p38 pathway kinases as anti-inflammatory drug targets.

Mitogen-activated protein kinases (MAPK) are intracellular signaling molecules involved in cytokine synthesis. Several classes of mammalian MAPK have been identified, including extracellular signal-regulated kinase, c-jun N-terminal kinase, and p38 MAP kinase. p38alpha is a key MAPK involved in tumor necrosis factor alpha and other cytokine production, as well as enzyme induction (cyclooxygenase-2, inducible nitric oxide synthase, and matrix metalloproteinases) and adhesion molecule expression. An understanding of the broad biologic and pathophysiological roles of p38 MAPK family members has grown significantly over the past decade, as has the complexity of the signaling network leading to their activation. Downstream substrates of MAPK include other kinases (e.g., mitogen-activated protein-kinase-activated protein kinase 2) and factors that regulate transcription, nuclear export, and mRNA stability and translation. The high-resolution crystal structure of p38alpha has led to the design of selective inhibitors that have good pharmacological activity. Despite the strong rationale for MAPK inhibitors in human disease, direct proof of concept in the clinic has yet to be demonstrated, with most compounds demonstrating dose-limiting adverse effects. The role of MAPK in inflammation makes them attractive targets for new therapies, and efforts are continuing to identify newer, more selective inhibitors for inflammatory diseases.

Haloalkane dehalogenases: structure of a Rhodococcus enzyme.

The hydrolytic haloalkane dehalogenases are promising bioremediation and biocatalytic agents. Two general classes of dehalogenases have been reported from Xanthobacter and Rhodococcus. While these enzymes share 30% amino acid sequence identity, they have significantly different substrate specificities and halide-binding properties. We report the 1.5 A resolution crystal structure of the Rhodococcus dehalogenase at pH 5.5, pH 7.0, and pH 5.5 in the presence of NaI. The Rhodococcus and Xanthobacter enzymes have significant structural homology in the alpha/beta hydrolase core, but differ considerably in the cap domain. Consistent with its broad specificity for primary, secondary, and cyclic haloalkanes, the Rhodococcus enzyme has a substantially larger active site cavity. Significantly, the Rhodococcus dehalogenase has a different catalytic triad topology than the Xanthobacter enzyme. In the Xanthobacter dehalogenase, the third carboxylate functionality in the triad is provided by D260, which is positioned on the loop between beta7 and the penultimate helix. The carboxylate functionality in the Rhodococcus catalytic triad is donated from E141. A model of the enzyme cocrystallized with sodium iodide shows two iodide binding sites; one that defines the normal substrate and product-binding site and a second within the active site region. In the substrate and product complexes, the halogen binds to the Xanthobacter enzyme via hydrogen bonds with the N(eta)H of both W125 and W175. The Rhodococcusenzyme does not have a tryptophan analogous to W175. Instead, bound halide is stabilized with hydrogen bonds to the N(eta)H of W118 and to N(delta)H of N52. It appears that when cocrystallized with NaI the Rhodococcus enzyme has a rare stable S-I covalent bond to S(gamma) of C187.

In vivo screening of haloalkane dehalogenase mutants.

Haloalkane dehalogenase (Dh1A) from Xanthobacter autotrophicus GJ10 catalyzes the dehalogenation of short chain primary alkyl halides. Due to the high Km and low turnover, wild type Dh1A is not optimal for applications in bioremediation. We have developed an in vivo screen, based on a colorimetric pH indicator, to identify Dh1A mutant with improved catalytic activity. After screening 50,000 colonies, we identified a Dh1A mutant with a lower pH optimum. Sequence analysis of the mutant revealed a single substitution, alanine 149 to threonine, which is located close to the active site of Dh1A. Replacement of alanine 149 via site-directed mutagenesis with threonine, serine or cysteine retained the mutant phenotype. Other substitutions at position 149 show little or no activity.

Haloalkane dehalogenases: steady-state kinetics and halide inhibition.

