Reactions of OH radicals with poly(U) in deoxygenated solutions: sites of OH radical attack and the kinetics of base release

Pulse radiolysis of N2O-saturated solutions of poly(U) in the presence of tetranitromethane showed that 81 per cent of the radicals formed are reducing in nature. Using data from other sources it has been estimated that 70 per cent of the OH radicals add to the base at C(5) and 23 per cent at C(6) while only 7 per cent abstract an H-atom from the sugar moiety. To a large extent the C(5) OH adduct radicals attack the sugar moiety of poly(U) thereby inducing strand breakage and base release. G (base release) = 2.9 can be subdivided into three components: (a) immediate (20 per cent), (b) fast (50 per cent) and (c) slow (30 per cent). The immediate base release must occur either during the free-radical stage or as a result of the rapid (t1/2 less than 4 min at 0 degree C) decomposition of a diamagnetic product. The fast and the slow processes are only readily observable at elevated temperatures, e.g. at 50 degrees C the half lives are 83 min and 26 h, respectively (Ea (fast) = 68 kJ mol-1, Ea (slow) = 89 kJ mol-1, A (fast) = 1.5 X 10(7) s-1, A (slow) = 1.9 X 10(9) s-1. It is concluded that there are three different types of sugar lesions giving rise to base release, structures for which are tentatively proposed.     

Kinetics of superoxide dismutase- and iron-catalyzed nitration of phenolics by peroxynitrite.

Superoxide dismutase and Fe3+EDTA catalyzed the nitration by peroxynitrite (ONOO-) of a wide range of phenolics including tyrosine in proteins. Nitration was not mediated by a free radical mechanism because hydroxyl radical scavengers did not reduce either superoxide dismutase or Fe3+EDTA-catalyzed nitration and nitrogen dioxide was not a significant product from either catalyst. Rather, metal ions appear to catalyze the heterolytic cleavage of peroxynitrite to form a nitronium-like species (NO2+). The calculated energy for separating peroxynitrous acid into hydroxide ion and nitronium ion is 13 kcal.mol-1 at pH 7.0. Fe3+EDTA catalyzed nitration with an activation energy of 12 kcal.mol-1 at a rate of 5700 M-1.s-1 at 37 degrees C and pH 7.5. The reaction rate of peroxynitrite with bovine Cu,Zn superoxide dismutase was 10(5) M-1.s-1 at low superoxide dismutase concentrations, but the rate of nitration became independent of superoxide dismutase concentration above 10 microM with only 9% of added peroxynitrite yielding nitrophenol. We propose that peroxynitrite anion is more stable in the cis conformation, whereas only a higher energy species in the trans conformation can fit in the active site of Cu,Zn superoxide dismutase. At high superoxide dismutase concentrations, phenolic nitration may be limited by the rate of isomerization from the cis to trans conformations of peroxynitrite as well as by competing pathways for peroxynitrite decomposition. In contrast, Fe3+EDTA appears to react directly with the cis anion, resulting in greater nitration yields.     

Intermolecular charge transfer involving tryptophan, tyrosine and three electron-bonded intermediates derived from methionine

Oxidation processes of radiation-generated three-electron-bonded intermediates derived from methionine Met2[S+...S] and Met[S...X] (X=Cl,Br) were investigated through reaction with tryptophan and tyrosine, using the optical pulse radiolysis method. Bimolecular rate constants have been measured for the reactions Met2[S+...S] with TrpH(k=3.8 x 10(8) dm3 mol-1 s-1 and k = 4.9 X 10(8) dm3 mol-1 s-1 at at ph 1 and 4.3, respectively) and Met2[S+...S] with tyrosine, k=3.8 x 10(7) dm3 mol-1 s-1. Rate constants for intermolecular transformation of Met[S...Br] and Met[S...Cl] into TrpH+. or Trp. were also estimated. They varied from 4.7 X 10(8) dm3 mol-1 s-1 (bromide species) to 1.0 X 10(9)dm3 mol-1 s-1 (chloride species). It has also been established azide radicals N-6, N.3 in contrast to dihalide radicals (X-2) do not form transients of Met[S...X] (X = N3)-type. However, oxidation of N-3 by Met2[S+...S] occurs with a bimolecular rate constant of 2.8 X 10(8) dm3 mol-1 s-1. These results are discussed in the light of some equilibria which have been proposed earlier for methionine-halide systems.     

