Structure of the ligand-binding domain of the EphB2 receptor at 2 A resolution.

Eph tyrosine kinase receptors, the largest group of receptor tyrosine kinases, and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, shape and mobility. Recently, several Eph receptors and ephrins have also been found to play important roles in the progression of cancer. Structural and biophysical studies have established detailed information on the binding and recognition of Eph receptors and ephrins. The initial high-affinity binding of Eph receptors to ephrin occurs through the penetration of an extended G-H loop of the ligand into a hydrophobic channel on the surface of the receptor. Consequently, the G-H loop-binding channel of Eph receptors is the main target in the search for Eph antagonists that could be used in the development of anticancer drugs and several peptides have been shown to specifically bind Eph receptors and compete with the cognate ephrin ligands. However, the molecular details of the conformational changes upon Eph/ephrin binding have remained speculative, since two of the loops were unstructured in the original model of the free EphB2 structure and their conformational changes upon ligand binding could consequently not be analyzed in detail. In this study, the X-ray structure of unbound EphB2 is reported at a considerably higher 2 A resolution, the conformational changes that the important receptor loops undergo upon ligand binding are described and the consequences that these findings have for the development of Eph antagonists are discussed.

Crystal structure of an Eph receptor-ephrin complex.

The Eph family of receptor tyrosine kinases and their membrane-anchored ephrin ligands are important in regulating cell-cell interactions as they initiate a unique bidirectional signal transduction cascade whereby information is communicated into both the Eph-expressing and the ephrin-expressing cells. Initially identified as regulators of axon pathfinding and neuronal cell migration, Ephs and ephrins are now known to have roles in many other cell-cell interactions, including those of vascular endothelial cells and specialized epithelia. Here we report the crystal structure of the complex formed between EphB2 and ephrin-B2, determined at 2.7 A resolution. Each Eph receptor binds an ephrin ligand through an expansive dimerization interface dominated by the insertion of an extended ephrin loop into a channel at the surface of the receptor. Two Eph-Ephrin dimers then join to form a tetramer, in which each ligand interacts with two receptors and each receptor interacts with two ligands. The Eph and ephrin molecules are precisely positioned and orientated in these complexes, promoting higher-order clustering and the initiation of bidirectional signalling.

Mutational analysis of sickle haemoglobin (Hb) gelation.

The use of recombinant Hb has provided the advantage that any amino acid substitution can be made at sites not represented by natural mutants or that cannot be modified by chemical procedures. We have recently reported the expression of human sickle Hb (HbS) in the yeast Saccharomyces cerevisiae that carries a plasmid containing the human alpha- and beta-globin cDNA sequences; N-terminal nascent protein processing is correct and a soluble correctly folded Hb tetramer is produced. The yeast system produces a recombinant sickle Hb that is identical by about a dozen biochemical and physiological criteria with the natural sickle Hb purified from the red cells of sickle-cell anaemia patients. Most importantly, the gelling concentration of this recombinant sickle Hb is the same as that of the HbS purified from human sickle red cells. The misfolding of Hb reported for the Escherichia coli-expressed protein is not apparent for Hb expressed in yeast by any of the criteria that we have used for characterization. These findings indicate that this system is well suited to the production of HbS mutants to explore those areas of the HbS tetramer whose roles in the gelation process are not yet defined and to measure quantitatively the strength of such interactions at certain inter-tetrameric contact sites in the deoxy-HbS aggregate. This article reviews our studies on a number of sickle Hb mutants, including polymerization-enhancing HbS mutants and polymerization-inhibiting HbS mutants.

Crystal structure of the ligand-binding domain of the receptor tyrosine kinase EphB2.

The Eph receptors, which bind a group of cell-membrane-anchored ligands known as ephrins, represent the largest subfamily of receptor tyrosine kinases (RTKs). They are predominantly expressed in the developing and adult nervous system and are important in contact-mediated axon guidance, axon fasciculation and cell migration. Eph receptors are unique among other RTKs in that they fall into two subclasses with distinct ligand specificities, and in that they can themselves function as ligands to activate bidirectional cell-cell signalling. We report here the crystal structure at 2.9 A resolution of the amino-terminal ligand-binding domain of the EphB2 receptor (also known as Nuk). The domain folds into a compact jellyroll beta-sandwich composed of 11 antiparallel beta-strands. Using structure-based mutagenesis, we have identified an extended loop that is important for ligand binding and class specificity. This loop, which is conserved within but not between Eph RTK subclasses, packs against the concave beta-sandwich surface near positions at which missense mutations cause signalling defects, localizing the ligand-binding region on the surface of the receptor.