The substrate specificities and product inhibition patterns of haloalkane dehalogenases from Xanthobacter autotrophicus GJ10 (XaDHL) and Rhodococcus rhodochrous (RrDHL) have been compared using a pH-indicator dye assay. In contrast to XaDHL, RrDHL is efficient toward secondary alkyl halides. Using steady-state kinetics, we have shown that halides are uncompetitive inhibitors of XaDHL with 1, 2-dichloroethane as the varied substrate at pH 8.2 (Cl-, Kii = 19 +/- 0.91; Br-, Kii = 2.5 +/- 0.19 mM; I-, Kii = 4.1 +/- 0.43 mM). Because they are uncompetitive with the substrate, halide ions do not bind to the free form of the enzyme; therefore, halide ions cannot be the last product released from the enzyme. The Kii for chloride was pH dependent and decreased more than 20-fold from 61 mM at pH 8.9 to 2.9 mM at pH 6.5. The pH dependence of 1/Kii showed simple titration behavior that fit to a pKa of approximately 7.5. The kcat was maximal at pH 8.2 and decreased at lower pH. A titration of kcat versus pH also fits to a pKa of approximately 7.5. Taken together, these data suggest that chloride binding and kcat are affected by the same ionizable group, likely the imidazole of a histidyl residue. In contrast, halides do not inhibit RrDHL. The Rhodococcus enzyme does not contain a tryptophan corresponding to W175 of XaDHL, which has been implicated in halide ion binding. The site-directed mutants W175F and W175Y of XaDHL were prepared and tested for halide ion inhibition. Halides do not inhibit either W175F or W175Y XaDHL.

A Raman spectroscopic characterization of bonding in the complex of horse liver alcohol dehydrogenase with NADH and N-cyclohexylformamide.

The binding of N-cyclohexylformamide (CXF) to the complex of horse liver alcohol dehydrogenase with NADH mimics that of the Michaelis complex for aldehyde reduction catalyzed by the enzyme. The Raman spectra of bound CXF and its 13C- and 15N-substituted derivatives have been obtained using Raman difference techniques, and the results are compared with CXF spectra in aqueous solution and in methylene chloride. The results indicate that the amide N-H bond is trans to the C=O bond of CXF both in solution and in the enzyme ternary complex. The C=O stretch and N-H bending modes of the amide of CXF shift -16 and -9 cm-1, respectively, in the enzyme ternary complex relative to that in aqueous solution and -48 and 36 cm-1, respectively, relative to that in methylene chloride. Ab initio normal mode calculations on various model systems of CXF show that the observed frequency changes of the C=O stretch mode have contributions from the frequency changes induced by the environmental changes near both the local C=O bond and the remote N-H bond. The same is true for the observed N-H bending frequency change. Our calculations also show that the environmentally induced frequency changes are additive so that it is possible to determine the C=O stretch (or N-H bending) frequency change that is due to the local interaction change near the C=O (or N-H) bond from the observed frequency changes. On the basis of these results and the empirical relationship between the C=O stretch frequency shift and the interaction enthalpy change on the C=O bond developed here, it is found that the C=O group of CXF in the enzyme/NADH/CXF complex binds with a favorable interaction enthalpy of approximately 5.5 kcal/mol relative to water. Similar analysis suggests that the N-H moiety of CXF is destabilized in the ternary complex by about 1.5 kcal/mol relative to water but is stabilized by about 1.5 kcal/mol relative to a hydrophobic environment. The analysis describes quantitatively the binding of the C=O of CXF with the catalytic zinc and the hydroxyl group of Ser-48 and the interaction of the N-H with the benzene ring of Phe-93 of the enzyme.

Inhibition of human alcohol dehydrogenases by formamides.

Human alcohol dehydrogenase (HsADH) comprises class I (alpha, beta, and gamma), class II (pi), and class IV (sigma) enzymes. Selective inhibitors of the enzymes could be used to prevent the metabolism of alcohols that form toxic products. Formamides are unreactive analogues of aldehydes and bind to the enzyme-NADH complex [Ramaswamy, S.; Scholze, M.; Plapp, B. V. Biochemistry 1997, 36, 3522-3527]. They are uncompetitive inhibitors against varied concentrations of alcohol, and this makes them effective even with saturating concentrations of alcohols. Molecular modeling led to the design and synthesis of a series of cyclic, linear, and disubstituted formamides. Evaluation of 23 compounds provided structure-function information and selective inhibitors for the enzymes, which have overlapping but differing substrate specificities. Monosubstituted formamides are good inhibitors of class I and II enzymes, and disubstituted formamides are selective for the alpha enzyme. Selective inhibitors, with Ki values at pH 7 and 25 degrees C of 0.33-0.74 microM, include N-cyclopentyl-N-cyclobutylformamide for HsADH alpha, N-benzylformamide for HsADH beta1, N-1-methylheptylformamide for HsADH gamma2, and N-heptylformamide for HsADH sigma and HsADH beta1.