Biostructural chemistry of magnesium ion: characterization of the weak binding sites on tRNA(Phe)(yeast). Implications for conformational change and activity

The thermodynamics and kinetics of magnesium binding to tRNA(Phe)(yeast) have been studied directly by 25Mg NMR. In 0.17 M Na+(aq), tRNA(Phe) exists in its native conformation and the number of strong binding sites (Ka greater than or equal to 10(4)) was estimated to be 3-4 by titration experiments, in agreement with X-ray structural data for crystalline tRNA(Phe) (Jack et al., 1977). The set of weakly bound ions were in slow exchange and 25Mg NMR resonances were in the near-extreme-narrowing limit. The line shapes of the exchange-broadened magnesium resonance were indistinguishable from Lorentzian form. The number of weak magnesium binding sites was determined to be 50 +/- 8 in the native conformation and a total line-shape analysis of the exchange-broadened 25 Mg2+ NMR resonance gave an association constant Ka of (2.2 +/- 0.2) X 10(2) M-1, a quadrupolar coupling constant (chi B) of 0.84 MHz, an activation free energy (delta G*) of 12.8 +/- 0.2 kcal mol-1, and an off-rate (koff) of (2.5 +/- 0.4) X 10(3) s-1. In the absence of background Na+(aq), up to 12 +/- 2 magnesium ions bind cooperatively, and 73 +/- 10 additional weak binding sites were determined. The binding parameters in the nonnative conformation were Ka = (2.5 +/- 0.2) X 10(2) M-1, chi B = 0.64 MHz, delta G* = 13.1 +/- 0.2 kcal mol-1, and koff = (1.6 +/- 0.4) X 10(3) s-1. In comparison to Mg2+ binding to proteins (chi B typically ca. 1.1-1.6 MHz) the lower chi B values suggest a higher degree of symmetry for the ligand environment of Mg2+ bound to tRNA. A small number of specific weakly bound Mg2+ appear to be important for the change from a nonnative to a native conformation. Implications for interactions with the ribosome are discussed.     

Electron acceptors in photosynthetic reaction centers from Rhodopseudomonas spheroides]

Using optical differential spectroscopy and EPR, a parallel study of light-induced electron transfer between the primary (X1) and secondary (X2) quinone-like acceptors in the preparations of reaction centers (RC) isolated from bacterial chromatophore membranes with sodium dodecyl sulfate was carried out. The data from direct measurements of the rate constant temperature dependence for the interaction between light-reduced X1 and X2 (KX1X2) are in good agreement with the data calculated from the kinetic analysis of dark reduction of photooxidized bacteriochlorophyll RC on the acceptors X1 and X2 (KX1X2 = 2.10(-1)S at 20 degrees; Ea = 11,8 kcal.mol-1 within the temperature range of 20 degrees-- -20 degrees). This evidence proves the efficiency of the previously used approach /1, 2/ for the evaluation of the X1-X2 interaction. The method proposed was used for a kinetic analysis of a low-temperature electron transfer from X1 to X2 in RC isolated with lauryldimethylaminoxide (KX1X2 = 2,3.10(2) S-1 at 20 degrees; Ea = 5,5 kcal.mol-1 within the temperature range of 10 degrees-- --70 degrees).     

Some redox properties of myohemerythrin from retractor muscle of Themiste zostericola

Distinct semimetmyohemerythrin species are produced by one-electron oxidation of deoxymyohemerythrin and one-electron reduction of metmyohemerythrin. The former, (semimetmyo)o, changes (greater than or equal to 90%) to the latter, (semimetmyo)R, with k = 1.0 x 10(-2) s-1, delta H = 15.1 kcal mol-1 and delta S = -17 eu. Oxidation of (semimetmyo)o by Fe(CN)6(3)- rapidly produces an unstable metmyohemerythrin form which converts to the final metmyohemerythrin with k = 4.6 x 10(-3) s-1, delta H = 16.8 kcal mol-1, and delta S = -13 eu. The two met forms react at the same rate with N3-, but the unstable form reacts very rapidly with S2O4(2-) in contrast to stable metmyohemerythrin. (Semimetmyo)R or a mixture of metmyohemerythrin and deoxymyohemerythrin equilibrate very slowly to a mixture containing all three species. The rate constants for disproportionation and comproportionation are 0.89 M-1 s-1 and 9.4 M-1 s-1, respectively. EPR spectra near liquid He temperatures and optical absorption spectra have been used to characterize and measure the rates at 25 degrees C, pH 8.2, and I = 0.15 M. The comparative behavior of octameric and monomeric protein is discussed.     

