Binding of substrate at the effector site of pyrophosphatase increases the rate of its hydrolysis at the active site

It is shown that in addition to the active site, each subunit of Escherichia coli inorganic pyrophosphatase (E-PPase) contains an extra binding site for the substrate magnesium pyrophosphate or its non-hydrolyzable analog magnesium methylenediphosphonate. The occupancy of the extra site stimulates the substrate conversion. Binding affinity of this site decreased or disappeared upon the conversion of E-PPase into a trimeric form or introduction of point mutations. However, when the slowly hydrolyzed substrate, lanthanum pyrophosphate (LaPP(i)), is used, the extra site was revealed in all enzyme forms of E-PPase and of Y-PPase (Saccharomyces cerevisiae PPase), resulting in about 100-fold activation of hydrolysis. A hypothesis on the localization of the extra site and the mechanism of its effect in E-PPase is presented.

Phosphate transfer from inositol pyrophosphates InsP5PP and InsP4(PP)2: A semi-empirical investigation

A novel phosphate transfer process involving the non-enzymatic transfer of a phosphate group from inositol pyrophosphates to serine residues in proteins has been recently reported. Semi-empirical calculations at the PM3/SM5.2 level were undertaken to explore the effect of inositol pyrophosphate structure and overall charge on the thermodynamics of this phosphate transfer.

Competitive inhibition of aristolochene synthase by phenyl-substituted farnesyl diphosphates: evidence of active site plasticity

Analogues of farnesyl diphosphate (FPP, ) containing phenyl substituents in place of methyl groups have been prepared in syntheses that feature use of a Suzuki-Miyaura reaction as a key step. These analogues were found not to act as substrates of the sesquiterpene cyclase aristolochene synthase from Penicillium roqueforti (AS). However, they were potent competitive inhibitors of AS with K(I)-values ranging from 0.8 to 1.2 microM. These results indicate that the diphosphate group contributes the largest part to the binding of the substrate to AS and that the active sites of terpene synthases are sufficiently flexible to accommodate even substrate analogues with large substituents suggesting a potential way for the generation of non-natural terpenoids. Molecular mechanics simulations of the enzyme bound inhibitors suggested that small changes in orientations of active site residues and subtle alterations of the conformation of the backbones of the inhibitors are sufficient to accommodate the phenyl-farnesyl-diphosphates.

Synthesis and biological evaluation of nucleoside dicarboxylates as potential mimics of nucleoside diphosphates

A series of nucleotide analogues wherein the diphosphate moiety has been replaced by a dicarboxylate were synthesized and tested for inhibitory activity against nucleoside diphosphate (NDP) kinase as well as several pathogenic bacterial strains.

A conjugated polyelectrolyte-based fluorescence sensor for pyrophosphate

A new fluorescence turn-on sensor consisting of PPE-CO(2)(-)/Cu(2+) shows high selectivity for pyrophosphate over other anions and is used to develop a real-time assay for alkaline phosphatase.

Simple but Effective Way to Sense Pyrophosphate and Inorganic Phosphate by Fluorescence Changes

A new fluorescent chemosensor based on the acridine-Zn(II) derivative effectively recognizes pyrophosphate and inorganic phosphate at pH 7.4. Acridine derivative 1 displayed a fluorescent quenching effect with pyrophosphate; on the other hand, a large fluorescent enhancement was observed with inorganic phosphate. [structure: see text].

FTIR features of lithium-iron phosphates as electrode materials for rechargeable lithium batteries

The essential structural features of lithium-metal phosphates (LMP) have been studied using FTIR spectroscopy which is a sensitive tool to probe the local environment in the solid materials. Various LMP materials where M is iron have been investigated including phospho-olivine LiFePO(4), diphosphate LiFeP(2)O(7), Nasicon-type phosphate Li(3)Fe(2)(PO(4))(3) and dihydrate FePO(4).2H(2)O. Vitreous and amorphous materials are also considered. Analysis of internal and external modes of vibration allows to distinguish between the different phases and the type of cationic environment in the framework. Results corroborate the contribution of the main factors which are responsible for the complexity of the spectra, i.e. departure from ideal symmetry, interactions between polyhedra, bridging atoms and lattice distortion.

