Pentahaem cytochrome c nitrite reductase: reaction with hydroxylamine,a potential reaction intermediate and substrate

The pentahaem enzyme cytochrome c nitrite reductase catalyses the reduction of nitrite to ammonia, a key reaction in the biological nitrogen cycle. The enzyme can also transform nitrogen monoxide and hydroxylamine, two potential bound reaction intermediates, into ammonia. Structural and mechanistic aspects of the multihaem enzyme are discussed in comparison with hydroxylamine oxidoreductase, a trimeric protein with eight haem molecules per subunit.     

The reaction force and the transition region of a reaction

The reaction force F(R) and the position-dependent reaction force constant κF(R) are defined by F(R)=-∂V(R)/∂R and κ(R)=∂²V(R)/∂R², where V(R) is the potential energy of a reacting system along a coordinate R. The minima and maxima of F(R) provide a natural division of the process into several regions. Those in which F(R) is increasing are where the most dramatic changes in electronic properties take place, and where the system goes from activated reactants (at the force minimum) to activated products (at the force maximum). κ(R) is negative throughout such a region. We summarize evidence supporting the idea that a reaction should be viewed as going through a transition region rather than through a single point transition state. A similar conclusion has come out of transition state spectroscopy. We describe this region as a chemically-active, or electronically-intensive, stage of the reaction, while the ones that precede and follow it are structurally-intensive. Finally, we briefly address the time dependence of the reaction force and the reaction force constant.     

Chemiluminescence of the Fenton reaction and a dihydroxybenzene-driven Fenton reaction

A dihydroxybenzenes(DHB)-driven Fenton reaction was found to be more efficient than a simple Fenton reaction based on OH radical and activated species production. The reason for this enhanced reactivity by [Fe DHB] complexes is not well understood, but results suggest that it may be explained by the formation of oxidation species different from those formed during the classic Fenton reactions. In previous work, greater concentrations, and more sustained production of OH over time were observed in DHB driven Fenton reactions versus neat Fenton and Fenton-like reactions. In this work, chemiluminescence (CL) was monitored, and compared to OH production kinetics. The CL of the DHB-driven Fenton reaction was shorter than that for sustained production of OH. CL appears to have been caused by excited Fe(IV) species stabilized by the DHB ligands initially formed in the reaction. Formation of this species would have to have occurred by the reaction between OH and Fe(III) in a DHB complex.     

Peroxydisulfate ion, a plant growth inhibitor, and its reaction with IAA

Germination and sprouting tests were used to demonstrate thatperoxydisulfate ion, S₂O₈^–2, reversibly inhibits turnipsprout growth but does not prevent germination. Peroxydisulfateion is kinetically inert to most organic compounds but readilyoxidizes IAA. Activation energy and rate constants for the reactionwere measured and the pH effect studied. Hormone oxidation isproposed as the effective mechanism of growth inhibition. (Received April 28, 1979; )     

Activation of a cyanobacterial adenylate cyclase, CyaC, by autophosphorylation and a subsequent phosphotransfer reaction.

The CyaC protein, a cyanobacterial adenylate cyclase, has a unique primary structure composed of the catalytic domain of adenylate cyclase and the conserved domains of bacterial two-component regulatory systems, one transmitter domain and two receiver domains. In the present work, CyaC was produced in Escherichia coli as a histidine-tagged recombinant protein and purified to homogeneity. CyaC showed ability to autophosphorylate in vitro with the gamma-phosphate of [gamma-32P]ATP. CyaC derivatives were constructed by site-directed mutagenesis in which the highly conserved phosphorylation sites in the transmitter domain (His572) and receiver domains (Asp60 or Asp895) were replaced by glutamine and alanine residues, respectively. After autophosphorylation of the CyaC derivatives, the chemical stabilities of the phosphoryl groups bound to the derivatives were determined. It was found that His572 is the initial phosphorylation site and that the phosphoryl group once bound to His572 is transferred to Asp895. The enzyme activities of the CyaC derivatives defective in His572 or Asp895 were considerably reduced. Asp895 is phosphorylated by acetyl [32P]phosphate, a small phosphoryl molecule, but Asp60 is not. Acetyl phosphate stimulates adenylate cyclase activity only when Asp895 is intact. These results suggest that the phosphorylation of Asp895 is essential for the activation of adenylate cyclase and that Asp60 functions differently from Asp895 in regulating the enzyme activity.     

