The salt dependence of DNA recognition by NF-kappaB p50 : a detailed kinetic analysis of the effects on affinityand specificity

The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the dissociation constants. Under previously established high affinity buffer conditions, the k a for both sequences was in the order of 10(7) M-1s-1whilst the k d values varied 600-fold in a sequence-dependent manner between 10(-1) and 10(-4 )s-1, suggesting that the selectivity of p50 for different sequences is mediated primarily through sequence-dependent dissociation rates. The calculated K D value for the Ig-kappaB sequence was 16 pM, whilst the K D for the non-specific sequence was 9.9 nM. As the ionic strength increased to levels which are closer to that of the cellular environment, the binding of p50 to the non-specific sequence was abolished whilst the specific affinity dropped to nanomolar levels. From these results, a mechanism is proposed in which p50 binds specific sequences with high affinity whilst binding non-specific sequences weakly enough to allow efficient searching of the DNA.

Superoxide does react with peroxides : direct observation of the haber-weiss reaction in the gas phase

The fact that nature provides specific enzymes to selectively remove superoxide (O2.−) from aerobic organisms, namely, the superoxide dismutase enzymes,1 has led to the suggestion that this radical ion may cause the oxidative damage associated with degradative disease and aging.2 Intriguingly, however, superoxide itself is relatively unreactive toward most cellular components, which suggests that dismutase enzymes may ultimately protect the cell against more pernicious oxidants formed from superoxide. As such, there is increasing interest in the endogenous chemistry of superoxide and the pathways by which it might beget more reactive oxygen species. Protonation of superoxide to form the hydroperoxyl radical (HOO.) and dismutation of the same species to hydrogen peroxide (HOOH), with subsequent metal-catalyzed reduction to the hydroxyl radical (HO.), are well-characterized processes in which both the HOO. and HO. radicals are significantly more reactive than their common progenitor.2 Recent examples, however, have also linked superoxide to the putative production of singlet oxygen3 and ozone,4, 5 although the definitive characterization of these chemistries in the cellular milieu has proved challenging

Heat of formation of the hydroperoxyl radical HOO via negative ion studies

We present a determination of Delta(f)H(298)(HOO) based upon a negative. ion thermodynamic cycle. The photoelectron spectra of HOO- and DOO- were used to measure the molecular electron affinities (EAs). In a separate experiment, a tandem flowing afterglow-selected ion flow tube (FA-SIFT) was used to measure the forward and reverse rate constants for HOO- + HCdropCH reversible arrow HOOH + HCdropC(-) at 298 K, which gave a value for Delta(acid)H(298)(HOO-H). The experiments yield the following values: EA(HOO) = 1.078 +/- 0.006 eV; T-0((X) over tilde HOO - (A) over tilde HOO) = 0.872 +/- 0.007 eV; EA(DOO) = 1.077 +/- 0.005 eV; T-0((X) over tilde DOO - (A) over tilde DOO) = 0.874 +/- 0.007 eV; Delta(acid)G(298)(HOO-H) = 369.5 +/- 0.4 kcal mol(-1); and Delta(acid)H(298)(HOO-H) = 376.5 +/- 0.4 kcal mol(-1). The acidity/EA thermochemical cycle yields values for the bond enthalpies of DH298(HOO-H) = 87.8 +/- 0.5 kcal mol(-1) and Do(HOO-H) = 86.6 +/- 0.5 kcal mol(-1). We recommend the following values for the heats of formation of the hydroperoxyl radical: Delta(f)H(298)(HOO) = 3.2 +/- 0.5 kcal mol(-1) and Delta(f)H(0)(HOO) = 3.9 +/- 0.5 kcal mol(-1); we recommend that these values supersede those listed in the current NIST-JANAF thermochemical tables.

Investigation of the gas phase reactivity of the 1-adamantyl radical using a distonic radical anion approach

The gas phase reactions of the bridgehead 3-carboxylato-1-adamantyl radical anion were observed with a series of neutral reagents using a modified electrospray ionisation linear ion trap mass spectrometer. This distonic radical anion was observed to undergo processes suggestive of radical reactivity including radical-radical combination reactions, substitution reactions and addition to carbon-carbon double bonds. The rate constants for reactions of the 3-carboxylato-1-adamantyl radical anion with the following reagents were measured ( in units 10(-12) cm(3) molecule(-1) s(-1)): O-18(2) ( 85 +/- 4), NO ( 38.4 +/- 0.4), I-2 ( 50 +/- 50), Br-2 ( 8 +/- 2), CH3SSCH3 ( 12 +/- 2), styrene ( 1.20 +/- 0.03), CHCl3 ( H abstraction 0.41 +/- 0.06, Cl abstraction 0.65 +/- 0.1), CDCl3 ( D abstraction 0.035 +/- 0.01, Cl abstraction 0.723 +/- 0.005), allyl bromide (Br abstraction 0.53 +/- 0.04, allylation 0.25 +/- 0.01). Collision rates were calculated and reaction efficiencies are also reported. This study represents the first quantitative measurement of the gas phase reactivity of a bridgehead radical and suggests that distonic radical anions are good models for the study of their elusive uncharged analogues.

