Reactivity and ionization of the active site cysteine residues of DsbA, a protein required for disulfide bond formation in vivo

DsbA is a periplasmic protein of Escherichia coli that appears to be the immediate donor of disulfide bonds to proteins that are secreted. Its active site contains one accessible and one buried cysteine residue, Cys30 and Cys33, respectively, which can form a very unstable disulfide bond between them that is 10(3)-fold more reactive toward thiol groups than normal. The two cysteine residues have normal properties when in a short peptide. In DsbA, the Cys30 thiol group is shown to be reactive toward alkylating reagents down to pH 4 and to be fully ionized, on the basis of the UV absorbance of the thiolate anion at 240 nm. Its reactivity is altered by another, unknown group on the reduced protein titrating with a pKa of about 6.7. The other cysteine residue is buried and unreactive and has a high pKa value. The ionization properties of the DsbA thiol groups can explain, at least partly, the high reactivity of its disulfide bonds and thiol groups at both neutral and acidic pH values.

One-disulfide intermediates of apamin exhibit native-like structure

The conformations of three peptide models of the one-disulfide and fully reduced forms of apamin were characterized by using nuclear magnetic resonance (NMR) spectroscopy. Apa-2 contains the native disulfide bond between Cys3 and Cys15 in apamin with the other two cysteines replaced by alanines. Apa-1 contains the native disulfide bond between Cys1 and Cys11. Apa-S has all cysteines replaced with serines, mimicking fully reduced apamin. Comparing NOESY cross peaks and coupling constants for amide protons in the peptide analogs with those in native apamin indicates that a significant portion of Apa-2 possesses native-like structural elements of apamin in addition to some random coil conformations. Apa-1 contains a short helical structure from Ala9 to Arg13, corresponding to the N-terminal portion of the alpha-helix observed in the native structure, along with some local and probably flexible secondary structures corresponding to the reverse turn region in native apamin. A larger portion of Apa-1 exists in the form of random coil conformations compared to Apa-2. Apa-S displays mainly random coil conformations with some localized helical structures from Glu7 to Arg14 which are similar to the "nascent helices" proposed by Wright et al. [Wright, P. E., Dyson, H. J., & Lerner, R. A. (1988) Biochemistry 27, 7167-7175]. Formation of the first disulfide bond in apamin seems to be important in the folding process by stabilizing native-like structure, presumably by reducing the conformational freedom and initiating formation of structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Serum sensitivity of Burkholderia (Pseudomonas) cepacia isolates from patients with cystic fibrosis

Bacterial strains which are sensitive to the bactericidal activity of serum are generally considered to be less virulent than serum-resistant strains and are seldom associated with bacteraemia. Burkholderia (Pseudomonas) cepacia is an important pathogen in cystic fibrosis and is associated with rapid fatal pulmonary decline and bacteraemia in 20% of colonised patients. In this study 19 isolates of B. cepacia expressing either rough or smooth LPS were investigated to determine the degree of serum sensitivity. Strains expressing rough-LPS were serum-sensitive: these included a highly transmissible strain of B. cepacia isolated from approximately 50 cystic fibrosis patients attending various U.K. regional centres and associated with cases of bacteraemia.

Densitometry: modern approaches advance an established technique

Densitometry is an established technique used in most biological research laboratories. Established techniques are often assumed to be stable and therefore not subject to advancement by the application of newer technology. However, when new technology is applied to an established technique, great advances can suddenly occur. Using the latest in laser optics design, semiconductor technology and state-of-the-art software implementation, Molecular Dynamics has developed and recently introduced a new Personal Densitometer SI that has performance capabilities considered impossible only a few years ago. In addition, the entire system can be priced lower than was previously possible.