Recombinant sickle hemoglobin containing a lysine substitution at Asp-85(alpha): expression in yeast, functional properties, and participation in gel formation.

Clinical modalities based on inhibition of gelation of HbS are hindered by the lack of quantitative information on the extent of participation of different amino acid residues in the aggregation process. One such site is Asp-85(alpha), which is involved in a parallel interdouble strand ionic interaction with Lys-144(beta) according to the crystal structure of HbS, but electron microscopy does not specifically show Asp-85(alpha) as a contact site for fiber formation. Using a yeast recombinant system, we have substituted this site by Lys to abolish ion pairing and to make a quantitative determination of its participation in aggregation. The purified double mutant was shown to have the expected pI, the calculated molecular weight, correct amino acid composition, and peptide map. The recombinant double mutant has an oxygen affinity of 10 mm Hg, which is identical to that for HbA and HbS under the same conditions; it also has high cooperativity with an average n value of 2.7. The change in P50 in response to chloride ions was about 25% less than that for HbA or HbS and is ascribed to the introduction of a new positive charge near one of the major oxygen-linked chloride binding sites of hemoglobin. The gelation concentration of the double mutant was measured by a new procedure (Bookchin et al, 1994); the maximal amount of soluble hemoglobin (Csat) in the presence of dextran indicated a decreased tendency for gelation with a Csat of 53 mg/mL compared with 34 mg/mL for HbS. This inhibitory effect is smaller than that of the E6V(beta)/L88A(beta) (Csat, 67 mg/mL) and the E6V(beta)/K95I(beta) (Csat, 90 mg/mL) recombinant hemoglobins. Thus, we would classify Asp-85(alpha) as a moderate contributor to the strength of the HbS aggregate. This wide range of gelation values demonstrates that some sites are more important than others in promoting HbS aggregation.

Nucleation and polymerization of sickle hemoglobin with Leu beta 88 substituted by Ala.

We have measured the solubility, and the rates of homogeneous and heterogeneous nucleation on sickle hemoglobin (HbS beta 6 Glu-->Val) additionally modified by site-directed mutagenesis to possess Ala rather than Leu at beta 88, which forms part of the receptor site for beta 6 Val in the sickle polymer. The solubility of the hemoglobin is increased at all temperatures, and is about 29 g/dl at 25 degrees C. Polymerization kinetics, induced by laser photolysis and observed by light-scattering intensity, showed exponential growth with rates about 300 times slower than experiments done on similar concentrations of HbS. When polymerization is carried out in small volumes, the time of measurable light-scattering signal to reach one-tenth of its final value (denoted as the tenth time) showed stochastic fluctuations, as is seen in pure HbS. Homogeneous nucleation rates were measured by observing distributions of tenth times and these rates were slowed by the mutation by almost 1000-fold relative to pure HbS. The kinetics, including the exponential progress curves and shape of the tenth time distributions, are well described by the double nucleation mechanism for polymerization. Analysis of the homogeneous nucleation rates leads to the surprising conclusion that the mutation has scarcely changed the energy of the intermolecular contacts despite the increase in solubility of the double mutant. This conclusion is supported by the stereochemistry of the modified contact site, in which the amount of exposed hydrophobic surface appears to be unchanged by the mutation. The increased solubility must therefore result from decreased motional freedom of molecules within the polymer, which could arise from tighter packing into the enlarged receptor pocket. This points up the ability of kinetic analysis to reveal important thermodynamic properties of assembly, and underlines the importance of the vibrational degrees of freedom in setting the final equilibrium constant. Chemical modifications to restrict vibrations and enhance the cost of polymerization may prove useful in constructing compounds to act as inhibitors of sickle cell gelation.

A recombinant sickle hemoglobin triple mutant with independent inhibitory effects on polymerization.