Conversion of cysteinyl residues to unnatural amino acid analogs. Examination in a model system.

Improved and efficient techniques have led to an explosive growth in the application of site-directed mutagenesis to the study of enzymes. However, the limited availability of only those 20 amino acids that are translated by the genetic code has prevented the systematic variation of an amino acid's properties in order to define more precisely its role in the catalytic mechanism of an enzyme. An approach is being examined that combines the high specificity of site-directed mutagenesis with the flexibility of chemical modification to overcome these limitations. A set of reagents has been synthesized and reacted with a cysteine model to produce a series of amino acid structural analogs at appreciable rates and in good overall yields. The selective incorporation of these analogs in place of important functional amino acids in a protein will allow a more detailed examination of the role of that amino acid.

Mechanism-based inactivation of L-aspartase from Escherichia coli.

The substrate analogue L-aspartate beta-semialdehyde (L-ASA) has been identified as a mechanism-based inactivator of L-aspartase from Escherichia coli. The enzyme catalyzes the deamination of L-ASA to yield fumaric acid semialdehyde (FAA) and NH4+, with the product FAA partitioning between subsequent release or irreversible enzyme inactivation. Complete protection against L-ASA inactivation is observed in the presence of the product fumarate and a divalent metal ion. However, protection against inactivation by the product FAA also requires the presence of an enzyme activator. In addition to functioning as a mechanism-based inactivator, L-ASA has also been shown to serve as an activator of L-aspartase. The mechanism of inactivation by FAA involves the attack of an active site nucleophilic at the alpha-carbon of FAA to yield a stable Michael type enzyme adduct. Subsequent formation of a hydrazone upon treatment of the enzyme adduct with 2,4-dinitrophenylhydrazine confirms the presence of the unreacted aldehydic group of FAA. Examination of a group of product analogues with different substituents has demonstrated a correlation between the electron-withdrawing ability of these functional groups and the rate of inactivation of L-aspartase.

Mutagenic investigation of conserved functional amino acids in Escherichia coli L-aspartase.

The potential importance of several functional amino acids in the activity of L-aspartase from Escherichia coli has been examined by site-directed mutagenesis. Amino acids whose importance in enzyme activity was suggested by chemical modification and pH dependence studies were chosen as candidates for investigation. The selection of the particular amino acid targets was guided by homology comparisons among the other sequenced bacterial L-aspartases and by the broader comparison among the fumarase-aspartase enzyme family. Substitution of the most highly conserved cysteine with either serine or alanine, or the most highly conserved histidine with leucine, had no significant effect on the activity of L-aspartase or on the sensitivity of these mutated L-aspartases to cysteine and histidine specific modifying reagents. However, alteration of each of the two conserved lysines to arginine did cause dramatic changes in the catalytic properties of the enzyme. Modification of lysine 54 results in the complete loss of enzyme activity. However, this activity loss appears to be related to changes in the subunit association properties of the arginine 54 mutant. Lysine 326 appears to be involved in substrate binding. Modification of this residue causes a 5-fold increase in the Km for aspartic acid, a drastic decrease in kcat/Km, and a change in the divalent metal ion requirements of the enzyme.

Crystallization and preliminary X-ray studies of L-aspartase from Escherichia coli.

Single crystals of L-aspartate ammonia-lyase (L-aspartase) from Escherichia coli have been obtained by microdialysis at room temperature using polyethylene glycol 3350 and sodium acetate as co-precipitants. The crystals exhibit the symmetry of space group P2(1)2(1)2 with a = 156.5 A, b = 147.6 A, c = 102.5 A and diffract at least to 2.8 A.

Protein-gold transport in the endocytic complex of trophotaenial absorptive cells in the embryos of a goodeid teleost.