Hydrolysis of triasulfuron, metsulfuron-methyl and chlorsulfuron in alkaline soil and aqueous solutions

The hydrolysis of triasulfuron, metsulfuron-methyl and chlorsulfuron in aqueous buffer solutions and in soil suspensions at pH values ranging from 5.2 to 11.2 was investigated. Hydrolysis of all three compounds in both aqueous buffer and soil suspensions was highly pH-sensitive. The rate of hydrolysis was much faster in the acidic pH range (5.2-6.2) than under neutral and moderately alkaline conditions (8.2-9.4), but it increased rapidly as the pH exceeded 10.2. All three compounds degraded faster at pH 5.2 than at pH 11.2. Hydrolysis rates of all three compounds could be described well with pseudo-first-order kinetics. There were no significant differences (P =0.05) in the rate constants (k, day-1) of the three compounds in soil suspensions from those in buffer solutions within the pH ranges studied. A functional relationship based on the propensity of nonionic and anionic species of the herbicides to hydrolyse was used to describe the dependence of the 'rate constant' on pH. The hydrolysis involving attack by neutral water was at least 100-fold faster when the sulfonylurea herbicides were undissociated (acidic conditions) than when they were present as the anion at near neutral pH. In aqueous buffer solution at pH > 11, a prominent degradation pathway involved O-demethylation of metsulfuron-methyl to yield a highly polar degradate, and hydrolytic opening of the triazine ring. It is concluded that these herbicides are not likely to degrade substantially through hydrolysis in most agricultural (C) 2000 Society of Chemical Industry.

Excited-state dynamics in diketopyrrolopyrrole-based copolymer for organic photovoltaics investigated by transient optical spectroscopy

We investigate the photoexcited state dynamics in a donor-acceptor copolymer, poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]- pyrrole-1,4-dione-alt-naphthalene} (pDPP-TNT), by picosecond fluorescence and femtosecond transient absorption spectroscopies. Timeresolved fluorescence lifetime measurements of pDPP-TNT thin films reveal that the lifetime of the singlet excited state is 185 ± 5 ps and that singlet-singlet annihilation occurs at excitation photon densities above 6 × 1017 photons/cm3. From the results of singlet-singlet annihilation analysis, we estimate that the single-singlet annihilation rate constant is (6.0 ± 0.2) × 109cm3 s-1 and the singlet diffusion length is -7 nm. From the comparison of femtosecond transient absorption measurements and picosecond fluorescence measurements, it is found that the time profile of the photobleaching signal in the charge-transfer (CT) absorption band coincides with that of the fluorescence intensity and there is no indication of long-lived species, which clearly suggests that charged species, such as polaron pairs and triplet excitons, are not effectively photogenerated in the neat pDPP-TNT polymer.

Hydrolysis of genotoxic methyl-substituted oxiranes : Experimental kinetic and semiempirical studies

The kinetics of acid-catalyzed hydrolysis of seven methylated aliphatic epoxides - R1R2C(O)CR3R4 (A: R1=R2=R3=R4=H; B: R1=R2=R3=H, R4=Me; C: R1=R2=H, R3=R4=Me; D: R1=R3=H, R2=R4=Me(trans); E: R1=R3=H, R2=R4=Me(cis); F: R1=R3=R4=Me, R2=H; G: R1=R2=R3=R4=Me) - has been studied at 36 ± 1.5°C. Compounds with two methyl groups at the same carbon atom of the oxirane ring exhibit highest rate constants (k(eff) in reciprocal molar concentration per second: 11.0 ± 1.3 for C, 10.7 ± 2.1 for F, and 8.7 ± 0.7 for G as opposed to 0.124 ± 0.003 for B, 0.305 ± 0.003 for D, and 0.635 ± 0.036 for E). Ethylene oxide (A) displays the lowest rate of hydrolysis (0.027 M-1 s-1). The results are consistent with literature data available for compounds A, B, and C. To model the reactivities we have employed quantum chemical calculations (MNDO, AM1, PM3, and MINDO/3) of the main reaction species. There is a correlation of the logarithm k(eff) with the total energy of epoxide ring opening. The best correlation coefficients (r) were obtained using the AM1 and MNDO methods (0.966 and 0.957, respectively). However, unlike MNDO, AM1 predicts approximately zero energy barriers for the oxirane ring opening of compounds B, C, E and G, which is not consistent with published kinetic data. Thus, the MNDO method provides a preferential means of modeling the acidic hydrolysis of the series of methylated oxiranes. The general ranking of mutagenicity in vitro, A > B > C, is in line with the concept that this sequence also gradually leaves the expoxide reactivity optimal for genotoxicity toward reactivities leading to higher biological detoxifications.

