Pt-staining of peroxidatic reaction products at the ultrastructural level

The use of H2PtCl6 is proposed for the selective visualization of the poly-DAB reaction product created, in aldehyde-fixed tissue, with the cytochemical reaction according to Graham and Karnovsky (1966) or to Hoefsmit (1975). At sites known to contain peroxidatic activity, at the ultrastructural level, an electron-dense reaction product is acquired in otherwise unstained ultrathin sections. The presence of the element platinum in these sites has been demonstrated by X-ray microanalysis, for both the endogenous peroxidase and peroxidase conjugated to antibodies. The absolute platinum concentration has been established in erythrocytes and the granules in eosinophils and monocytes by co-embedded, Pt-containing Chelex ion-exchange beads next to the cells. By the application of the method of integrated morphometrical and chemical analysis (de Bruijn and Zeelen 1984; de Bruijn 1985; de Bruijn and Cleton 1985), both the elemental concentration and the area occupied have been calculated for eosinophil granules. The mean Pt net-intensity values of the cytoplasmic areas, known not to contain the enzyme peroxidase has been measured, and compared to the mean net-intensity Pt values of the granules. It was noted that the cytoplasmic Pt net-intensity values were not zero. The two sets of values are expressed as a mean Pt granule/cytoplasm ratio, this ratio creates a value for the "selectivity" of the reaction. The application of a postfixation reaction with OsO4- containing media, at pH 7.4, in addition to the H2PtCl6 reaction, resulted in a contrasted poly-DAB reaction product at all sites known to contain peroxidatic activity. However, X-ray microanalysis revealed that in addition to platinum, osmium was present.(ABSTRACT TRUNCATED AT 250 WORDS)     

Pt-Staining of peroxidatic reaction products at the ultrastructural level

Summary The use of H₂PtCl₆ is proposed for the selective visualization of the poly-DAB reaction product created, in aldehyde-fixed tissue, with the cytochemical reaction according to Graham and Karnovsky (1966) or to Hoefsmit (1975).At sites known to contain peroxidatic activity, at the ultrastructural level, an electron-dense reaction product is acquired in otherwise unstained ultrathin sections. The presence of the element platinum in these sites has been demonstrated by X-ray microanalysis, for both the endogenous peroxidase and peroxidase conjugated to antibodies.The absolute platinum concentration has been established in erythrocytes and the granules in eosinophils and monocytes by co-embedded, Pt-containing Chelex ion-exchange beads next to the cells.By the application of the method of integrated morphometrical and chemical analysis (de Bruijn and Zeelen 1984; de Bruijn 1985; de Bruijn and Cleton 1985), both the elemental concentration and the area occupied have been calculated for eosinophil granules. The mean Pt net-intensity values of the cytoplasmic areas, known not to contain the enzyme peroxidase has been measured, and compared to the mean net-intensity Pt values of the granules. It was noted that the cytoplasmic Pt net-intensity values were not zero. The two sets of values are expressed as a mean Pt granule/cytoplasm ratio, this ratio creates a value for the selectivity of the reaction.The application of a postfixation reaction with OsO₄-containing media, at pH 7.4, in addition to the H₂PtCl₆ reaction, resulted in a contrasted poly-DAB reaction product at all sites known to contain peroxidatic activity. However, X-ray microanalysis revealed that in addition to platinum, osmium was present.A reaction mechanism for the cytochemical poly-DAB contrast-staining at low pH, based upon the reaction proposed by Wild (1963), is postulated.In honour of Prof. P. van Duijn     

Characterization at atomic resolution of peptide helical structures.

A survey of literature for the various types of helices experimentally observed in high-resolution single crystal x-ray diffraction analyses of peptides has allowed to determine accurate conformational and helical parameters for the various secondary structures such as the alpha-helix, the 3(10)-helix, the fully extended conformation (2(5)-helix) and the beta-bend ribbon spiral. For each of these structures the characteristic phi, psi conformational parameters, n, the number of residues per turn, h, the height per residues and p, the pitch of the helix are described.     

