Binding Mechanism of Metal⋅NTP Substrates and Stringent-Response Alarmones to Bacterial DnaG-Type Primases

Primases are DNA-dependent RNA polymerases found in all cellular organisms. In bacteria, primer synthesis is carried out by DnaG, an essential enzyme that serves as a key component of DNA replication initiation, progression, and restart. How DnaG associates with nucleotide substrates and how certain naturally prevalent nucleotide analogs impair DnaG function are unknown. We have examined one of the earliest stages in primer synthesis and its control by solving crystal structures of the S.?aureus DnaG catalytic core bound to metal ion cofactors and either individual nucleoside triphosphates or the nucleotidyl alarmones, pppGpp and ppGpp. These structures, together with both biochemical analyses and comparative studies of enzymes that use the same catalytic fold as DnaG, pinpoint the predominant nucleotide-binding site of DnaG and explain how the induction of the stringent response in bacteria interferes with primer synthesis.     

Determination of sulfite radical (SO 3 ⋅ −) reaction rate constants by means of competition kinetics

Summary The sulfite radical anion (SO ₃ ^–) was found to react rapidly with the flavonoid quercetin (k = 2.5 × 10⁸ dm³mol^–1 s^–1) and the carotenoids crocin (k = 1.0 × 10⁹ dm³mol^–1 s^1–) and crocetin (k = 1.5 × 10⁹ dm³mol^1– s^1–). The reactions can easily be monitored due to the strong absorptions of the substrates and, in the case of quercetin, the formation of a strongly absorbing transient species. Using these substances, we determined by means of competition kinetics rate constants of SO ₃ ^– reactions with nucleic acid components, polyunsaturated fatty acids, and glutathione.Abbreviations ABTS 2,2-azinobis(3-ethyl-6-benzothiazolinesulfonate) - cmc critical micellization concentration - GSH Glutathione - PUFA polyunsaturated fatty acids Preliminary results were presented at the Third Biennial Meeting of the Society for Free Radical Research in Düsseldorf in July, 1986     

Pulse sequences for detection of NH2···N hydrogen bonds in sheared G⋅A mismatches via remote, non-exchangeable protons

The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch.     

EPR spin trapping and 2-deoxyribose degradation studies of the effect of pyridoxal isonicotinoyl hydrazone (PIH) on ⋅OH formation by the Fenton reaction

The search for effective iron chelating agents was primarily driven by the need to treat iron-loading refractory anemias such as β-thalassemia major. However, there is a potential for therapeutic use of iron chelators in non-iron overload conditions. Iron can, under appropriate conditions, catalyze the production of toxic oxygen radicals which have been implicated in numerous pathologies and, hence, iron chelators may be useful as inhibitors of free radical-mediated tissue damage. We have developed the orally effective iron chelator pyridoxal isonicotinoyl hydrazone (PIH) and demonstrated that it inhibits iron-mediated oxyradical formation and their effects (e.g. 2-deoxyribose oxidative degradation, lipid peroxidation and plasmid DNA breaks). In this study we further characterized the mechanism of the antioxidant action of PIH and some of its analogs against ^⋅OH formation from the Fenton reaction. Using electron paramagnetic resonance (EPR) with 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) as a spin trap for ^⋅OH we showed that PIH and salicylaldehyde isonicotinoyl hydrazone (SIH) inhibited Fe(II)-dependent production of ^⋅OH from H₂O₂. Moreover, PIH protected 2-deoxyribose against oxidative degradation induced by Fe(II) and H₂O₂. The protective effect of PIH against both DMPO hydroxylation and 2-deoxyribose degradation was inversely proportional to Fe(II) concentration. However, PIH did not change the primary products of the Fenton reaction as indicated by EPR experiments on ^⋅OH-mediated ethanol radical formation. Furthermore, PIH dramatically enhanced the rate of Fe(II) oxidation to Fe(III) in the presence of oxygen, suggesting that PIH decreases the concentration of Fe(II) available for the Fenton reaction. These results suggest that PIH and SIH deserve further investigation as inhibitors of free-radical mediated tissue damage.     

