Platelet endothelial cell adhesion molecule 1 (PECAM-1) and its interactions with glycosaminoglycans: 2. Biochemical analyses

Platelet endothelial cell adhesion molecule 1 (PECAM-1) (CD31), a member of the immunoglobulin (Ig) superfamily of cell adhesion molecules with six Ig-like domains, has a range of functions, notably its contributions to leukocyte extravasation during inflammation and in maintaining vascular endothelial integrity. Although PECAM-1 is known to mediate cell adhesion by homophilic binding via domain 1, a number of PECAM-1 heterophilic ligands have been proposed. Here, the possibility that heparin and heparan sulfate (HS) are ligands for PECAM-1 was reinvestigated. The extracellular domain of PECAM-1 was expressed first as a fusion protein with the Fc region of human IgG1 fused to domain 6 and second with an N-terminal Flag tag on domain 1 (Flag-PECAM-1). Both proteins bound heparin immobilized on a biosensor chip in surface plasmon resonance (SPR) binding experiments. Binding was pH-sensitive but is easily measured at slightly acidic pH. A series of PECAM-1 domain deletions, prepared in both expression systems, were tested for heparin binding. This revealed that the main heparin-binding site required both domains 2 and 3. Flag-PECAM-1 and a Flag protein containing domains 1-3 bound HS on melanoma cell surfaces, but a Flag protein containing domains 1-2 did not. Heparin oligosaccharides inhibited Flag-PECAM-1 from binding immobilized heparin, with certain structures having greater inhibitory activity than others. Molecular modeling similarly identified the junction of domains 2 and 3 as the heparin-binding site and further revealed the importance of the iduronic acid conformation for binding. PECAM-1 does bind heparin/HS but by a site that is distinct from that required for homophilic binding.

Lipid assisted membrane entry in specific phospholipid targeted protein systems

The purpose of this thesis project is to study changes in the physical state of cell membranes during cell entry, including how these changes are connected to the presence of ceramide. The role of enzymatical manipulation of lipids in bacterial internalization is also studied. A novel technique, where a single giant vesicle is chosen under the microscope and an enzyme coupled-particle attached to the micromanipulator pipette towards the vesicle, is used. Thus, the enzymatic reaction on the membrane of the giant vesicle can be followed in real-time. The first aim of this study is to develop a system where the localized sphingomyelinase membrane interaction could be observed on the surface of the giant vesicle and the effects could be monitored with microscopy. Domain formation, which resembles acid sphingomyelinase (ASMase), causes CD95 clustering in the cell membrane due to ceramide production (Grassmé et al., 2001a; Grassmé et al., 2001b) and the formation of small vesicles inside the manipulated giant vesicle is observed. Sphingomyelinase activation has also been found to be an important factor in the bacterial and viral invasion process in nonphagocytic cells (Grassmé et al., 1997; Jan et al., 2000). Accordingly, sphingomyelinase reactions in the cell membrane might also give insight into bacterial or viral cellular entry events. We found sphingomyelinase activity in Chlamydia pneumonia elementarybodies (EBs). Interestingly, the bacterium enters host cells by endocytosis but the internalization mechanism of Chlamydia is unknown. The hypothesis is that sphingomyelin is needed for host cell entry in the infection of C. pneumonia. The second project focuses on this subject. The goal of the third project is to study a role of phosphatidylserine as a target for a membrane binding protein. Phosphatidylserine is chosen because of its importance in fusion processes. This will be another example for the importance of lipids in cell targeting, internalization, and externalization.

Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 ILL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles. (c) 2007 Elsevier B.V. All rights reserved.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase{triangledown}

The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (–)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase{triangledown}

The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (–)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory

