more favorable environment for the charge on the ferric heme coordination center.