Evidence for catalytic dismutation of superoxide by cobalt(II) derivatives of bovine superoxide dismutase in aqueous solution as studied by pulse radiolysis.

By using the technique of pulse radiolysis to generate O2-., it is demonstrated that Co(II) derivatives of bovine superoxide dismutase in which the copper alone and both the copper and zinc of the enzyme have been substituted by Co(II), resulting in (Co,Zn)- and (Co,Co)-proteins, are capable of catalytically dismutating O2-. with 'turnover' rate constants of 4.8 X 10(6) dm3.s-1.mol-1 and 3.1 X 10(6) dm3.s-1.mol-1 respectively. The activities of the proteins are independent of the pH (7.4-9.4) and are about three orders of magnitude less than that of the native (Cu,Zn)-protein. The rate constants for the initial interaction of O2-. with the Co-proteins were determined to be (1.5-1.6) X 10(9) dm3.s-1.mol-1; however, in the presence of phosphate, partial inhibition is apparent [k approximately (1.9-2.3) X 10(8) dm3.s-1.mol-1]. To account for the experimental observations, two reaction schemes are presented, involving initially either complex-formation or redox reactions between O2-. and Co(II). This is the first demonstration that substitution of a metal into the vacant copper site of (Cu,Zn)-protein results in proteins that retain superoxide dismutase activity.     

On the reaction of molecular oxygen with thiyl radicals: a re-examination

Absolute rate constants for the addition of oxygen to thiyl radicals, i.e. RS. + O2----RSOO., have been determined by applying a new competition method based on RS. formation via one-electron reduction of the corresponding disulphides, and the competition between RS. reacting with O2 and an electron donor such as ascorbate. Bimolecular rate constants have been obtained for the thiyl radicals derived from cysteine (6.1 X 10(7) mol-1 dm3 s-1), penicillamine (2.5 X 10(7) mol-1 dm3 s-1), homocysteine (8.0 X 10(7) mol-1 dm3 s-1), cysteamine (2.8 X 10(7) mol-1 dm3 s-1), 3-thiopropionic acid (2.2 X 10(8) mol-1 dm3 s-1) and glutathione (3.0 X 10(7) mol-1 dm3 s-1), respectively. The values obtained for the O2 addition to the thiyl radicals from glutathione and cysteine are considerable lower (by about two orders of magnitude) than those previously published. This indicates that the RS. + O2 reaction may be of complex nature and is generally a process which is not solely controlled by the diffusion of the reactants.     

Nitrogenase of Klebsiella pneumoniae. Kinetic studies on the Fe protein involving reduction by sodium dithionite, the binding of MgADP and a conformation change that alters the reactivity of the 4Fe-4S centre.

The kinetics of reduction of indigocarmine-dye-oxidized Fe protein of nitrogenase from Klebsiella pneumoniae (Kp2ox) by sodium dithionite in the presence and absence of MgADP were studied by stopped-flow spectrophotometry at 23 degrees C and at pH 7.4. Highly co-operative binding of 2MgADP (composite K greater than 4 X 10(10) M-2) to Kp2ox induced a rapid conformation change which caused the redox-active 4Fe-4S centre to be reduced by SO2-.(formed by the predissociation of dithionite ion) with k = 3 X 10(6) M-1.s-1. This rate constant is at least 30 times lower than that for the reduction of free Kp2ox (k greater than 10(8) M-1.s-1). Two mechanisms have been considered and limits obtained for the rate constants for MgADP binding/dissociation and a protein conformation change. Both mechanisms give rate constants (e.g. MgADP binding 3 X 10(5) less than k less than 3 X 10(6) M-1.s-1 and protein conformation change 6 X 10(2) less than k less than 6 X 10(3) s-1) that are similar to those reported for creatine kinase (EC 2.7.3.2). The kinetics also show that in the catalytic cycle of nitrogenase with sodium dithionite as reductant replacement of 2MgADP by 2MgATP occurs on reduced and not oxidized Kp2. Although the Kp2ox was reduced stoichiometrically by SO2-. and bound two equivalents of MgADP with complete conversion into the less-reactive conformation, it was only 45% active with respect to its ability to effect MgATP-dependent electron transfer to the MoFe protein.     