Binding mechanism of affinity ligands for purification of plasmid DNA

Plasmid DNA for therapeutic and vaccination purposes must be highly purified. The high selectivity of affinity chromatography makes it ideal for the isolation of pDNA from complex biological feed stocks. Affinity chromatography makes use of the biological function and/or individual chemical structure of the interacting molecules. However, the success of any affinity purification protocol is dependent on the availability of suitable ligands. In this study, surface plasmon resonance (SPR) based Biacore system has been employed for the detection and quantification of the binding between lac operon (lacO) sequence contained in a pDNA and synthetic peptides based on the DNA-binding domain of the lac repressor protein, lad. The equilibrium dissociation constant (K D) and association and dissociation rate constants (ka, kd) for the interaction between plasmid DNA and designed peptides were determined.

A comprehensive mechanistic kinetic model for dilute acid hydrolysis of switchgrass cellulose to glucose, 5-HMF and levulinic acid

Switchgrass was treated by 1% (w/w) H₂SO₄in batch tube reactors at temperatures ranging from 140–220°C for up to 60 minutes. In this study, release patterns of glucose, 5-hydroxymethylfurfural (5-HMF), and levulinic acid from switchgrass cellulose were investigated through a mechanistic kinetic model. The predictions were consistent with the measured products of interest when new parameters reflecting the effects of reaction limitations, such as cellulose crystallinity, acid soluble lignin–glucose complex (ASL–glucose) and humins that cannot be quantitatively analyzed, were included. The new mechanistic kinetic model incorporating these parameters simulated the experimental data with R² above 0.97. Results showed that glucose yield was most sensitive to variations in the parameter regarding the cellulose crystallinity at low temperatures (140–180°C), while the impact of crystallinity on the glucose yield became imperceptible at elevated temperatures (200–220 °C). Parameters related to the undesired products (e.g. ASL–glucose and humins) were the most sensitive factors compared with rate constants and other additional parameters in impacting the levulinic acid yield at elevated temperatures (200–220°C), while their impacts were negligible at 140–180°C. These new findings provide a more rational explanation for the kinetic changes in dilute acid pretreatment performance and suggest that the influences of cellulose crystallinity and undesired products including ASL–glucose and humins play key roles in determining the generation of glucose, 5-HMF and levulinic acid from biomass-derived cellulose.

Synthesis of some copper(II)-chelating (dialkylamino)pyridine amphiphiles and evaluation of their esterolytic capacities in cationic micellar media

Three new (dialkylamino)pyridine (DAAP)-based ligand amphiphiles 3-5 have been synthesized. All of the compounds possess a metal ion binding subunit in the form of a 2,6-disubstituted DAAP moiety. In addition, at least one ortho-CH2OH substituent is present in all the ligands. Complex formation by these ligands with various metal ions were examined under micellar conditions, but only complexes with Cu(II) ions showed kinetically potent esterolytic capacities under micellar conditions. Complexes with Cu(II) were prepared in host comicellar cetyltrimethylammonium bromide (CTABr) media at pH 7.6. Individual complexes were characterized by UV-visible absorption spectroscopy and electron paramagnetic resonance spectroscopy. These metallomicelles speed the cleavage of the substrates p-nitrophenyl hexanoate or p-nitrophenyl diphenyl phosphate. To ascertain the nature of the active esterolytic species, the stoichiometries of the respective Cu(II) complexes were determined from the kinetic version of Job's plot. In all the instances, 2:1 complex ligand/Cu(II) ion are the most kinetically competent species. The apparent pK(a) values of the Cu(II)-coordinated hydroxyl groups of the ligands 3, 4, and 5, in the comicellar aggregate, are 7.8, 8.0, and 8.0, respectively, as estimated from the rate constant vs pH: profiles of the ester cleavage reactions. The nucleophilic metallomicellar reagents and the second-order "catalytic" rate constants toward esterolysis of the substrate p-nitrophenyl hexanoate (at 25 degrees C, pH 7.6) are 37.5 for 3, 11.4 for 4, and 13.8 for 5. All catalytic systems comprising the coaggregates of 3, 4, or 5 and CTABr demonstrate turnover behavior in the presence of excess substrate.