Juvenile hormone biosynthesis in M. sexta: substrate specificity of insect prenyltransferase utilizing homologous diphosphate analogs

Analogs of dimethylallyl diphosphate (DMAPP) and geranyl diphosphate (GPP) were prepared and tested as potential substrates of prenyltransferase of the tobacco hornworm, Manduca sexta, and of a sesquiterpene synthase derived from pig liver. Enzyme derived from corpora allata homogenates of both the larval and adult stage of M. sexta coupled each of the DMAPP analogs to produce homologous geranyl and farnesyl diphosphate products in the order (Z)-3-ethyl>(Z)-3-n-propyl>(Z)-3-methyl (DMAPP)>(Z)-3-i-propyl(Z)-3-n-butyl. In competition studies, the ethyl and n-propyl analogs either enhanced or had no effect on DMAPP coupling, whereas the larger analogs were inhibitors. (Z)-7-ethyl and (2Z,6Z)-3,7-diethyl analogs of GPP were as good, if not better substrates of larval prenyltransferase, while the C-3 ethyl analog of GPP, which is precursor to an isomeric form of juvenile hormone (JH) that is not typically found in insects, was poorly coupled by the enzyme. While similarities were seen for whole-cell extracts derived from adult and larval M. sexta, adult prenyltransferase derived from cytosolic and 16,000xg pellet fractions displayed distinct competitive coupling of GPP and its homologs, suggesting differences in substrate specificity as a result of enzyme localization. In contrast to M. sexta, the pig liver enzyme poorly coupled each of the homologous DMAPP derivatives, and the homologous derivatives of GPP were less efficiently coupled than GPP. These results indicate that prenyltransferase in M. sexta possesses high steric latitude at the (Z)-C-3 and C-7 alkyl positions of DMAPP and GPP, respectively, in contrast to other animal prenyltransferases but in keeping with the enzyme's presumptive role in homologous JH metabolism.

Phosphorus sorption by sediments in a southeastern coastal plain in-stream wetland

A close relationship has been reported between sediment organic C (SedOC) content and its P sorption capacity (P(max)) and total P (TP) concentration. Phosphorus sorbed to organically complexed cations is a proposed explanation for this relationship. The objectives of this study were (i) to determine relationships between in-stream wetland SedOC content and both the sediment's P(max) and TP concentrations, and (ii) to ascertain the role of both organically complexed and oxalate-extractable cations on the sediment P(max) and TP values. The sediment's oxalate-extractable Fe (Fe(ox)) and Al (Al(ox)) contents were determined using acidified ammonium oxalate, while sodium pyrophosphate was used to extract organically complexed cations (Al(pryo), Ca(pyro), Fe(pyro), Mg(pyro), and Mn(pyro)). Both the sediment's P(max) and TP contents were strongly correlated with its SedOC concentration (r(2) > 0.90, P < 0.001). Only the Al(ox) contents were significantly correlated with TP and P(max), suggesting that amorphous Al forms have an important role in P sorption. All five pyrophosphate-extracted cations were significantly correlated with SedOC contents. Regression analyses showed that the Al(pyro) accounted for 88% of the variation in sediment P(max) values, whereas a combination of Al(pyro) and Ca(pyro) accounted for 98% of the variation in sediment TP concentrations. Additionally, Al and Ca chelated by SedOC compounds also have an important role in P binding and indicate that a linkage exists between the wetlands SedOC and P(max) content and its ability to accumulate TP. This study identified that two different mechanisms have significant roles in regulating P sorption by sediments in a southeastern Coastal Plain in-stream wetland.

DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples

Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato.