Site-directed mutagenesis of rabbit muscle phosphofructokinase cDNA. Mutations at glutamine 200 affect the allosteric properties of the enzyme

Full-length cDNA for rabbit muscle phosphofructokinase has been cloned and characterized (Li, J., Chen, Z., Lu, L., Byrnes, M., and Chang, S. H. (1990) Biochem. Biophys. Res. Commun. 170, 1056-1060). The 2.8-kilobase cDNA was inserted in the plasmid vector pPL2 and transformed into Escherichia coli cells deficient in endogenous phosphofructokinase activity (DF 1020). The recombinant phosphofructokinase so prepared is nearly identical in kinetic properties and size of subunits to the enzyme isolated from rabbit muscle. On the basis of the sequence homology between the muscle and the bacterial phosphofructokinases and the crystallographic structure of the latter, the glutamine at position 200 of the muscle enzyme is implicated in the allosteric transitions. This residue was replaced by alanine (Q200A), glutamate (Q200E), or arginine (Q200R). The purified enzymes were analyzed for quaternary structure, activity, and allosteric properties. The native and all the altered enzymes are tetramers. At pH 7.0, the wild-type enzyme is sensitive to inhibition by ATP at concentration above 0.6 mM, and its activity responds to fructose 6-phosphate concentration cooperatively at high ATP concentration. In contrast, the mutated enzyme Q200R is virtually insensitive to ATP inhibition up to 7 mM. Thus at high ATP concentration, its activity responds to fructose 6-phosphate concentration is a manner similar to the activated form of the native enzyme. Under the same conditions, mutant Q200E exhibits cooperative behavior only at much higher concentration of fructose 6-phosphate. Mutant Q200A is active at pH 8.0 but inactive at pH 7.0. The native enzyme and all three mutants are activated by inorganic phosphate and fructose 2,6-bisphosphate and inhibited by citrate.

Strategies for selecting mutation sites for methionine enhancement in the bean seed storage protein phaseolin

The complete three-dimensional structure of the bean seed storage protein phaseolin was generated from alpha-carbon coordinates by using molecular mechanic calculations. This structure was used as a template to simulate modifications aimed at increasing the methionine content of phaseolin. A hydrophilic, methionine-rich looping insert sequence was designed. Simulated mutagenesis shows that the insert might be accommodated in turn and loop regions of the protein, but not within an alpha-helix. Methionine content was also increased by the replacement of hydrophobic amino acids with methionine in the central core beta-barrels of the phaseolin protein. Calculations indicated that methionine can effectively replace conserved or variant leucine, isoleucine, and valine residues. However, alanine residues were much more sensitive to substitution, and demonstrated high variability in the effects of methionine replacement. Introduction of multiple substitutions in the barrel interior demonstrated that the replaced residues could interact favorably to relieve local perturbations caused by individual substitutions. Molecular dynamics simulations were also utilized to study the structural organization of phaseolin. The calculations indicate that there are extensive packing interactions between the major domains of phaseolin, which have important implications for protein folding and stability. Since the proposed mutant proteins can be produced and studied, the results presented here provide an ideal test to determine if there is a correlation between the effects obtained by computer simulation and the effects of the mutations on the protein structure expressed in vivo.

Solution structure of tertiapin determined using nuclear magnetic resonance and distance geometry

The solution structure of tertiapin, a 21-residue bee venom peptide, has been characterized by circular dichroism (CD), two-dimensional nuclear magnetic resonance (NMR) spectroscopy, and distance geometry. A total of 21 lowest error structures were obtained from distance geometry calculations. Superimposition of these structures shows that the backbone of tertiapin is very well defined. One type-I reverse turn from residue 4 to 7 and an alpha-helix from residue 12 to 19 exist in the structure of tertiapin. The alpha-helical region is best defined from both conformational analysis and structural superimposition. The overall three-dimensional structure of tertiapin is highly compact resulting from side chain interactions. The structural information obtained from CD and NMR are compared for both tertiapin and apamin (ref. 3), another bee venom peptide. Tertiapin and apamin have some similar secondary structure, but display different tertiary structures.