Serine hydroxymethyltransferase (SHMT) belongs to the alpha-family of pyridoxal 5'-phosphate-dependent enzymes and catalyzes the reversible conversion of L-Ser and etrahydrofolate to Gly and 5,10-methylene tetrahydrofolate. 5,10-Methylene tetrahydrofolate serves as a source of one-carbon fragment in many biological processes. SHMT also catalyzes the tetrahydrofolate-independent conversion of L-allo-Thr to Gly and acetaldehyde. The crystal structure of Bacillus stearothermophilus SHMT (bsSHMT) suggested that E53 interacts with the substrate, L-Ser and etrahydrofolate. To elucidate the role of E53, it was mutated to Q and structural and biochemical studies were carried out with the mutant enzyme. The internal aldimine structure of E53QbsSHMT was similar to that of the except for significant changes at Q53, Y60 and Y61. The wild-type enzyme, carboxyl of Gly and side chain of L-Ser were in two conformations in the respective external aldimine structures. The mutant enzyme was completely inactive for tetrahydrofolate-depen dent cleavage of L-Ser, whereas there was a 1.5-fold increase in the rate of tetrahydrofolate-independent reaction with L-allo-Thr. The results obtained from these studies suggest that E53 plays an essential role in tetrahydrofolate/5-formyl tetrahydrofolate binding and in the proper positioning of C beta of L-Ser for direct attack by N5 of tetrahydrofolate. Most interestingly, the structure of the complex obtained by cocrystallization of E53QbsSHMT with Gly and 5-formyl tetrahydrofolate revealed the gem-diamine form of pyridoxal 5'-phosphate bound to Gly and active site Lys. However, density for 5-formyl tetrahydrofolate was not observed. Gly carboxylate was in a single conformation, whereas pyridoxal 5'-phosphate had two distinct conformations. The differences between the structures of this complex and Gly external aldimine suggest that the changes induced by initial binding of 5-formyl tetrahydrofolate are retained even though 5-formyl tetrahydrofolate is absent in the final structure. Spectral studies carried out with this mutant enzyme also suggest that 5-formyl tetrahydrofolate binds to the E53QbsSHMT-Gly complex forming a quinonoid intermediate and falls off within 4 h of dialysis, leaving behind the mutant enzyme in the gemdiamine form. This is the first report to provide direct evidence for enzyme memory based on the crystal structure of enzyme complexes.

Thermal ignition studies on metallized fuel-oxidizer systems

The thermal ignition behaviour of various mixtures of organic fuels, magnesium and ammonium nitrate (AN) has been examined by differential thermal analysis technique. It has been observed that the thermal decomposition/ignition of organic fuel-AN mixtures is modified significantly in the presence of magnesium metal. The decomposition characteristics of the binary mixtures of AN with various metals indicate the specific action of magnesium and zinc in lowering the decomposition temperature. A possible explanation for the low temperature decomposition is given in terms of the solid state reaction causing the fusion of AN which further reacts with the metal resulting in a highly exothermic reaction.

Chemical Aspects of the Synergistic Hypergolic Ignition in Hybrid Systems with N2O4 as Oxidizer

Synergistic hypergolic ignition with nitrogen tetroxide ( N2O4) as oxidizer has been observed in hybrid systems comprising of a mixture of magnesium and Schiff bases as fuels. The ignition delays (IDs) measured using a modified device, have been compared with those of magnesium-Schiff base-WFNA systems under identical conditions. The ID has been found to vary with the nature of the substitution in both the benzene rings. A linear relationship emerges when the ignition delays are plotted against the Hammett substitution constants (σ). The preignition products of the reaction of N2O4 with magnesium and benzylidineaniline have been analysed to be Mg(NO3)2, benzenediazonium salt and benzaldehyde. Based on the preignition products isolated, a probable reaction mechanism has been proposed. The previously proposed preignition mechanism for the Schiff base-magnesium-WFNA system has been further supported from the present ignition delay data.

Studies on neurotransmitter-stimulated phospholipid metabolism with cerebral tissue suspensions: A possible biochemical correlate of synaptogenesis in normal and undernourished rats

The phenomenon of neurotransmitter-stimulated incorporation of32Pi into phosphatidic acid and inositol phosphatides (neurotransmitter effect) in developing brain was studied in vitro as a possible measure of synaptogenesis. While the neurotransmitter effect was not observed with brain homogenates, highly consistent and significant effects were noted with brain tissue suspensions obtained by passing the tissue through nylon bolting cloth. The magnitude of the effect decreased with the increase in mesh number. Maximum stimulations obtained with the 33 mesh adult brain cortex preparations (mean±S.E.M. of6experiments) were203 ± 8%, 316 ± 11 % and150 ± 8% with 10−3 M acetylcholine (ACh) + 10−3 M eserine; 10−2 M norepinephrine (NE) and 10−2 M serotonin (5-HT), respectively. Experiments with developing rat brain at 7, 14 and 21 days of age showed that the neurotransmitter effects due to ACh, NE and 5-HT increase progressively in different regions of the brain but that there are marked regional differences. It is suggested that the neurotransmitter effect is a valid biochemical correlate of synaptogenesis. In rats undernourished from birth t0 21 days of age, by increasing the litter size, the neurotransmitter effect with ACh, NE or 5-HT was not altered in the cortex but was significantly reduced in the brain stem. In cerebellum the effects due to ACh and NE were significantly altered, while that with 5-HT was unaffected. It is concluded that cholinergic, adrenergic and serotonergic synapses are relatively unaffected in the cortex but are significantly affected in the brain stem by undernutrition. In the cerebellum of undernourished rats the adrenergic and cholinergic, but not serotonergic systems, are altered.

Metabolome based reaction graphs of M.tuberculosis and M.leprae: A comparative network analysis

Background. Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. Methodology/Principal Findings. Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. Conclusions. We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension.