Thermodynamic and kinetic studies on saccharide binding to soya-bean agglutinin.

The fluorescence of N-dansylgalactosamine [N-(5-dimethylaminonaphthalene-1-sulphonyl)galactosamine] was enhanced 11-fold with a 25 nm blue-shift in the emission maximum upon binding to soya-bean agglutinin (SBA). This change was used to determine the association constants and thermodynamic parameters for this interaction. The association constant of 1.51 X 10(6) M-1 at 20 degrees C indicated a very strong binding, which is mainly due to a relatively small entropy value, as revealed by the thermodynamic parameters: delta G = -34.7 kJ X mol-1, delta H = -37.9 kJ X mol-1 and delta S = -10.9 J X mol-1 X K-1. The specific binding of this sugar to SBA shows that the lectin can accommodate a large hydrophobic substituent on the C-2 of galactose. Binding of non-fluorescent ligands, studied by monitoring the fluorescence changes when they are added to a mixture of SBA and N-dansylgalactosamine, indicates that a hydrophobic substituent at the anomeric position increases the affinity of the interaction. The C-6 hydroxy group also stabilizes the binding considerably. Kinetics of binding of N-dansylgalactosamine to SBA studied by stopped-flow spectrofluorimetry are consistent with a single-step mechanism and yielded k+1 = 2.4 X 10(5) M-1 X s-1 and k-1 = 0.2 s-1 at 20 degrees C. The activation parameters indicate an enthalpicly controlled association process.     

Reaction of azide radicals with amino acids and proteins.

The azide radical N3 reacts selectively with amino acids, in neutral solution preferentially with tryptophan (k (N3 + TrpH) = 4.1 X 10(9) dm3 mol(-1s-1) and in alkaline solution also with cysteine and tyrosine (k(N3 + CyS-) = 2.7 X 10(9) dm3 mol-1s-1) and k(N3 + TyrO-) equals 03.6 X 10(9) dm3 mol-1s-1). Oxidation of the enzyme yADH by N3 involves primary attacks, mainly at tryptophan residues, and subsequent slow secondary reactions. N3-induced inactivation of yADH is likely to occur upon oxidation of tryptophan residues in the substrate binding pocket (58-TrpH and 93-TrpH) since the substrate ethanol although unreactive with N3, protects yADH and since elADH, which does not contain tryptophan in the substrate pocket, is comparatively resistant against N3-attack. N3 exhibits low reactivity with nucleic acid derivatives and it is inert towards aliphatic compounds such as methanol and sodium dodecylsulphate.     

The reverse of the 'repair' reaction of thiols: H-abstraction at carbon by thiyl radicals

Thiyl radicals (RS) formed by the reaction of radiolytically generated OH radicals with thiols, e.g. 1,4-dithiothreitol (DTT), react with cis- and trans-2,5-dimethyltetrahydrofuran by abstracting an H atom in the alpha-position to the ether function (k approximately equal to 5 X 10(3) dm3 mol-1 s-1). The so-formed planar ether radical is 'repaired' by the thiol (k = 6 X 10(8) dm3 mol-1 s-1) thereby regenerating a cis- or trans-2,5-dimethyltetrahydrofuran molecule. In this reaction a thiyl radical is reproduced. Thus trans-2,5-Me2THF from cis-2,5-Me2THF and vice versa are formed in a chain reaction: at a dose rate of 2.8 X 10(-3) Gys-1 and a trans-2,5-Me2THF concentration of 1 X 10(-2) mol dm-3 using DTT as the thiol, G(cis-2,5-Me2THF) = 160 has been found. The chain reaction is very sensitive to impurities and also to disulphides such as those radiolytically formed. 2,5-Me2THF can be regarded as a model for the sugar moiety of DNA where the C(4')-radical is known to lead to DNA strand breakage. The possible role of cellular thiols in the repair of the C(4') DNA radical, and also the conceivable role of thiyl radicals inducing DNA strand breakage, are discussed.     