Repair of O6-methylguanine in rat pancreatic beta-cells after exposure to N-methyl-N-nitrosourea

Because of the possible involvement of O6-methyldeoxyguanosine as a cytotoxic and carcinogenic lesion in pancreatic beta-cells, studies were undertaken to assess the ability of rat beta-cells to repair this DNA lesion. Primary cultures of neonatal rat beta-cells were shown to contain very low levels of O6-methylguanine-DNA-methyltransferase activity, the predominant mechanism for repairing O6-methyldeoxyguanosine in mammalian cells. However, using a 32P-endlabeling assay to measure O6-methyldeoxyguanosine in cells after exposure to N-methyl-N-nitrosourea, it was determined that rat beta-cells repaired O6-methyldeoxyguanosine to a substantial extent over a 24-h period. To elucidate the mechanism of O6-methyldeoxyguanosine repair in the virtual absence of constitutive O6-methylguanine-DNA-methyltransferase expression, studies were performed to determine if O6-methylguanine-DNA-methyltransferase expression was enhanced in N-methyl-N-nitrosourea-treated beta-cells. No increase in O6-methylguanine-DNA-methyltransferase activity was detected 24 or 48 h after exposure. However, Northern blot analysis showed a two- to threefold elevation in O6-methylguanine-DNA-methyltransferase messenger RNA levels in beta-cells 12 and 24 h after N-methyl-N-nitrosourea treatment. This finding is the first demonstration of a change in O6-methylguanine-DNA-methyltransferase messenger RNA levels in a cell type with low constitutive activity.

Evidence for transmission of Pseudomonas cepacia by social contact in cystic fibrosis

Pulmonary colonisation with Pseudomonas cepacia in patients with cystic fibrosis can be associated with increased morbidity and mortality. The modes of transmission of P cepacia are, however, unclear. We used selective media and phenotypic and genomic typing systems to investigate the acquisition of P cepacia by adults with cystic fibrosis. An analysis of isolates from 210 patients attending regional clinics in Edinburgh and Manchester between 1986 and 1992 showed that the main cause of increased isolations of P cepacia from 1989 was the emergence of an epidemic strain that had spread between patients in both clinics. Epidemiological evidence indicated that social contact was important in spread of the epidemic strain within and between clinics. We suggest that guidelines to limit the acquisition of P cepacia should not be restricted to patients in hospital, and that intimate or frequent social contact is associated with a high risk of cross-infection.

Serum IgG and sputum IgA antibody to core lipopolysaccharide antigen from Pseudomonas cepacia in patients with cystic fibrosis

The immunological response of cystic fibrosis (CF) patients to lipopolysaccharide (LPS) antigens of Pseudomonas cepacia was investigated. Enzyme-linked immunosorbent assays (ELISA) with either P. cepacia whole cells or extracted core LPS from a clinical isolate of P. cepacia as antigen were used to measure serum IgG and sputum IgA anti-P. cepacia antibodies. The ELISA with core LPS distinguished nine CF patients colonised by P. cepacia from nine age- and sex-matched non-colonised CF patients. The rate of increase of anti-P. cepacia IgG antibodies after bacteriologically proven P. cepacia colonisation varied in individual patients: in some patients the first isolation of P. cepacia was preceded or accompanied by a two-to-four-fold rise in anti-P. cepacia LPS IgG titres. Absorption studies and immunoblot analysis of serum from patients colonised with P. cepacia demonstrated that a significant component of the anti-P. cepacia core LPS antibodies was specific for P. cepacia and did not react with the core LPS of P. aeruginosa. Immunoblotting also illustrated that there may be a degree of core heterogeneity between different isolates of P. cepacia. Detection of P. cepacia LPS specific antibodies in serum (IgG) and sputum (IgA) from CF patients is recommended to assist the identification of P. cepacia colonisation in CF patients.

Microbiology of cystic fibrosis lung infections: themes and issues

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Microbiology of lung infection in cystic fibrosis

Bronchopulmonary infection in cystic fibrosis (CF) patients is associated with chronic progressive lung disease and episodes of acute exacerbation. Infection is predominantly caused by bacteria, although infections with viruses, mycoplasma and fungi may play undervalued roles. Bacteria commonly isolated from CF sputum include Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa. Colonisation of the airways by mucoid, alginate-producing variants of P. aeruginosa is recognised as a major cause of pulmonary deterioration. In addition, there is now considerable concern relating to the clinical consequences of colonisation and cross-infection with P. cepacia. This review discusses the microbiology of CF focussing on the pathogenesis and epidemiology of P. aeruginosa and P. cepacia.