Physiological reaction of women during exercise and recovery, in a comfortable environment and a hot environment

Physiological reaction and oxygen intake during exercise and recovery were measured in fourteen young female Japanese during the follicular phase of their menstrual cycle at 25 degree C with 50% relative humidity and at 35 degree C with 50% relative humidity. Subjects, clad in bathing suits only, performed a bicycle ergometer exercise at a constant work load of 600 kg . m/min at a cycling rate of 50 rpm for 20 min and recovered while remaining on the bicycle ergometer for 40 min. The mean values of sweat volume and skin temperature were significantly greater at 35 degree C than at 25 degree C. It has been shown that heart rate and rectal temperature during exercise were slightly higher at 35 degree C than at 25 degree C, while those during recovery were significantly higher at 35 degree C than at 25 degree C. Oxygen intake, oxygen debt, and the fall in diastolic blood pressure after exercise were considerably greater at 35 degree C than at 25 degree C. The increase in oxygen intake in a hot environment might result from an increased metabolism due to higher body temperature and increased energy requirement for heat dissipation such as profuse sweating, higher heart rate, and increased ventilatory volume. The increase in oxygen debt in a hot environment might reflect the increased metabolism caused by higher body temperature and the increased production of lactic acid in the working muscle as a result of an insufficient blood supply to the muscle. The increases in sweat volume, oxygen intake during exercise, and oxygen debt in women in a hot environment were considerably smaller than corresponding values for men. The smaller increase in sweat volume in women in a hot environment could reflect a smaller oxygen intake and a more marked dilation of skin vessels in women than in men.     

A zone phenomenon and a progressive reaction occurring with a radioactive hemolysin,sodium erucate,I 131

Sodium erucate reacts progressively (i.e., once the reaction is started in a time which is so short that the lysin is in contact with the red cells for 30 seconds, it cannot be stopped even by being diluted 10-fold) with human red cells at pH 7. At the same time, systems containing the lysin and human red cells show a zone phenomenon, lysis occurring most readily in a certain concentration of lysin but more slowly in larger or smaller concentrations. Sodium erucate-I¹³¹ can be used to investigate both the zone phenomenon and the progressive character of the reaction. As regards the former, large concentrations of the lysin react relatively poorly with the red cell surfaces and the resistance of the red cells is relatively high. This may be due to the presence of an admixed inhibitor or to the development of an inhibitory state. The lysin is taken up and fixed by material in the red cell surface, so that the "internal phase" of lysin attached to the cell surfaces is so firmly fixed that a 10-fold dilution has no effect on it. It follows that lysis in these systems is progressive, as it is found to be.     

Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase

A previously determined crystal structure of the ternary complex of trehalose-6-phosphate synthase identified a putative transition state-like arrangement based on validoxylamine A 6'-O-phosphate and uridine diphosphate in the active site. Here linear free energy relationships confirm that these inhibitors are synergistic transition state mimics, supporting front-face nucleophilic attack involving hydrogen bonding between leaving group and nucleophile. Kinetic isotope effects indicate a highly dissociative oxocarbenium ion-like transition state. Leaving group (18)O effects identified isotopically sensitive bond cleavages and support the existence of a hydrogen bond between the nucleophile and departing group. Br?nsted analysis of nucleophiles and Taft analysis highlight participation of the nucleophile in the transition state, also consistent with a front-face mechanism. Together, these comprehensive, quantitative data substantiate this unusual enzymatic reaction mechanism. Its discovery should prompt useful reassessment of many biocatalysts and their substrates and inhibitors.     

Synthesis of guanine nucleosides by fusion,and a mechanistic aspect of the reaction

N²-Acetylguanine (1) was condensed by fusion with the fully acetylated derivatives of the following sugars: β-D-ribofuranose (2), β-D-ribopyranose (3), α-D-xylopyranose (4), β-D-xylopyranose (5), α-D-glucopyranose (6), and β-D-gluco-pyranose (7). The reaction of 1 with either 2 or 3 gave a mixture of 7-β, 9-α, and 9-β isomers, whereas only the 7-β and 9-β isomers, and virtually no 9-α isomer, were obtained when 4, 5, 6, and 7 were used. When each isomeric acetylated ribofuranosylguanine was heated in the presence of an acidic catalyst, a mixture of 7-β, 9-α, and 9-β nucleosides was formed. Close examination of the product ratios showed that the ratio of 7:9 isomers remained unchanged throughout the reactions, but the anomeric nature of the 9-substituted nucleoside was dependent on the sugar used.     

Isolation, purification and characterization of histidino-threosidine, a novel Maillard reaction protein crosslink from threose, lysine and histidine

We isolated a novel acid-labile yellow chromophore from the incubation of lysine, histidine and d-threose and identified its chemical structure by one and two-dimensional NMR spectroscopy combined with LC-tandem mass spectrometry. This new cross-link exhibits a UV absorbance maximum at 305 nm and a molecular mass of 451 Da. The proposed structure is 2-amino-5-(3-((4-(2-amino-2-carboxyethyl)-1H-imidazol-1-yl)methyl)-4-(1,2-dihydroxyethyl)-2-formyl-1H-pyrrol-1-yl)pentatonic acid, a cross-link between lysine and histidine with addition of two threose molecules. It was in part deduced and confirmed through synthesis of the analogous compound from n-butylamine, imidazole and d-threose. We assigned the compound the trivial name histidino-threosidine. Systemic incubation revealed that histidino-threosidine can be formed in low amounts from fructose, glyceraldehyde, methylglyoxal, glycolaldehyde, ascorbic acid, and dehydroascorbic acid, but at a much higher yield with degradation products of ascorbic acid, i.e. threose, erythrose, and erythrulose. Bovine lens protein incubated with 10 and 50 mM threose for two weeks yielded 560 and 2840 pmol/mg histidino-threosidine. Histidino-threosidine is to our knowledge the first Maillard reaction product known to involve histidine in a crosslink.     