As part of a comprehensive effort to map the most important regions of sickle hemoglobin that are involved in polymerization, we have determined whether two sites previously shown to be involved, Leu-88(beta) and Lys-95(beta), had additive effects when substituted. The former site is part of the hydrophobic pocket that binds Val-6(beta), the natural mutation of HbS, and the latter site is a prominent part of the hemoglobin exterior. A sickle hemoglobin triple mutant with three amino acid substitutions on the beta-chain, E6V/L88A/K95I, has been expressed in yeast and characterized extensively. Its oxygen binding curve, cooperativity, response to allosteric effectors, and the alkaline Bohr effect showed that it was completely functional. The polymer solubility of the deoxy triple mutant, measured by a new micromethod requiring reduced amounts of hemoglobin, was identical to that of the E6V(beta)/K95I(beta) mutant, i.e. when the K95I(beta) substitution was present on the same tetramer together with the naturally occurring E6V(beta) substitution, the L88A(beta) replacement had no additive effect on polymer inhibition. The results suggest that Lys-95(beta) on the surface of the tetramer and its complementary binding region on the adjoining tetramer are potential targets for the design of an effective antisickling agent.

Phosphoserine aminotransferase from Bacillus circulans subsp. alkalophilus: purification, gene cloning and sequencing.

Two peaks of aspartate aminotransferase (AspAT) catalytic activity were observed during DEAE chromatography of a protein extract from alkalophilic B. circulans. The enzyme purified from the major peak appeared to be not aspartate but phosphoserine aminotransferase (PSAT) with a considerably high AspAT side activity. The sequence of the enzyme N-terminus was determined, and the PSAT gene was cloned as two separate fragments. DNA sequencing revealed the open reading frame for the PSAT starting from TTG, putative ribosomal binding site and terminator of transcription. The PSAT gene encodes a protein of 361 amino acids (M(r) 39793) which shows moderate homology to other known phosphoserine aminotransferases (36-46% of identity, 60-64% of similarity). The PSAT from the alkalophile shares with all of them the consensus sequence pattern around the pyridoxal 5'-phosphate attachment site.

Solubility of sickle hemoglobin measured by a kinetic micromethod.

We have developed a photolytic method to determine the concentration of reactive hemes in a solution in the presence of a trace amount of CO. By measurement of the bimolecular rate of CO binding, and by calibration of the rate constant under equivalent conditions, the concentration of the reactive hemes can be determined. In a solution of sickle hemoglobin, the molecules in the gel contribute negligibly to the recombination rate, allowing the concentration of the molecules in the solution phase to be determined. To optimize signal to noise, modulated excitation methods were employed, although the method could also be used with pulse techniques and suitable signal averaging. Because the optical method employs a microspectrophotometer, only a few microliters of concentrated Hb solution is required to reproduce the entire temperature dependence of the solubility previously determined by centrifugation using milliliter quantities of solutions of the same concentration. This should be especially useful for studies of site-directed mutants, and we present results obtained on one such HbS in which Leu 88 beta has been replaced by Ala. The free energy difference in the polymerization of the Leu 88 beta double mutant is consistent with known differences in the amino acid hydrophobicities. The calibration required for these experiments also provides an excellent determination of the activation energy for binding the first CO to deoxy Hb.

Participation and strength of interaction of lysine 95(beta) in the polymerization of hemoglobin S as determined by its site-directed substitution by isoleucine.

The role of Lys-95(beta), which is on the exterior of the hemoglobin (HbS) tetramer, in the aggregation process has been addressed because there is a lack of agreement on its importance. The early studies on the aggregation of HbS in the presence of other mutant hemoglobins are consistent with the subsequent electron microscopic studies in demonstrating the participation of Lys-95(beta) in gelation; the results of the crystal structure do not agree with these conclusions. Therefore, with the objective of clarifying its role we have carried out site-directed substitution of Lys-95(beta) to an isoleucine residue. The mutation was introduced by polymerase chain reaction recombination methodology, and the absence of other mutations in the beta-globin gene was established by sequencing the gene in its entirety. The recombinant mutant hemoglobin was expressed in yeast and characterized by peptide mapping and sequencing, which demonstrated that the only different tryptic peptide had the Ile substitution at position 95(beta). The recombinant hemoglobin had the correct amino acid composition and molecular weight by mass spectrometric analysis. It was also pure as judged by isoelectric focusing. It was fully functional because it had an average Hill coefficient of 3.1 and responded normally to the allosteric regulators, chloride, 2,3-diphosphoglycerate, and inositol hexaphosphate. Of particular interest was the finding that this hemoglobin mutant aggregated at a concentration of about 40 g/dl, nearly twice that at which HbS itself aggregated (24 g/dl). Therefore, Lys-95(beta) has a very important role in the aggregation process and is a good candidate site for the design of a therapeutic agent for sickle cell anemia.

Biological activities of lipoteichoic acid and peptidoglycan-teichoic acid of Bacillus subtilis 168 (Marburg).