Biophysical analysis of phaseolin denaturation induced by urea, guanidinium chloride, pH, and temperature

The structural stability of phaseolin was determined by using absorbance, circular dichroism (CD), fluorescence emission, and fluorescence polarization anisotropy to monitor denaturation induced by urea, guanidinium chloride (GdmCl), pH changes, increasing temperature, or a combination thereof. Initial results indicated that phaseolin remained folded to a similar extent in the presence or absence of 6.0 M urea or GdmCl at room temperature. In 6.0 M GdmCl, phaseolin denatures at approximately 65 degrees C when probed with absorbance, CD, and fluorescence polarization anisotropy. The transition occurs at lower temperatures by decreasing pH. Kinetic measurements of denaturation using CD indicated that the denaturation is slow below 55 degrees C and is associated with an activation energy of 52 kcal/mol in 6.0 M GdmCl. In addition, kinetic measurement using fluorescence emission indicated that the single tryptophan residue was sensitive to at least two steps of the denaturation process. The fluorescence emission appeared to reflect some other structural perturbation than protein denaturation, as fluorescence inflection occurred approximately 5 degrees C prior to the changes observed in absorbance, CD, and fluorescence polarization anisotropy.

Cooperative disulfide bond formation in apamin

Apamin is being studied as a model for the folding mechanism of proteins whose structures are stabilized by disulfide bonds. Apamin consists of 18 amino acid residues and forms a stable structure consisting of a C-terminal alpha-helix and two reverse turns. This structure is stabilized by two disulfide bonds connecting Cys-1 to Cys-11 and Cys-3 to Cys-15. We used glutathione and dithiothreitol as reference thiols to measure the stabilities of the two disulfide bonds as a function of urea concentration and temperature in order to understand what contributes to the stability of the native structure. The results demonstrate modest contributions from secondary structure to the overall stability of the two disulfide bonds. The equilibrium constants for disulfide bond formation between the fully reduced peptide and the native structure with two disulfide bonds at 25 degrees C and pH 7.0 are 0.42 M2 using glutathione and 2.7 x 10(-5) using dithiothreitol. The equilibrium constant decreases by a factor of approximately 4 in 8 M urea and decreases by a factor of 3 between 0 and 60 degrees C. At least three one-disulfide intermediates are found at low concentrations in the equilibrium mixture. Using glutathione, the equilibrium constants for forming the one-disulfide intermediates with respect to the reduced peptide are approximately 0.025 M. The second disulfide bond forms with an equilibrium constant of approximately 17 M. Thus, apamin folding is very cooperative, but the native structure is only modestly stabilized by urea- or temperature-denaturable secondary structure.

Production and characterisation of mouse monoclonal antibodies reactive with the lipopolysaccharide core of Pseudomonas aeruginosa

Monoclonal antibodies (MAbs) to the core antigen region of lipopolysaccharide (LPS) of Pseudomonas aeruginosa were produced from mice immunised with whole cells of heat-killed rough mutants of Pseudomonas aeruginosa expressing partial or complete core LPS. MAbs were screened in an enzyme-linked immunosorbent assay (ELISA) against three different antigen cocktails: S-form LPS from three P. aeruginosa strains, R-form LPS from six P. aeruginosa strains and, as a negative control, R-form LPS from Salmonella typhimurium and Escherichia coli. Selected MAbs were subsequently screened against a range of extracted LPS and whole cells from both reference strains and clinical isolates of P. aeruginosa. The antibodies were also screened in ELISA against whole-cell antigens from other Pseudomonas spp. as well as strains of Haemophilus influenzae, Neisseria subflava and Staphylococcus aureus. Five MAbs reacting with the core component of P. aeruginosa LPS were finally selected. Two of these, MAbs 360.7 and 304.1.4, were particularly reactive in immunoblots against unsubstituted core LPS, including that from O-antigenic serotypes of P. aeruginosa. The MAbs also reacted with some of the other Pseudomonas spp., but not with P. cepacia or Xanthomonas (Pseudomonas) maltophilia. Cross-reactivity with whole cells from other bacterial species was minimal or not observed. Reactivity of MAbs with some Staph. aureus strains was observed, and binding to the protein A component was implicated. The reactivity of the MAbs was investigated further by flow cytometry and immunogold electronmicroscopy. The suitability of the MAbs for an immunological assay for detection of P. aeruginosa in respiratory secretions from CF patients is discussed.