Transient state kinetics of transcription elongation by T7 RNA polymerase

The single subunit DNA-dependent RNA polymerase (RNAP) from bacteriophage T7 catalyzes both promoter-dependent transcription initiation and promoter-independent elongation. Using a promoter-free substrate, we have dissected the kinetic pathway of single nucleotide incorporation during elongation. We show that T7 RNAP undergoes a slow conformational change (0.01-0.03 s(-1)) to form an elongation competent complex with the promoter-free substrate (dissociation constant (Kd) of 96 nM). The complex binds to a correct NTP (Kd of 80 microM) and incorporates the nucleoside monophosphate (NMP) into RNA primer very efficiently (220 s(-1) at 25 degrees C). An overall free energy change (-5.5 kcal/mol) and internal free energy change (-3.7 kcal/mol) of single NMP incorporation was calculated from the measured equilibrium constants. In the presence of inorganic pyrophosphate (PPi), the elongation complex catalyzes the reverse pyrophosphorolysis reaction at a maximum rate of 0.8 s(-1) with PPi Kd of 1.2 mM. Several experiments were designed to investigate the rate-limiting step in the pathway of single nucleotide addition. Acid-quench and pulse-chase kinetics indicated that an isomerization step before chemistry is rate-limiting. The very similar rate constants of sequential incorporation of two nucleotides indicated that the steps after chemistry are fast. Based on available data, we propose that the preinsertion to insertion isomerization of NTP observed in the crystallographic studies of T7 RNAP is a likely candidate for the rate-limiting step. The studies here provide a kinetic framework to investigate structure-function and fidelity of RNA synthesis and to further explore the role of the conformational change in nucleotide selection during RNA synthesis.

Novel design of osmotic chitosan capsules characterized by asymmetric membrane structure for in situ formation of delivery orifice

In this study, chitosan capsules with asymmetric membrane to induce osmotic effects and in situ formation of the delivery orifice were optimally prepared and characterized. Chitosan capsules were formed on stainless steel mold pins by dipping the pins into a chitosan solution followed by forming asymmetric structure by dipping into a quenching solution containing tripolyphosphate (TPP) to cause an ionic cross-linking reaction between the outer layer of chitosan and TPP. Factors influencing the properties of the capsule membrane, such as the molecular weight of chitosan, the dipping solution and dipping time, and the quenching solution and time, were optimized to successfully produce osmotic chitosan capsules with asymmetric membrane using chitosans that possessed different viscosities. In situ formation of a delivery orifice on the asymmetric membrane of the chitosan capsule was proven by the observation of a jet stream of chlorophyll being released from the capsule. Drugs with different solubility were selected, and a linear correlation between drug solubility and the initial drug release rate calculated from the slope of the drug release profile was used to verify that the delivery orifices that were in situ formed on the asymmetric membrane of the chitosan capsules induced by osmotic effect was responsible for the drug release. Water permeability across the optimally produced asymmetric membrane of the capsule from chitosan of 500 cps (300-700 cps) quenched with TPP for 30 min (C500/TPP30) was determined to be 1.40 x 10(-6)cm(2)h(-1)atm(-1) at 37.0+/-0.5 degrees C. The encapsulation of poorly water-soluble drugs, felodipine (FE) and nifedipine (NF), in such an asymmetric chitosan capsule was capable of creating a sufficient osmotic effect to activate the release of the drug with the addition of SLS and HPMC. The multiple regression equations of maximal release percent at 24h for FE and NF confirmed that both sodium lauryl sulfate (SLS) and hydroxypropyl methylcellulose (HPMC) positively influenced this response factor, and the effect of SLS was greater than that of HPMC.