This paper reports adsorptive endocytosis of exogenous proteins by the trophotaenial absorptive cells (TACs) in the viviparous goodeid teleost, Ameca splendens. In vitro incubations were performed with gold conjugated to bovine serum albumin (Au-BSA), human transferrin (Au-HTf), fetuin (Au-Fet), and asialofetuin (Au-ASFet). Localization of gold label on the TAC surface was nearly exclusive to patches of an amorphous coat associated with part of the intermicrovillous plasma membrane. On addition of excess BSA, HTf, Fet, or ASFet to incubation media containing, respectively, Au-BSA, Au-HTf, Au-Fet, or Au-ASFet, the density of gold particles adsorbed on the TAC surface decreased drastically. Moreover, attachment of the four protein-gold complexes to the same plasma membrane sites was suggested by reciprocal inhibitory effects. Further proteins such as hemoglobin, myoglobin, and cytochrome c were as well potent inhibitors of Au-BSA and Au-HTf binding and uptake. Binding of TACs of native BSA or HTf was visualized by immunogold labeling. The interactions between proteins and binding sites required both the presence of Ca2+ and appropriate pH greater than 6.6. Analyses of the concentration-dependent BSA and HTf binding curves, plotted from morphometric data, resulted in apparent dissociation constants, Kds, of approximately 5 x 10(-7) M and 4 x 10(-7) M, respectively. Following binding at the TAC surface and internalization via clathrin-coated pits and vesicles the several ligands were routed along the lysosomal pathway with transit through the endosomal compartment. Prolonged incubation periods led to massive intracellular accumulation of tracer proteins. The effects of NH4Cl (10 mM) treatment on TACs included enormous cytoplasmic vacuolation, a reversible loss of protein binding sites on the plasma membrane, and a block in the transport of protein-gold complexes to lysosomes.

Retrograde trafficking of tracer protein by the internal ovarian epithelium in gravid goodeid teleosts.

Gravid goodeid females harbor embryos in a preformed ovarian cavity for prolonged periods of gestation. Various nutrients for embryonic growth are provided by the internal ovarian epithelium (IOE). Its cells flatten during late stages of gestation and form an attenuated layer of cytoplasm covering a dense network of protruding capillaries, with the nuclear domains mostly recessing between the vascular meshes. The IOE in both Xenotoca eiseni and Girardinichthys viviparus exhibit morphological features associated with vesicular transport of macromolecules. The amounts of rough endoplasmic reticulum in the IOE cells seem insufficient to effectively synthesise proteinaceous secretions. Apparently, it rather serves as a transit route for serum-derived products. Cationized ferritin (CF) was injected into the ovarian cavity of gravid females. The electrostatic ligand spotwise attached to the luminal surface of the IOE and gained access by adsorptive micropinocytosis. Many tracer molecules were sequestered into lysosome-like vacuoles that became increasingly swollen after prolonged incubation intervals. In addition, CF traversed the IOE within small vesicles. At the basal pole of the cells the contents of transcytotic vesicles were evacuated, and localization of small CF-clusters was regularly in the basement lamina, in the underlying connective tissue, in vacuoles within migrant cells, in vesicular compartments of the capillary endothelia, in capillary lumina, and in intravascular leucocytes. Tracer molecules were never observed to enter stacked Golgi cisternae. Since the cationic marker probably follows retrograde pathways of the protein secretion, the experimental data support the morphologically derived conclusions that postulate a major role for the IOE in transepithelial transport.

Polarized distribution of binding sites for concanavalin A and wheat-germ agglutinin in the zona pellucida of goodeid oocytes (teleostei).

Zonae pellucidae of the viviparous goodeid teleosts Girardinichthys viviparus, Xenoophorus captivus, and Xenotoca eiseni were investigated ultrastructurally, and binding sites for ConA and WGA were localized on cross-sections using a colloidal gold technique. In late stages of development, the oocytes are surrounded by a three-zonated acellular matrix multiply perforated by pore canals allowing long microvilli of the oocyte to penetrate interstices of the follicle epithelium. Together, the surface of the microvilli and zona pellucida is coated by a thin layer of homogeneous slightly electron-dense material. In early oogenesis, the thin acellular layer is entirely packed with binding sites for WGA, whereas those for ConA occur only sparsely. Three-zonated zonae pellucidae amply contain both WGA and ConA receptors. The asymmetric labelling pattern obtained with both lectin protein gold preparations indicates a polarized organization of the different glycoconjugates. WGA receptors are concentrated within the outer region of the zona pellucida. Labelling with ConA-HRP-Au complexes produced heavy deposits of marker beads within the inner two thirds of the zona pellucida and weak labelling of the superficial coat. After prolonged digestion with neuraminidase, WGA binding sites were no longer detectable.

Age-dependent changes in volume and haemoglobin content of erythrocytes in the carp (Cyprinus carpio L.).