Stabilities of disulfide bond intermediates in the folding of apamin

Apamin is an 18-residue bee venom peptide with the sequence CNCKAPETALCARRCQQH-amide and contains 2 disulfide bonds connecting C-1 to C-11 and C-3 to C-15. In the folding of reduced, unfolded apamin to native apamin with two disulfide bonds, the one-disulfide folding intermediate states are not populated to significant levels. To study the properties of the one-disulfide intermediates, we have synthesized two peptide models to mimic the one-disulfide intermediates, Apa-1 and Apa-2, in which two cysteines in the sequence have been replaced by alanines. These peptides can form only one of the native disulfide bonds, C-1 to C-11 in the case of Apa-1 and C-3 to C-15 in the case of Apa-2. The stabilities of these disulfide bonds have been measured as a function of pH, concentration of urea, and temperature, in order to understand which contributions stabilize the disulfide-bonded structures. Using oxidized and reduced glutathione, the equilibrium constants for forming the disulfide bonds at 25 degrees C and pH 7.0 are 0.018 M for Apa-1 and 0.033 M for Apa-2 and show little dependence on pH or temperature. Both disulfide bonds are destabilized slightly (by approximately a factor of 2) between 0 and 8 M urea. Circular dichroism spectra indicate that although both Apa-1 and Apa-2 exhibit some structure, Apa-2 exhibits more than Apa-1. The results suggest that in the folding of apamin, the one-disulfide intermediate containing the C-3 to C-15 disulfide bond, as in Apa-2, is favored slightly. Secondary structure provides modest stabilization to this intermediate.

Direct measurement of the equilibrium between glutathione and dithiothreitol by high performance liquid chromatography

The equilibrium constant between reduced glutathione (GSH), oxidized glutathione (GSSG), reduced dithiothreitol (DTTSHSH), and oxidized dithiothreitol (DTTSS) has been directly measured by high performance liquid chromatography analysis of equilibrium mixtures. The equilibrium constant at 25 degrees C for the reaction GSSG + DTTSHSH in equilibrium 2GSH + DTTSS varies from approximately 200 M, below pH 8, to approximately 2800 M, above pH 11. The observed pH dependence is generally consistent with published values of acid dissociation constants of these thiols.

Preferential DNA repair of alkali-labile sites within the active insulin gene

DNA damage and repair were studied in a DNA fragment containing the insulin gene after treatment of cells with methylnitrosourea. For these studies, two clonal isolates from the same rat insulinoma cell line which differ in that the insulin gene is transcribed in one (RINr 38) and is silent in the other (RINr B2) were utilized. Both the determination of immunologically reactive insulin released and the expression of insulin mRNA were used to verify that the gene was transcribed in the RINr 38 cells and not in the RINr B2 cells. Repair kinetics for the removal of alkali-labile sites were comparable across the entire genome in the RINr 38 and RINr B2 cells as determined using alkaline sucrose gradient sedimentation and a 32P end-labeling assay for the quantitation of N7-methylguanine. Quantitative DNA blot analysis was utilized to assess the formation and repair of alkali-labile sites within the restriction fragment containing the insulin gene. Alkali-labile sites appeared to be formed equally within the restriction fragment containing the insulin gene in both the RINr 38 and RINr B2 cells. However, at 24 h, 60% of the lesions were removed from the fragment in the RINr 38 cells, where the gene was transcribed, compared to the removal of only 20% in the RINr B2 cells, where the gene was silent. Thus, it appears that alkali-labile sites induced by exposure to methylnitrosourea are repaired more efficiently in the DNA fragment containing the insulin gene when it is actively transcribed.