Study of molecular dynamics and the solid state phase transition mechanism for unsymmetrical thiopyrophosphate using X-ray diffraction, DFT calculations and NMR spectroscopy

Differential scanning calorimetry (DSC) and low-temperature X-ray diffraction studies showed that 2-thio-(5,5-dimethyl-1,3,2-dioxaphosphorinanyl)2'-oxo-dineopentyl-thiophosphate (compound 1) undergoes reversible phase transition at 203 K related to the change of symmetry of the crystallographic unit. Solid state NMR spectroscopy was used to establish the dynamic processes of aliphatic groups and the phosphorus skeleton. 13C and 31P variable temperature NMR studies as well as T1 and T1rho measurements of relaxation times revealed the different mode of molecular motion for each neopentyl residue directly bonded to phosphorus. It is concluded that molecular dynamics of aliphatic groups causes different van der Waals interactions in the crystal lattice and is the driving force of phase transition for compound 1. Finally, we showed that very sharp phase transition temperature makes compound 1 an excellent candidate as a low-temperature NMR thermometer in the solid phase.

A modified back-etch method for preparation of plan-view high-resolution transmission electron microscopy samples

A modified back-etch method is described that has been successfully used to prepare samples of thin films and nanoparticles on Si wafer substrates for examination by high-resolution transmission electron microscopy (HRTEM). This process includes ultrasonic cutting, abrasive pre-thinning and a two-stage etching procedure. Unlike previous reports of back-etching methods, tetramethyl ammonium hydroxide, which has a very high-etching selectivity of Si to SiO(2), is used for the final etching to allow removal of the Si without degradation of the SiO(2) membrane. An innovative wrapping method is also described. This novel approach reduces the preparation time for HRTEM samples to <1 h per sample for groups of 10 or more samples. As an example, the preparation of FePt nanoparticle samples for HRTEM imaging is described.

Comparison of efficacy of three extractants to solubilize glomalin on hyphae and in soil

Glomalin, a glycoprotein produced by arbuscular mycorrhizal (AM) fungi, is a major component of the humus fraction of soil organic matter. Glomalin is extracted from soil and hyphae of AM fungi by using sodium citrate at 121 degrees C in multiple 1-h cycles, but extensive extraction does not solubilize all glomalin in all soils. Efficacies of 100 mM sodium salts of citrate, borate or pyrophosphate (pH 9.0, 121 degrees C) were tested for two 1-h cycles for hyphae from four AM fungal isolates and four 1-h cycles for seven soils from four US geographic regions. Residual soil glomalin was examined by pyrophosphate extraction of soils previously extracted with citrate or borate followed by extraction of all soils after treatment with NaOH. Hyphal extracts were compared using Bradford-reactive total protein (BRTP) values, and extracts from soils were compared using BRTP, percentage C and C weight. No difference among extractants was detected for AM fungal isolates or across soils. The residual glomalin across soils for extractants contained the following percentages of the total BRTP: pyrophosphate, 14%; borate, 17%; and citrate, 22%. Comparisons among individual soils indicated that pyrophosphate extracted significantly more BRTP (10-53%) than borate or citrate in six soils and borate was equal to pyrophosphate in one soil. Extraction with borate should be compared with pyrophosphate before initiating an experiment. For routine extractions of ca. 85% of the glomalin across a variety of soils, sodium pyrophosphate appears to be equal to or better than borate and better than citrate.

Structure of synthetic calcium hydroxyapatite particles modified with pyrophosphoric acid

Synthetic colloidal calcium hydroxyapatite (Ca(10)(PO(4))(6)(OH)(2): CaHap) was treated with pyrophosphoric acid (H(4)P(2)O(7): PP) in acetone and the materials were characterized by XRD, TEM, FTIR, and N(2) and H(2)O adsorption measurements. XRD patterns and morphology of CaHap particles were essentially not changed by the modification. The additional amount of PO(4) of CaHap was increased with an increase of PP concentration and the Ca/P molar ratio of the particles decreased from 1.62 to 0.81. IR results indicated that the isolated surface POH band developed with increasing the PP concentration up to 6.0 mmol dm(-3) by the reaction of isolated surface POH groups of CaHap and pyrophosphoric acids. Above 10.2 mmol dm(-3), a hydrogen-bonding surface POH band appeared at 2913 cm(-1) and enlarged with increasing the PP concentration, while the isolated surface POH band was weakened. The results of N(2) and H(2)O adsorption measurements revealed that the modified particles aggregated compared to the unmodified ones, which would be due to the formation of hydrogen-bonding surface POH groups among the particles.