Crystal structures of Yersinia enterocolitica salicylate synthase and its complex with the reaction products salicylate and pyruvate

The salicylate synthase, Irp9, from Yersinia enterocolitica is involved in the biosynthesis of the siderophore yersiniabactin. It is a bifunctional enzyme that forms salicylate and pyruvate from chorismate and water via the intermediate isochorismate. Here we report the first crystal structure of Irp9 and also of its complex with the reaction products salicylate and pyruvate at 1.85 A and 2.1 A resolution, respectively. Like other members of the chorismate-utilizing enzyme family, e.g. the TrpE subunit of anthranilate synthase and the PabB subunit of 4-amino-4-deoxychorismate synthase, Irp9 has a complex alpha/beta fold. The crystal structure of Irp9 contains one molecule each of phosphate and acetate derived from the crystallization buffer. The Irp9-products complex structure was obtained by soaking chorismate into Irp9, demonstrating that the enzyme is still catalytically active in the crystal. Both structures contain Mg(2+) in the active site. There is no evidence of the allosteric tryptophan binding site found in TrpE and PabB. Mutagenesis of Glu240, His321 and Tyr372 provided some insight into the mechanism of the two transformations catalyzed by Irp9. Knowledge of the structure of Irp9 will guide the search for potent inhibitors of salicylate formation, and hence of bacterial iron uptake, which is directly related to the virulence of Yersinia.     

Proteome analysis at the level of subcellular structures.

The targeting of proteins to particular subcellular sites is an important principle of the functional organization of cells at the molecular level. In turn, knowledge about the subcellular localization of a protein is a characteristic that may provide a hint as to the function of the protein. The combination of classic biochemical fractionation techniques for the enrichment of particular subcellular structures with the large-scale identification of proteins by mass spectrometry and bioinformatics provides a powerful strategy that interfaces cell biology and proteomics, and thus is termed 'subcellular proteomics'. In addition to its exceptional power for the identification of previously unknown gene products, the analysis of proteins at the subcellular level is the basis for monitoring important aspects of dynamic changes in the proteome such as protein transloction. This review summarizes data from recent subcellular proteomics studies with an emphasis on the type of data that can retrieved from such studies depending on the design of the analytical strategy.     

Crystal structures of myoglobin-ligand complexes at near-atomic resolution.

We have used x-ray crystallography to determine the structures of sperm whale myoglobin (Mb) in four different ligation states (unligated, ferric aquomet, oxygenated, and carbonmonoxygenated) to a resolution of better than 1.2 A. Data collection and analysis were performed in as much the same way as possible to reduce model bias in differences between structures. The structural differences among the ligation states are much smaller than previously estimated, with differences of <0.25 A root-mean-square deviation among all atoms. One structural parameter previously thought to vary among the ligation states, the proximal histidine (His-93) azimuthal angle, is nearly identical in all the ferrous complexes, although the tilt of the proximal histidine is different in the unligated form. There are significant differences, however, in the heme geometry, in the position of the heme in the pocket, and in the distal histidine (His-64) conformations. In the CO complex the majority conformation of ligand is at an angle of 18 +/- 3 degrees with respect to the heme plane, with a geometry similar to that seen in encumbered model compounds; this angle is significantly smaller than reported previously by crystallographic studies on monoclinic Mb crystals, but still significantly larger than observed by photoselection. The distal histidine in unligated Mb and in the dioxygenated complex is best described as having two conformations. Two similar conformations are observed in MbCO, in addition to another conformation that has been seen previously in low-pH structures where His-64 is doubly protonated. We suggest that these conformations of the distal histidine correspond to the different conformational substates of MbCO and MbO(2) seen in vibrational spectra. Full-matrix refinement provides uncertainty estimates of important structural parameters. Anisotropic refinement yields information about correlated disorder of atoms; we find that the proximal (F) helix and heme move approximately as rigid bodies, but that the distal (E) helix does not.     

New group of xylene linker-containing acetylcholinesterase reactivators as antidotes against the nerve agent cyclosarin

Nerve agents such as sarin, cyclosarin and tabun are organophosphorus substances able to inhibit the enzyme acetylcholinesterase (AChE; EC 3.1.1.7). AChE reactivators and anticholinergics are generally used as antidotes in the case of intoxication with these agents. None of the known AChE reactivators is able to reactivate AChE inhibited by all nerve agents used. In this work, reactivation potency of nine newly developed AChE reactivators with an incorporated xylene ring in their structure was measured in vitro. Cyclosarin was chosen as an appropriate member of the nerve agent family. Reactivation potency of the tested AChE reactivators was compared with the gold standard of AChE reactivators--pralidoxime. Two oximes (K107 and K108) surpassed the reactivation potency of pralidoxime. Moreover, from the obtained results it could be deduced that AChE reactivators with a functional oxime group in position-2 are the most potent AChE reactivators in the case of cyclosarin intoxications.     