Lack of correlation between TBARS production and PUFA degradation during incubation of membrane erythrocytes in an OH⋅ (Fe2+/H2O2) generator system

We investigated the effects of an OH^⋅ (Fe²⁺/H₂O₂) generator system of erythrocyte membrane, particularly the time-course of lipid peroxidation as estimated by measurement of conjugated dienes, thiobarbituric reactive substances (TBARS), lipofuscin-like pigments, and α-tocopherol. Polyunsaturated fatty acids (PUFAs), especially arachidonic acid (20∶4 ω 6) and docosahexenoic acid (22∶6 ω 3), were also measured. Erythrocyte membranes were suspended in phosphate buffer containing Fe²⁺ (200 μM) and H₂O₂ (1.42 mM), and incubated in a shaking water bath at 37°C. Initially, there was an increase in TBARS and lipofuscin-like pigments, two well-known end products of PUFA oxidative degradation, whereas PUFAs remained unchanged (incubation time: 1 h). After two or more hours of incubation, marked lipid peroxidation was noted, with the appearance of conjugated dienes and a decrease of PUFAs, indicating that lipid peroxidation had occurred after a lag phase during which TBARS were not produced from PUFAs. This suggests that another OH^⋅ target was involved.     

Automated hydrodynamic modelling of a complex between a human IgE fragment (FcÂ3–4) and the IgE high affinity receptor FcÂRI ⋅-chain

The binding of IgE to its high affinity receptor FcεRI plays an important role in the allergic response. The interaction between soluble FcεRIα-chain (sFcεRIα) and Fcε3–4, a fragment of IgE consisting of the Cε3 and Cε4 heavy chain constant domains, has been studied using analytical ultracentrifugation (Keown et al. this volume). Here we describe the development of a simple automated hydrodynamic modelling technique and its application to this interaction. This procedure utilises sphere models of the two molecules and performs an automated systematic translational search of sFcεRIα relative to Fcε3–4. The result of this is the generation of 40,359 individual models of how the receptor can be placed relative to Fcε3–4. These are then assessed for consistency by comparing the sedimentation coefficients generated for the models to the experimentally determined sedimentation coefficients, and are displayed graphically to show allowed and disallowed complexes. From this analysis, it is clear that the complex between sFcεRIα and Fcε3–4 is compact, with the most elongated models being excluded. In addition, sFcεRIα appears not to interact with the C-terminal end of Fcε3–4, and probably binds either to the sides or face, observations which are consistent with other experimental data on the FcεRIα/IgE interaction. Automated hydrodynamic modelling also has the potential to be used for other interactions, providing a simple way of looking at a large number of models, and making rigorous studies of interacting components more feasible. Received: 31 July 1996 / Accepted: 1 December 1996     

Biological Activation of Heteropoly Complex of Molybdotungstosilicate Containing Lanthanum K10H3La(SiMo6W5O39)2⋅26H2O: Spectroscopic Approach and Microcalorimetry

In this paper, the biological activation of heteropoly complex of molybdotungstosilicate containing lanthanum K₁₀H₃La(SiMo₆W₅O₃₉)₂?26H₂O (LaW₅) was investigated by spectroscopic approach and microcalorimetry under the human physiological conditions. Fluorescence spectroscopy in combination with UV–Vis absorption spectroscopy was employed to investigate the binding of LaW₅ to bovine serum albumin (BSA). In the mechanism discussion, it was proved that the fluorescence quenching of BSA by LaW₅ is a result of the formation of LaW₅–BSA complex. Binding parameters were determined using the Stern–Volmer equation. The results of thermodynamic parameters ?G, ?H, ?S at different temperatures indicate that van der Waals interactions and hydrogen bonds play a major role for LaW₅–BSA association. The distance r between donor (BSA) and acceptor (LaW₅) was obtained according to fluorescence resonance energy transfer. Furthermore, the calorimetric method was used to monitor the biological activity of LaW₅ in Escherichia coli.