An In-Vitro Study of Microleakage Around Class V Cavities Bonded with a Self-Etching Material Versus a Conventional Two-Bottle System

Objective

To evaluate the microleakage around class V restorations restored with either a self-etching adhesive system or a conventional two-bottle adhesive system used with ‘total etch’ technique, and their recommended resin-based composites (RBC).

Methods

Two types of adhesive systems were used. A self-etching adhesive, Etch and Prime 3.0 (Degussa AG, Hanau, Germany), and a conventional two-bottle adhesive, Gluma Solid Bond (Heraeus Kulzer, Dormagen, Germany). The bonding systems were used in strict accordance with the manufacturers’ instructions, except that, with the two-bottle adhesive system, the cavities were filled with either a ‘wet’ or a ‘dry’ bonding technique, subsequent to acid-etching with 20% phosphoric acid. Etch & Prime 3.0 was used in conjunction with Degufill Mineral (Degussa, Hanau, Germany) RBC and Gluma Solid Bond with Flow Line RBC (Heraeus Kulzer, Dormagen, Germany). Standardised bucco-cervical cavities were prepared on the buccal and lingual surfaces of 15 extracted maxillary first premolar teeth; all cavity margins were in enamel. Ten of the resulting cavities (Group A) were restored using Etch & Prime 3.0 and Degufill Mineral, ten (Group B) using Gluma Solid Bond (Wet Bond), and ten (Group C) using Gluma Solid Bond (Dry Bond). Leakage scores at occlusal and gingival margins were calculated after thermocycling 500 times between baths, held at 5°C and 55°C, respectively, with 30 seconds dwell time in both. Data were analysed by the Fisher Exact Test.

Results

There was no statistically significant difference between the self-etching adhesive and conventional two-bottle adhesive systems at either the occlusal or the gingival margins. With the self-etching adhesive, there was no statistically significant difference in leakage scores between occlusal and gingival margins. There was a statistically significant difference between the occlusal and the gingival margins when a ‘wet’ or ‘dry’ bonding technique was used with the conventional two-bottle adhesive system.

Conclusions

The results suggest that the application of a conventional two-bottle bonding system used with a ‘total etch’ technique is better than that of a self-etching adhesive system. With the former, the use of a ‘wet’ bonding does not give better results than a ‘dry’ bonding technique.

Association studies of aggregated aqueous lutein diphosphate with human serum albumin and α1-acid glycoprotein in vitro: Evidence from circular dichroism and electronic absorption spectroscopy

Water-dispersible C40 carotenoid derivatives, with increased utility in mammalian therapeutic applications, include natural stereoisomer-based (3R,3'R,6'R)-lutein (beta,epsilon-carotene-3,3'-diol) derivatives. Esterification with inorganic phosphate and conversion to the sodium salt produced compounds (lutein diphosphate sodium salt; 'LdP') capable of forming red-orange aqueous suspensions after addition to USP-purified water. The aqueous dispersibility of this diphosphate salt reached 29 mg/mL without the addition of heat, detergents, co-solvents, or other additives, and was a potent direct scavenger of superoxide anion (by EPR spectroscopy) in an isolated human neutrophil assay. In the current study, preliminary evidence of the aqueous aggregation of this compound in EPR studies was confirmed using circular dichroism (CD) and electronic absorption (UV-vis) spectroscopy. Evidence for H-type ('card-pack') and J-type ('head-to-tail') self-assemblies was obtained. In vitro analysis of the potential binding interaction between LdP and human serum albumin (HSA) and alpha1-acid glycoprotein (AGP) revealed only non-specific binding with HSA (and none with AGP), contrasting with previous reports of direct interaction between astaxanthin-based soft drugs and the major plasma protein albumin. The rapid in vivo cleavage of this phosphodiester by promiscuous mammalian phosphatases may overcome the aqueous aggregation of the formulated compound. This difference in potential plasma protein interaction with prior reports reflects the subtle structural differences inherent in either the parent carotenoid scaffolds and/or the esterifying moieties.