Carp erythrocytes were fractionated by angle-head centrifugation which yielded fractions with a linear increase in density. Haematological examinations revealed that the heavier red blood cells of carp had greater volumes (MCV), more haemoglobin (MCH) and higher haemoglobin concentrations (MCHC) than light ones. The same experiments with human red cell fractions yielded a decrease in MCV, constant MCH and an increase in MCHC. Haemoglobin content in individual erythrocytes was also determined by scanning stage absorbance cytophotometry to establish the frequency distribution of the cellular haemoglobin contents. In carp, the distribution was symmetrical with the means increasing with density. No such change with cell density was found in human erythrocytes. Both carp and human erythrocytes incorporated [2-14C]glycine in vitro. After gel filtration, radioactivity was detected in carp, but not in human, haemoglobin fractions. 14C was found in all three haemoglobin fractions, obtained by isoelectric focusing, and was present in the haem and in the globin. [2-14C]glycine-labelled erythrocytes were reinjected into chronically cannulated carp and followed in vivo for several months. With time, the main peak of scintillation counts shifted from red cell fractions of low to high density. This is considered as evidence that density and age of red cells in carp are positively correlated and that erythrocytes can synthesize haemoglobin while circulating in the peripheral blood.

Maternal-embryonic relationships in the goodeid teleost, Xenoophorus captivus. The vacuolar apparatus in trophotaenial absorptive cells and its role in macromolecular transport.

The endodermal trophotaenial epithelium in goodeid embryos acts as a placental exchange site. Fine structural and cytochemical data indicate that the trophotaenial absorptive cells are endocytotically highly active. To test their micropinocytotic capacity and characterize the cellular mechanisms involved in membrane, solute and ligand movements, living embryos of Xenoophorus captivus were incubated in saline media containing horseradish peroxidase (HRP) and/or cationized ferritin (CF) in vitro, and the uptake of these tracer proteins examined by both time sequence analysis and pulse-chase procedures. In some embryos, the effects of prolonged exposure to CF injected into the ovarian cavity, was also investigated. Labelling of the free cell surface was detectable with CF only, but interiorization of both probes was quick from all incubation media. Adsorptive pinocytosis of CF and fluid-phase uptake of HRP sequentially labelled pinocytic vesicles, endosomes, and lysosome-like bodies. In addition, CF-molecules were sequestered within apical tubules and small vesicles. HRP was largely excluded from both organelles and ended up in the lysosomal compartment. For CF, two alternative pathways were indicated by the pulse-chase experiments; transcellular passage and regurgitation of tracer molecules to the apical cell surface. The latter procedure involves membrane and receptor recycling, in which apical tubules are thought to mediate. In double-tracer experiments, using an 8:1 excess of HRP, external labelling with CF was light or lacking after 1-3 min, and the initial uptake-phase produced pinocytic vesicles and endosomes that mainly contained HRP-reaction product. Prolonged incubation, however, resulted in densely CF-labelled plasmalemmal invaginations and pinocytic vesicles that predominantly carried ferritin granules. After 60 min, the vacuoles of the endosomal compartment contained either high concentrations of HRP-reaction product, both tracers side by side, or virtually exclusively CF.

Microspectrophotometric and scanning microphotometric studies of carp (Cyprinus carpio L.) erythrocytes.

Carp (Cyprinus carpio) hemoglobin readily autoxidizes in blood smears. Quantification of Soret-band absorbance in individual erythrocytes by means of scanning cytophotometry therefore requires more elaborate methods of preparation of blood samples. Of the fixatives that have been tested, suspension of whole blood in isotonic salt solutions containing glutaraldehyde was most suitable. Glutaraldehyde-fixed red blood cells are totally resistant to hemolysis. In the course of fixation, hemoglobin is transformed to methemoglobin. Spectrophotometry indicated extensive similarities between glutaraldehyde-fixed carp methemoglobin and human methemoglobin. In aqueous solutions, the intensity of the Soret-peak was pH-dependent. The allosteric modifier organic polyphosphate caused an R----T transition, resulting in increased molar extinctions. Dried preparations showed Soret-spectra that were not influenced from either pH or organic polyphosphate concentration of the aqueous suspensions in which the erythrocytes had been stored. The same was true for slide preparations of cyanomethemoglobin, easily derived from methemoglobin on addition of potassium cyanide. In the absence of oxygen fresh blood cells from carp slowly transform their hemoglobin into deoxyhemoglobin. Spectra of the intermediate stages of deoxygenation, Hb4(O2)3, Hb4(O2)2 and Hb4(O2), as well as mixtures of these intermediates, could be monitored.