Covalent attachment of two important dicopper(II) systems in a one-dimensional polymeric chain: An x-ray structure of [Cu2(en)2(OH)2·Cu2(O2CMe)4](PF6)2·0.5EtOH]α showing the shortest Cucdots, three dots, centeredCu Distance in the tetraacetato core

Reaction of Cu2(O2CMe)4(H2O)2 with 1,2-diaminoethane(en) in ethanol, followed by the addition of NH4PF6, led to the formation of a covalently linked 1D polymeric copper(II) title complex showing alternating [Cu2(en)2(OH)22+] and [Cu2(O2CMe)4] units in the chain and the shortest Cucdots, three dots, centeredCu separation of 2.558(2) Å in the tetraacetato core.

Phase relations in the systems Cu–O–R2O3(R = Tm, Lu) and Gibbs energies of formation of Cu2R2O5 compounds

The phase relations in the systems Cu–O–R2O3(R = Tm, Lu) have been determined at 1273 K by X-ray diffraction, optical microscopy and electron probe microanalysis of samples equilibrated in evacuated quartz ampules and in pure oxygen. Only ternary compounds of the type Cu2R2O5 were found to be stable. The standard Gibbs energies of formation of the compounds have been measured using solid-state galvanic cells of the type, Pt|Cu2O + Cu2R2O5+ R2O3‖(Y2O3)ZrO2‖CuO + Cu2O‖Pt in the temperature range 950–1325 K. The standard Gibbs energy changes associated with the formation of Cu2R2O5 compounds from their binary component oxides are: 2CuO(s)+ Tm2O3(s)→Cu2Tm2O5(s), ΔG°=(10400 – 14.0 T/K)± 100 J mol–1, 2CuO(s)+ Lu2O3(s)→Cu2Lu2O5(s), ΔG°=(10210 – 14.4 T/K)± 100 J mol–1 Since the formation is endothermic, the compounds become thermodynamically unstable with respect to component oxides at low temperatures, Cu2Tm2O5 below 743 K and Cu2Lu2O5 below 709 K. When the chemical potential of oxygen over the Cu2R2O5 compounds is lowered, they decompose according to the reaction, 2Cu2R2O5(s)→2R2O3(s)+ 2Cu2O(s)+ O2(g) The equilibrium oxygen potential corresponding to this reaction is obtained from the emf. Oxygen potential diagrams for the Cu–O–R2O3 systems at 1273 K are presented.

A novel double friedel-crafts reaction: A new entry into bicyclo[3.2.2]nonane system

A novel synthesis of dibenzobicyclo[3.2.2]nonane systems is described through a double Friedel-Crafts reaction.

Synthesis of Cuprates of Perovskite Structure in the Ba-Pb-Cu-O, Ba-Bi-Cu-O, and Ba-Pb-Tl-Cu-O Systems: Possible High Tc Superconductivity in a Perovskite-like Phase in the Ba-Pb-Tl-Cu-O System

Cubic cuprates (a not, vert, similar 18.6 Å) with a BaCuO2-type structure were obtained in the Ba-Pb-Cu-O and Ba-Bi-Cu-O systems by the reaction of the component oxides at a high temperature (1370-1420 K), followed by quenching. By annealing these phases in oxygen at 1070-1120 K, perovskite-like phase (a not, vert, similar 4.3 Å) of the formulae BaPb1-xCuxO3-y and BaBi1-xCuxO3-y (0 < x ? 0.5) were obtained. A perovskite of nominal composition BaPb0.25Tl0.25 Cu0.5O3-y, prepared by a similar procedure, was found to be superconducting with a Tc of not, vert, similar 70 K.

Electron transfer reaction in the marcus inverted region: role of high frequency vibrational modes

A theoretical study of the dynamics of photo-electron transfer reactions in the Marcus inverted regime is presented. This study is motivated partly by the recent proposal of Barbara et al. (J. Phys. Chem. 96, 3728, 1991) that a minimal model of an electron transfer reaction should consist of a polar solvent mode (X), a low frequency vibrational mode (Q) and one high frequency mode (q). Interplay between these modes may be responsible for the crossover observed in the dynamics from a solvent controlled to a vibrational controlled electron transfer. The following results have been obtained. (i) In the case of slowly relaxing solvents, the proximity of the point of excitation to an effective sink on the excited surface is critical in determining the decay of the reactant population. This is because the Franck-Condon overlap between the reactant ground and the product excited states decreases rapidly with increase in the quantum number of the product vibrational state. (ii) Non-exponential solvation dynamics has an important effect in determining the rates of electron transfer. Especially, a biphasic solvation and a large coupling between the reactant and the product states both may be needed to explain the experimental results. ©1996 American Institute of Physics