Analysis of polymerase chain reaction amplifications through phosphate detection using an enzyme–based microbiosensor in a microfluidic device

An electrochemical method was developed for analyzing PCR amplification through the detection of inorganic phosphates (Pi). This method coupled a microchip to a nanoparticle comprising poly-5,2'-5',2''-terthiophene-3'-carboxylic acid (poly-TTCA)/pyruvate oxidase (PyO) modified microbiosensor. It detects Pi produced from the pyrophosphate (PPi), which is released as a byproduct of PCR. After completion of PCR, PPi is hydrolyzed to Pi by inorganic pyrophosphatase. On the microbiosensor surface, pyruvate was converted to H2O2 by PyO in the presence of Pi and oxygen, and subsequently, the anodic current of enzymatically generated H2O2 was detected at +0.5 V versus Ag/AgCl. The CE-EC analysis was completed within 2 min in a coated channel with 75.0 mm separation length at the field strength of -200 V/cm. Excellent operation stability of poly-TTCA/PyO was observed for a long period of analysis. The reproducibility of the analysis yielded an RSD of 3.4% (n = 22) for the peak areas and 1.8% (n = 22) for the migration times. The sensitivity of the analysis was 0.59 +/- 0.01 nA/cycle with a regression coefficient of 0.971.

Rational design of polymerase inhibitors as antiviral drugs

Almost all viruses have polymerases which are suitable targets for antiviral drugs. The development of selective polymerase inhibitors started with screening of compounds in virus-infected cell cultures and the mechanism of action was investigated once an inhibitor had been found. Especially nucleoside analogs were screened as their triphosphates were potential substrates for polymerases. However, the stepwise phosphorylation by cellular, and sometimes viral, kinases to the active triphosphate prevented a truly rational design of polymerase inhibitors. Nucleotide analogs offers a type of compounds which could be designed in a more rational way than nucleoside analogs since the first, most selective, phosphorylation step is eliminated in the path to the active inhibitor. The development of pyrophosphate analogs made rational design possible since these compounds act directly on the viral enzyme, but the room for structural variation was limited. The non-nucleoside HIV reverse transcriptase inhibitors are direct inhibitors and can thus be designed in a truly rational way by use of structure information on the enzyme-inhibitor complex by use of X-ray and NMR. This rational design of allosteric inhibitors is also being used in the development of inhibitors to other viral polymerases.

Preparation of UDP-galacturonic acid using UDP-sugar pyrophosphorylase

UDP-galacturonic acid, the activated form of galacturonic acid (GalUA), is synthesized both de novo and by salvage pathways. The UDP-GalUA pyrophosphorylase gene involved in the salvage pathway has not been identified. Here we show that UDP-sugar pyrophosphorylase from Pisum sativum with a broad specificity has UDP-GalUA pyrophosphorylase activity. The enzyme catalyzed the formation of UDP-GalUA and pyrophosphate from GalUA 1-phosphate and UTP with an equilibrium constant value of 0.24. The recombinant UDP-sugar pyrophosphorylase had optimal pH of 6.0, and the apparent K(m) values for GalUA 1-phosphate, UTP, UDP-GalUA, and pyrophosphate were 2.27, 1.15, 0.70, and 1.26 mM, respectively. In the presence of inorganic pyrophosphatase, the recombinant enzyme produced UDP-GalUA in an 84% yield (based on the GalUA 1-phosphate substrate) on a preparative scale. Thus, this UDP-sugar pyrophosphorylase is useful for the highly efficient production of UDP-GalUA for studies on pectin biosynthesis.