To evaluate the suitability of Bacillus subtilis as a production host of heterologous proteins for pharmaceutical purposes, we assessed the biological activity of this bacterium and its major cell envelope components, lipoteichoic acid (LTA) and peptidoglycan-teichoic acid complex (PG-TA) in several eukaryotic effector assays. LTA and PG-TA were found to be non-toxic for mice and guinea-pigs in a short-term toxicity assay. PG-TA was weakly pyrogenic and weakly mitogenic. Both LTA and PG-TA acted as immunologic adjuvants in mice and when injected in mice, also caused an increase in the number of granulocyte-monocyte colony-forming cells in the bone marrow probably via stimulation of production of granulocyte-macrophage colony-stimulating factor.

Evaluation of pooled and individual components of Bordetella pertussis as antigens in an enzyme immunoassay for diagnosis of pertussis.

Six different antigen preparations for use in an enzyme immunoassay (EIA) to detect IgM, IgA and IgG antibodies to Bordetella pertussis were evaluated using sera from 13 randomly selected culture-positive patients and from 87 patients with suspected pertussis during a pertussis outbreak. Based on results in 80 healthy control sera a specificity limit of 99.9% was selected. Sera from all culture-positive patients reacted with at least one of the antigens. The sensitivity of the EIA using the individual antigen preparations was 85% for filamentous hemagglutinin, 92% for pertussis toxin, 62% for 69 kDa outer membrane protein, 85% for a pool of these three antigens, 54% for sonicated whole bacteria and 69% for 21 kDa pertussis toxin subunit S1. In the outbreak patient group 49 (56%) of the initial sera reacted with at least one of five antigen preparations. The EIA using sonicated bacteria detected only 41% of all seropositive cases compared with 51% using filamentous hemagglutinin, 61% using pertussis toxin, 65% using 69 kDa OMP and 65% using pooled antigen. It is concluded that either the pooled antigen or pertussis toxin antigen are suitable antigen preparations for use in the EIA for diagnosis of pertussis.

Assessment of non-protein impurities in potential vaccine proteins produced by Bacillus subtilis.

The levels of non-protein impurities at different stages of purification of model vaccine proteins produced by Bacillus subtilis were assessed with special emphasis on peptidoglycan-wall teichoic acid and lipoteichoic acid. Intracytoplasmically produced proteins were purified by disrupting the lysozyme protoplasts using osmotic shock, depositing the inclusion bodies by low-speed centrifugation, and washing them with detergent. By this procedure most of the cell envelope-derived impurities could be removed. The final product contained less than 1% (w/w) of neutral sugars, fatty acids, phosphate, hexosamine, diaminopimelic acid and glycerol. A secreted protein was purified from the culture supernatant by successive ion-exchange and adsorption chromatography. The cell envelope-derived impurities were efficiently removed by the cation-exchanger, and the final product contained only minute amounts of non-protein components. The amounts of non-protein components such as peptidoglycan and lipoteichoic acid in proteins produced in either mode were shown to be negligible in relation to their potentially harmful biological effects.

Secretion of the Escherichia coli outer membrane proteins OmpA and OmpF in Bacillus subtilis is blocked at an early intracellular step.

When the genes coding for the outer membrane (OM) proteins OmpA and OmpF of Escherichia coli are fused to a signal sequence of a bacillar exoenzyme and expressed in Bacillus subtilis they remain cell-bound and the signal sequence is not cleaved. To identify the step of arrest in the export of these proteins we studied their accessibility to protease applied to intact protoplasts; they remained resistant indicating fully intracellular localization. Both proteins appeared associated with the cell membranes in sedimentation and flotation centrifugation experiments. However, OmpA and OmpF proteins synthesized in B. subtilis without a signal sequence were similarly associated with membranes in centrifugation experiments whereas electron microscopy showed the presence of intracytoplasmic inclusion bodies not obviously attached to the cytoplasmic membrane. We conclude that OmpA and OmpF proteins even when provided with a functional signal sequence do not enter the export pathway in B. subtilis, probably owing to lack of a specific export component in B. subtilis.

The 20 kDa C-terminally truncated form of pertussis toxin subunit S1 secreted from Bacillus subtilis.