New group of xylene linker-containing acetylcholinesterase reactivators as antidotes against the nerve agent cyclosarin

Nerve agents such as sarin, cyclosarin and tabun are organophosphorus substances able to inhibit the enzyme acetylcholinesterase (AChE; EC 3.1.1.7). AChE reactivators and anticholinergics are generally used as antidotes in the case of intoxication with these agents. None of the known AChE reactivators is able to reactivate AChE inhibited by all nerve agents used. In this work, reactivation potency of nine newly developed AChE reactivators with an incorporated xylene ring in their structure was measured in vitro. Cyclosarin was chosen as an appropriate member of the nerve agent family. Reactivation potency of the tested AChE reactivators was compared with the gold standard of AChE reactivators – pralidoxime. Two oximes (K107 and K108) surpassed the reactivation potency of pralidoxime. Moreover, from the obtained results it could be deduced that AChE reactivators with a functional oxime group in position-2 are the most potent AChE reactivators in the case of cyclosarin intoxications.     

Evidence for P-N bond scission in phosphoroamidate nerve agent adducts of human acetylcholinesterase

Acetylcholinesterases (AChEs) form conjugates with certain highly toxic organophosphorus (OP) agents that become gradually resistant to reactivation. This phenomenon termed "aging" is a major factor limiting the effectiveness of therapy in certain cases of OP poisoning. While AChE adducts with phosphonates and phosphates are known to age through scission of the alkoxy C-O bond, the aging path for adducts with phosphoroamidates (P-N agents) like the nerve agent N,N-dimethylphosphonocyanoamidate (tabun) is not clear. Here we report that conjugates of tabun and of its butyl analogue (butyl-tabun) with the E202Q and F338A human AChEs (HuAChEs) age at similar rates to that of the wild-type enzyme. This is in marked contrast to the large effect of these substitutions on the aging of corresponding adducts with phosphates and phosphonates, suggesting that a different aging mechanism may be involved. Both tabun and butyl-tabun appear to be similarly accommodated in the active center, as suggested by molecular modeling and by kinetic studies of phosphylation and aging with a series of HuAChE mutants (E202Q, F338A, F295A, F297A, and F295L/F297V). Mass spectrometric analysis shows that HuAChE adduct formation with tabun and butyl-tabun occurs through loss of cyanide and that during the aging process both of these adducts show a mass decrease of 28 +/- 4 Da. Due to the nature of the alkoxy substituent, such mass decrease can be unequivocally assigned to loss of the dimethylamino group, at least for the butyl-tabun conjugate. This is the first demonstration that AChE adducts with toxic P-N agents can undergo aging through scission of the P-N bond.     

Kinemage of action - proposed reaction mechanism of glutamate-1-semialdehyde aminomutase at an atomic level

Glutamate-1-semialdehyde aminomutase (GSAM), a key enzyme in tetrapyrrole cofactor biosynthesis, performs a unique transamination on a single substrate. The substrate, glutamate-1-semialdehyde (GSA), undergoes a reaction that exchanges the position of an amine and a carbonyl group to produce 5-aminolevulinic acid (ALA). This transamination reaction is unique in the fact that is does not require an external cofactor to act as a nitrogen donor or acceptor in this transamination reaction. One of the other remarkable features of the catalytic mechanism is the release free in the enzyme active site of the intermediate 4,5-diaminovaleric acid (DAVA). The action of a gating loop prevents the escape of DAVA from the active site. In a MD simulation approach, using snapshots provided by X-ray crystallography and protein crystal absorption spectrometry data, the individual catalytic steps in this unique intramolecular transamination have been elucidated.     

Coexistence of nitrergic and acetylcholinesterase (ACHE)-positive nerve structures of the phaesant spleen

The coexistence of neuronal NADPH-diaphorase and ACHE activities were investigated in the phaesant spleen by successive double histochemical staining of the same sections. Two types of nerve structures were found in pheasant the spleen: nerve cells and nerve fibres. NADPH-d and ACHE-positive nerve fibres in colocalization enter the spleen in its hilum in the vicinity of splenic artery branches and are gradually distributed in periarterial topography in the white pulp. Only NADPH-d positive nerve cells were seen around the splenic vessels. In the red pulp and splenic capsule, only ACHE-positive nerve fibres were present.     

Attachment of acetylcholinesterase to structures of the motor endplate.