Mucinophilic and chemotactic properties of Pseudomonas aeruginosa in relation to pulmonary colonization in cystic fibrosis

Representative isolates of nonmucoid Pseudomonas aeruginosa were studied to investigate the hypothesis that mucinophilic and chemotactic properties in this species act as potential factors in the initial stages of pulmonary colonization in patients with cystic fibrosis (CF). Transmission electron microscopy with a surfactant monolayer technique was used in a novel manner to demonstrate the adhesion of all 10 P. aeruginosa strains examined to porcine gastric mucin and tracheobronchial mucin from a patient with CF. Control experiments showed that Escherichia coli K-12 and single representatives of Proteus mirabilis and Klebsiella aerogenes did not bind to these mucins. The Adler capillary technique, used to measure bacterial chemotactic response, showed that purified CF mucin acted as a chemoattractant for most P. aeruginosa strains, with the exception of the nonmotile mutant M2Fla- and the nonchemotactic mutant WR-5. The ability of the major sugar and amino acid components of mucin to act as chemoattractants was investigated. The degree of chemotaxis was strain specific; optimum chemotaxis was observed toward serine, alanine, glycine, proline, and threonine. No strain showed chemotaxis to N-acetylneuraminic acid, but all strains showed a strain-dependent chemotactic response to the sugars L-fucose, D-galactose, N-acetyl-D-galactosamine, and N-acetyl-D-glucosamine. These results provide new information on the mucinophilic and chemotactic properties of nonmucoid P. aeruginosa and support the hypothesis that these properties could play a role in the initial stages of pulmonary colonization in patients with CF.

Distribution of charged residues stabilizes individual helices in myoglobins

The effect of the distribution of charged residues on stability of alpha helices in isolated peptides and in globular proteins exemplified by myoglobins from 62 different species is discussed. A highly simplified set of rules is used to account for the interaction of charged groups with the dipole of an alpha helix. Only the position and sign of a charge with respect to the center of the helix and its ability to participate in intrahelical salt bridges determine its effect. These rules lead to a linear correlation between the helicity in variant C-peptide helices from RNAse and the extent to which the charge distribution opposes the helix dipole. Of the sample of 496 helices in the myoglobins studied, 456 exhibit arrangements of charges which oppose the effective dipole moment of the helix according to this calculation. A number of variants occur which leave the backbone moment of helices A-D unchanged, or even add to it. However no such variants exist in the sequences of helices E-H. We suggest that the E, F, G and H helices in myoglobins which show the strongest reversal of the helix dipole participate in the structures of early intermediates in folding of the chain. Stable helix structures should be more likely to occur in these isolated sequences also, and introduction of charge alterations in helices E to H should affect the initial refolding rate of mutant myoglobins.

Persistence of the alpha-helix stop signal in the S-peptide in trifluoroethanol solutions

alpha-Helix formation in the S-peptide (residues 1-19 of ribonuclease A) was studied in detail by use of two-dimensional 1H nuclear magnetic resonance to monitor the effects of 2,2,2-trifluoroethanol (TFE) at 0 degrees C and pH* 2.07. TFE stabilizes the S-peptide alpha-helix. Helix formation by a particular amino acid was monitored by the chemical shifts of the C alpha, C beta, and C gamma protons while increasing the concentration of TFE: large changes in chemical shift of a particular residue indicate that it is induced to go helical, whereas small chemical shift changes indicate little helix formation. Residues Thr-3 to Met-13 undergo chemical shift changes consistent with helix formation, whereas the other residues do not. Earlier work [Kim, P. S., & Baldwin, R. L. (1984) Nature 307, 329-334] reported that residues Thr-3 to His-12 become helical in aqueous solution. The existence of a "helix stop signal" was inferred from this behavior. We thus conclude that this helix stop signal persists in TFE solutions.