The subunit S1 of pertussis toxin (PT) was purified as the recombinant product BacS1 from the culture supernatant of a Bacillus subtilis strain containing a secretion vector with a DNA fragment coding for the mature subunit S1 inserted downstream of the signal sequence of the alpha-amylase gene. The method of purification was successive ion exchange and adsorption chromatography. BacS1 occurred in two forms (28 and 20 kDa) of which the truncated 20-kDa peptide was the main one in the supernatant. The truncated BacS1 was purified and shown to have the same NH2-terminus as the full-size (28 kDa) BacS1. It was also enzymatically active indicating correct conformation. The truncated BacS1 was also shown to elicit neutralizing and protective antibodies when injected into mice or rabbits.

Immunogenicity and protective efficacy of pertussis toxin subunit S1 produced by Bacillus subtilis.

Pertussis toxin (PT) subunit S1 was produced in Bacillus subtilis as a secretory protein designated BacS1. BacS1 was partially purified and used to immunize mice. The sera were tested for PT-neutralizing antibodies and for protective capacity in a mouse model. Unlike previous findings with recombinant S1 from Escherichia coli, the recombinant BacS1 protein induced antibodies that were both neutralizing and protective. An adjuvant was necessary for efficient immunization with BacS1 but not with PT. Of the four adjuvants tested, aluminium phosphate gel was insufficient whereas Freund's incomplete adjuvant, Klebsiella lipopolysaccharide and Ribi's monophosphoryl lipid A-trehalose dimycolate emulsion all resulted in protective antibody production in NIH mice.

Expression of pertussis toxin subunit S4 as an intracytoplasmic protein in Bacillus subtilis.

The expression and secretion of pertussis toxin subunits S1 to S5 in Bacillus subtilis by the aid of a bacillary signal sequence has been reported. While secretion of subunit S1 was high, that of others was low. Ways have now been explored to improve the yield, using S4 as an example. The addition of a protease inhibitor was found to increase the amount of S4 in the culture supernatant, but the final amount was still much below that of S1. However, intracellular expression of S4 gave a high yield (500 mg l-1) and the aggregated protein could easily be isolated in a few simple steps.

Phosphorus-31 nuclear magnetic resonance of aspartate aminotransferase from chicken heart cytosol.

31P-nuclear magnetic resonance and absorption spectra of cytosolic chicken aspartate aminotransferase (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) have been recorded in the pH range from 5 to 8.5. The 31P chemical shift was found to be pH-dependent with a pK of 6.85; the chemical shift change was 0.35 ppm. The pK value found by spectrophotometric titration of the enzyme proved to be about 6.0. The monoanion-dianion transition of the 5'-phosphate group of a model Schiff base of pyridoxal phosphate with 2-aminobutanol in methanol is accompanied by a change in the 31P chemical shift of 5.2 ppm. It is inferred that the phosphate group of the protein-bound coenzyme is in a dianionic form throughout the investigated pH range; the pH-dependence of the 31P chemical shift may be due to a conformational change at the active site. In the presence of 100 mM succinate, 6 mM aminooxyacetate or 25 mM cycloserine, the 31P chemical shift is insensitive to pH variations.

[31P-NMR spectra of aspartate aminotransferase from cytosol of the chicken heart]. / Issledovanie spektrov 31P-IaMR aspartat-aminotransferazy iz tsitozolia kurinykh serdets.

31P NMR spectra of the cytosolic chicken aspartate aminotransferase have been recorded at 161.7 MHz in the pH range of 5.7 to 8.2. The 31P chemical shift was found to be pH-dependent with a pK of 6.85; difference in the chemical shift at pH 5.7 and 8.2 is only 0.35 ppm. The monoanion-dianion transition of 5'-phosphate group of a model Schiff base of pyridoxal phosphate with 2-aminobutanol in methanol is accompanied by a change in 31P chemical shift of 5.2 ppm. It is inferred that the phosphate group of the protein--bound coenzyme is in dianionic form throughout the investigated pH range; the small pH-dependent change of chemical shift may be due to a protein conformational change that affects O-P-O bond angle. In the presence of the 0.1 M succinate, 31P chemical shift of the enzyme remains constant in the pH range of 5.0 to 8.3.

Equilibria between vitamin B6-compounds and cyclodextrins.

Convenient chromatographic methods to measure equilibrium constants between cyclodextrins and aromatic compounds were developed. The use of 'Hummel-Dreyer' elution profile allows us to determine values above 15-20 M-1. The weaker associations (below 15-20 M-1) can be measured with cyclo-dextrin-derivatized Biogel P-2 column. The latter method is very suitable to determine the equilibrium constants between cyclodextrins and vitamin B6-compounds which can't be measured with the conventional photometric procedure.