Cuprous oxide catalyzed air oxidation of thiosulfate and tetrathionate

Thiosulfate (S2O32−) and tetrathionate (S4O62−)are oxidized to sulfate by air at atmospheric pressure and 50–70°C in the presence of cuprous oxide (Cu2O) as catalyst. Sulfate is produced from S2O32− by series-parallel reaction paths involving S4O62− as an intermediate. The rate data obtained for air oxidation of S2O32− on Cu2O agree well with a pseudo-homogeneous first order kinetic scheme, yielding values of rate constants for series parallel reaction paths which have been used in modelling the catalyzed air oxidation of S2O32−. Air oxidation of S4O62− on Cu2O proceeds at a higher rate in the presence of S2O32− than in its absence. Cu2O is less active than Cu2S for the air oxidation of S2O32−, as shown by the rate constant values which for Cu2O catalyzed oxidation are an order of magnitude smaller than those for the Cu2S catalyzed oxidation.

Identification of amino acid residues essential for enzyme activity of sheep liver 5,10-methylenetetrahydrofolate reductase

Sheep liver 5,10-methylenetetrahydrofolate reductase was subjected to specific chemical modification with phenylglyoxal, diethyl pyrocarbonate and N-bromosuccinimide. The second-order rate constants for inactivation were calculated to be 54 M-1 X min-1, 103 M-1 X min-1 and 154 M-1 X min-1 respectively. This inactivation could be prevented by incubation with substrates or products, suggesting that the residues modified, namely arginine, histidine and tryptophan, are essential for enzyme activity.

Kinetic mechanism of the interaction of D-cycloserine with serine hydroxymethyltransferase

The kinetic mechanism for the interaction of D-cycloserine with serine hydroxymethyltransferase (EC2.1.2.1) from sheep liver was established by measuring changes in the activity, absorbance, and circular dichoism (CD) of the enzyme. The irreversible inhibition of the enzyme was characterized by three detectable steps: an initial rapid step followed by two successive steps with rate constants of 5.4 X s-l and 1.4 X lo4 s-l. The first step was distinguished by a rapid disappearance of the enzyme absorbance peak at 425 nm, a decrease in the enzyme activity to 25% of the uninhibited velocity, and a lowering of the CD intensity at 432 nm to about 65% of the original value. The second step of the interaction was accompanied by a complete loss of enzyme.

Triplet-state Photophysics and Transient Photochemistry of Cyclic Enethiones A Laser Flash Photolysis Study

The triplets of four cyclic enethiones, including thiocoumarin, have been investigated by nanosecond laser flash photolysis. Data are presented for transient spectra and kinetics associated with triplets, quantum yields of intersystem crossing and singlet oxygen photosensitization. The quenching of the thiocoumarin triplet (A:, = 485 nm, E:,, = 8.8 x lo3 dm3 mol-' cm-'in benzene) by several olefins, amines and hydrogen donors occurs with rate constants of 107-5 x lo9 dm3 mol-' s-'; the lower limits of quantum yields ( c#+~) for the related photoreactions, estimated from ground-state depletion, are generally small (0.0-0.1 1 in benzene, except for good hydrogen donors, namely, p-methoxythiophenol and tri-n-butylstannane) . The radical anion of thiocoumarin (A,,, = 405-435 nm) is formed in two stages upon triplet quenching by triethylamine in acetonitrile; the fast component is the result of direct electron transfer to the triplet and the slower component is assigned to secondary photoreduction of the thione ground state by the a-aminoalkyl radical derived from the triethylamine radical-cation.

Identification of active-site residues of sheep liver serine hydroxymethyltransferase

Chemical modification of amino acid residues with phenylglyoxal, N-ethylmaleimide and diethyl pyrocarbonate indicated that at least one residue each of arginine, cysteine and histidine were essential for the activity of sheep liver serine hydroxymethyltransferase. The second-order rate constants for inactivation were calculated to be 0.016 mM-1 X min-1 for phenylglyoxal, 0.52 mM-1 X min-1 for N-ethylmaleimide and 0.06 mM-1 X min-1 for diethyl pyrocarbonate. Different rates of modification of these residues in the presence and in the absence of substrates and the cofactor pyridoxal 5'-phosphate as well as the spectra of the modified protein suggested that these residues might occur at the active site of the enzyme.