The kinetics of AChE solubilization from intact motor endplates of mouse diaphragm, by collagenase, papain and hyaluronidase, was studied in parallel with the ultrastructural localization of AChE in treated neuromuscular junctions. Hyaluronidase did not solubilize more AChE from isolated motor endplate regions than Ringer's solution itself. Residual AChE activity could be demonstrated histochemically in motor endplates even after the plateau of solubilization by collagenase or papain was reached. Less than 35% of junctional AChE is left after collagenase, and less than 20% after papain treatment, as estimated by the percentage of AChE activity left in the isolated endplate region of the diaphragm after protease treatment. Cytochemically, both proteases had a similar effect on postsynaptic AChE. Residual AChE activity was distributed randomly, adhering to the sarcolemma of junctional clefts. Presynaptic AChE localized in the gap between axon terminal and Schwann cell appears to be resistant to collagenase but not to papain treatment. The mode of AChE attachment or the composition of the intercellular material in this gap may differ from that of the primary and secondary clefts.     

Crystal structures of cephaibols.

The crystal structures of the peptaibol antibiotics cephaibol A, cephaibol B and cephaibol C have been determined at ca. 0.9 A resolution. All three adopt a helical conformation with a sharp bend (of about 55 degrees) at the central hydroxyproline. All isovalines were found to possess the D configuration, superposition of all four models (there are two independent molecules in the cephaibol B structure) shows that the N-terminal helix is rigid and the C-terminus is flexible. There are differences in the hydrogen bonding patterns for the three structures that crystallize in different space groups despite relatively similar unit cell dimensions, but only in the case of cephaibol C does the packing emulate the formation of a membrane channel believed to be important for their biological function.     

Crystal polymorphism of pharmaceuticals: probing crystal nucleation at the molecular level

Paracetamol, sulfathiazole and l-glutamic acid are presented as examples of pharmaceutical crystal polymorphic systems. The effect of N-acylated sulfathiazole derivatives (3–6) on sulfathiazole crystallisation is discussed, and possible modes of action presented. Methods for the control of the crystal polymorphism of l-glutamic acid which utilise the principles of conformation mimicry and co-operative binding are presented. The preparation of a series of bis-amides of EDTA derived from sulfathiazole, 5-aminoisophthalic acid and 4-hydroxyaniline (i.e. compounds 9a–c) is presented, as is data on the effect of these compounds on the crystallisation of, respectively, sulfathiazole, l-glutamic acid and paracetamol.     

Crystal polymorphism of pharmaceuticals: probing crystal nucleation at the molecular level

Paracetamol, sulfathiazole and L-glutamic acid are presented as examples of pharmaceutical crystal polymorphic systems. The effect of N-acylated sulfathiazole derivatives (3-6) on sulfathiazole crystallisation is discussed, and possible modes of action presented. Methods for the control of the crystal polymorphism of L-glutamic acid which utilise the principles of conformation mimicry and co-operative binding are presented. The preparation of a series of bis-amides of EDTA derived from sulfathiazole, 5-aminoisophthalic acid and 4-hydroxyaniline (i.e. compounds 9a-c) is presented, as is data on the effect of these compounds on the crystallisation of, respectively, sulfathiazole, L-glutamic acid and paracetamol.     

Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.

Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from alpha-D-5-phosphoribosyl-1-pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure-based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 A resolution), the UPRTase bound to its substrate, uracil (2.2 A resolution), its product, UMP (2.5 A resolution), and the prodrug, 5-fluorouracil (2.3 A resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone-water-exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil-binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T. gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel beta-arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate-binding water molecule.     

Self-recognition at the atomic level: understanding the astonishing molecular diversity of homophilic Dscams

The Drosophila Dscams are immunoglobulin superfamily members produced from a single gene that is diversified by alternative splicing to produce a family of cell-surface proteins with over 19,000 different ectodomain isoforms. Dscams are critical for neuronal wiring, and mounting evidence suggests that they play a key role in self-avoidance between sister branches from neurons, which depends on homophilic self-recognition by Dscams. Two recent papers shed new light on Dscam recognition: first by showing that the vast majority of Dscam isoforms mediate specific homophilic binding and second by revealing the essence of the molecular basis of homophilic recognition by Dscams through high-resolution structural studies.     

Crystal structures of E. coli laccase CueO at different copper concentrations

CueO protein is a hypothetical bacterial laccase and a good laccase candidate for large scale industrial application. Four CueO crystal structures were determined at different copper concentrations. Low copper occupancy in apo-CueO and slow copper reconstitution process in CueO with exogenous copper were demonstrated. These observations well explain the copper dependence of CueO oxidase activity. Structural comparison between CueO and other three fungal laccase proteins indicates that Glu106 in CueO constitutes the primary counter-work for reconstitution of the trinuclear copper site. Mutation of Glu106 to a Phe enhanced CueO oxidation activity and supported this hypothesis. In addition, an extra alpha-helix from Leu351 to Gly378 covers substrate biding pocket of CueO and might compromises the electron transfer from substrate to type I copper.