Synthesis, characterization, and reaction pathways for the formation of a GMP adduct of a cytotoxic thiocyanato ruthenium arene complex

The organoruthenium complex [(η⁶-hmb)Ru(en)(Cl)][PF₆] (hmb is hexamethylbenzene, en is ethylenediamine) undergoes facile aquation and then reacts with KSCN in unbuffered solution to give the S-coordinated thiocyanato product [(η⁶-hmb)Ru(en)(S-SCN)]⁺ which slowly converts to the thermodynamically favored N-bound complex [(η⁶-hmb)Ru(en)(N-NCS)]⁺ (1 ⁺). Complex 1 was synthesized and characterized by X-ray crystallography and mass spectrometry. Despite its lack of hydrolysis over 24 h, complex 1 exhibits moderate cytotoxicity (IC₅₀ 24 μM) towards the human ovarian cancer cell line A2780, comparable with that of the chlorido analogue which is thought to be activated (towards potential target DNA) via a rapid aquation (Wang et. al. in Proc Natl Acad Sci USA 102:18269–18274, 2005). Detailed kinetic studies suggest that complex 1 binds to guanosine 5′-monophosphate (GMP) through direct N7 substitution of the N-bound SCN ligand. In the presence of a high concentration of chloride (104 mM), however, complex 1 may bind partly to GMP via Cl substitution.     

Superoxide, amine buffers and tetranitromethane: a novel free radical chain reaction

The amine buffer Tris slowly reduces tetranitromethane (TNM) to the nitroform anion in a non-accelerating reaction. The amine buffers HEPES and MOPS also (slowly) react with TNM but the dialkylaminoalkyl radicals formed from these two buffers undergo further reactions resulting in a rapid, accelerating, free radical chain process whereby the amine is oxidized and TNM reduced. The chemical functionality in any reaction component, not necessarily the buffer, required for this radical chain mechanism is >N-CH<. In the presence of such groups, the quantification of superoxide by TNM is impossible.     

Ubiquinone binding, ubiquinone exclusion, and detailed cofactor conformation in a mutant bacterial reaction center

The X-ray crystal structure of a Rhodobacter sphaeroides reaction center with the mutation Ala M260 to Trp (AM260W) has been determined. Diffraction data were collected that were 97.6% complete between 30.0 and 2.1 A resolution. The electron density maps confirm the conclusions of a previous spectroscopic study, that the Q(A) ubiquinone is absent from the AM260W reaction center (Ridge, J. P., van Brederode, M. E., Goodwin, M. G., van Grondelle, R., and Jones, M. R. (1999) Photosynthesis Res. 59, 9-26). Exclusion of the Q(A) ubiquinone caused by the AM260W mutation is accompanied by a change in the packing of amino acids in the vicinity of the Q(A) site that form part of a loop that connects the DE and E helices of the M subunit. This repacking minimizes the volume of the cavity that results from the exclusion of the Q(A) ubiquinone, and further space is taken up by a feature in the electron density maps that has been modeled as a chloride ion. An unexpected finding is that the occupancy of the Q(B) site by ubiquinone appears to be high in the AM260W crystals, and as a result the position of the Q(B) ubiquinone is well-defined. The high quality of the electron density maps also reveals more precise information on the detailed conformation of the reaction center carotenoid, and we discuss the possibility of a bonding interaction between the methoxy group of the carotenoid and residue Trp M75. The conformation of the 2-acetyl carbonyl group in each of the reaction center bacteriochlorins is also discussed.     

KRDS, a new peptide derived from human lactotransferrin, inhibits platelet aggregation and release reaction

KRDS (Lys-Arg-Asp-Ser), a tetrapeptide from human lactotransferrin, was tested in vitro on human platelet function, and its effects were compared to those of RGDS, a tetrapeptide from human fibrinogen. Both peptides had a high probability of initiating a beta-turn and were highly hydrophilic. KRDS inhibited ADP-induced platelet aggregation [median inhibitory concentration (IC50) 350 microM] and fibrinogen binding (IC50 360 microM) to a lesser extent than RGDS (IC50 75 microM and 20 microM, respectively). Different from RGDS, thrombin-induced serotonin release was inhibited by KRDS (750 microM) on normal platelets (55 +/- 10%) and type I Glanzmann's thrombasthenia platelets (43% +/- 1). However, KRDS had no effect on cytoplasmic Ca2+ mobilization, inositol phospholipid metabolism or protein phosphorylation (myosin light chain P20 and P43). In contrast to RGDS, KRDS does not inhibit the binding of monoclonal antibody PAC-1 to activated platelets. KRDS and RGDS inhibited 4 beta-phorbol-12-myristate-13-acetate (PMA)-induced aggregation and fibrinogen binding, while proteins were normally phosphorylated. Thus, the tetrapeptide KRDS is (a) an inhibitor of serotonin release by a mechanism independent of protein phosphorylation and (b) an inhibitor of fibrinogen binding and, hence, aggregation by a mechanism that may not necessarily involve its direct binding to the glycoprotein IIb-IIIa-complex.