Substrate-assisted movement of the catalytic Lys 215 during domain closure: site-directed mutagenesis studies of human 3-phosphoglycerate kinase

3-Phosphoglycerate kinase (PGK) is a two-domain hinge-bending enzyme. It is still unclear how the geometry of the active site is formed during domain closure and how the catalytic residues are brought into the optimal position for the reaction. Comparison of the three-dimensional structures in various open and closed conformations suggests a large (10 A) movement of Lys 215 during domain closure. This change would be required for direct participation of this side chain in both the catalyzed phospho transfer and the special anion-caused activation. To test the multiple roles of Lys 215, two mutants (K215A and K215R) were constructed from human PGK and characterized in enzyme kinetic and substrate binding studies. For comparison, mutants (R38A and R38K) of the known essential residue, Arg 38, were also produced. Drastic decreases (1500- and 500-fold, respectively), as in the case of R38A, were observed in the kcat values of mutants K215A and K215R, approving the essential catalytic role of Lys 215. In contrast, the R38K mutation caused an only 1.5-fold decrease in activity. This emphasizes the importance of a very precise positioning of Lys 215 in the active site, in addition to its positive charge. The side chain of Lys 215 is also responsible for the substrate and anion-dependent activation, since these properties are abolished upon mutation. Among the kinetic constants mainly the Km values of MgATP and 1,3-BPG are increased (approximately 20- and approximately 8-fold, respectively) in the case of the neutral K215A mutant, evidence of the interaction of Lys 215 with the transferring phospho group in the functioning complex. Weakening of MgATP binding (a moderate increase in Kd), but not of MgADP binding, upon mutation indicates an initial weak interaction of Lys 215 with the gamma-phosphate already in the nonfunctioning open conformation. Thus, during domain closure, Lys 215 possibly moves together with the transferring phosphate; meanwhile, this group is being positioned properly for catalysis.

Monoglycosyl, diglycosyl, and dinucleoside methylenediphosphonates: direct synthesis and antiviral activity

A direct and general access to D-glycosyl 3-, 5-, or 6-methylenediphosphonates, di-D-glycosyl 1,5-, 3,5-, 3,6-, 5,5-, or 6,6-methylenediphosphonates and dithymidine 3',5'-methylenediphosphonate is described. The method involves the one-pot alkylidenediphosphorylation of glycosyl or thymidine derivatives. No antiviral activity was detected against a panel of RNA and DNA viruses.

Extraction and identification by mass spectrometry of undecaprenyl diphosphate-MurNAc-pentapeptide-GlcNAc from Escherichia coli

Undecaprenyl diphosphate-MurNAc-pentapeptide-GlcNAc (lipid II) is extracted from Escherichia coli cells by utilizing its unusual pH-dependent solubility property in a Bligh-Dyer system, and identified by electrospray ionization mass spectrometry in conjunction with a novel 15N mass shift analysis. The described approach will facilitate the structural characterization of lipid II variants from diverse bacteria, including antibiotic-resistant mutants, as well as the numerous minor uncharacterized lipids present in all biological systems.

Host–guest interaction between cyclen based macrotricyclic ligands and phosphate anions. A potentiometric investigation

The host-guest interaction between orthophosphate, pyrophosphate and triphosphate anions and three cyclen based macrotricyclic ligands possessing ortho- (TOC), meta- (TMC) and para-xylenyl (TPC) linkers was investigated by potentiometric measurements. The ternary species present in solution and their stability constants have been determined. The different behaviours are explained in terms of hydrogen bond formation and coulombic attraction between the organic host and the inorganic guest. The selectivity, illustrated with species distribution diagrams, is discussed. The results unambiguously showed the importance of the distance between the two cyclen cores and emphasized the increasing of the triphosphate species selectivity together with the cavity size of the ligand. A comparison of the present results with those obtained with their mono-bridged homologues is also discussed.