Estimation and Analysis of Cucumber (Cucumis sativus L.) Leaf Cellular Heat Sensitivity

Triphenyl tetrazolium chloride (TTC) reduction by cucumber (Cucumis sativus L. cv Poinsett 76 and cv Ashley) leaf discs was used as a viability assay to examine the effect of temperature pretreatment on the tissue response to acute hyperthermia. Semi-logarithmic plots of TTC reduction as a function of incubation time at different temperatures from 40 to 60[deg]C resembled the heat survival curves of animal cells. Heat inactivation rates were obtained and subjected to "quasi" Arrhenius analyses by analytical methods derived from the animal studies. The Arrhenius plots of TTC reduction rates for cv Ashley leaf discs preincubated at 25 or 37[deg]C and for cv Poinsett 76 preincubated at 37[deg]C were linear with the same activation energy (Ea) of about 80 kcal mol-1. The Arrhenius plot of cv Poinsett 76 preincubated at 25[deg]C was nonlinear with an Ea of about 80 kcal mol-1 at temperatures below 46[deg]C and an Ea of about 27.5 kcal mol-1 at temperatures above 47[deg]C. The significance of these differences is discussed in terms of the role of protein denaturation in the thermal sensitivity of cucumber disc reduction of TTC and the applicability of these methods to the analysis of plant cellular heat sensitivity.     

The influence of temperature and osmolyte on the catalytic cycle of cytochrome c oxidase.

The influence of temperature on cytochrome c oxidase (CCO) catalytic activity was studied in the temperature range 240-308 K. Temperatures below 273 K required the inclusion of the osmolyte ethylene glycol. For steady-state activity between 278 and 308 K the activation energy was 12 kcal x mol-1; the molecular activity or turnover number was 12 s-1 at 280 K in the absence of ethylene glycol. CCO activity was studied between 240 and 277 K in the presence of ethylene glycol. The activation energy was 30 kcal x mol-1; the molecular activity was 1 s-1 at 280 K. Ethylene glycol inhibits CCO by lowering the activity of water. The rate limitation in electron transfer (ET) was not associated with ET into the CCO as cytochrome a was predominantly reduced in the aerobic steady state. The activity of CCO in flash-induced oxidation experiments was studied in the low temperature range in the presence of ethylene glycol. Flash photolysis of the reduced CO complex in the presence of oxygen resulted in three discernable processes. At 273 K the rate constants were 1500 s-1, 150 s-1 and 30 s-1 and these dropped to 220 s-1, 27 s-1 and 3 s-1 at 240 K. The activation energies were 5 kcal.mol-1, 7 kcal.mol-1, and 8 kcal.mol-1, respectively. The fastest rate we ascribe to the oxidation of cytochrome a3, the intermediate rate to cytochrome a oxidation and the slowest rate to the re-reduction of cytochrome a followed by its oxidation. There are two comparisons that are important: (a). with vs. without ethylene glycol and (b). steady state vs. flash-induced oxidation. When one makes these two comparisons it is clear that the CCO only senses the presence of osmolyte during the reductive portion of the catalytic cycle. In the present work that would mean after a flash-induced oxidation and the start of the next reduction/oxidation cycle.     

Pulse radiolytic study of the interaction of SO4.- with deoxynucleosides. Possible implications for direct energy deposition

Using the technique of pulse radiolysis it has been demonstrated that the interaction of SO4.- with deoxynucleosides (k approximately less than 2 X 10(8)-2.3 X 10(9) dm3 mol-1 s-1) in aqueous solution at pH 7.0 results in the formation of the corresponding one-electron oxidized radicals which either deprotonate or hydrate to yield OH adducts. Based upon the ease of oxidation of the deoxynucleosides, dG, dA, dC, dT, by SO4.-, the apparent redox potentials are in the order dG much greater than dA approximately equal to dC greater than dT. With the exception of deoxyuridine, the deoxynucleoside radicals produced on interaction with SO4.- have been shown to have oxidizing properties based upon the interactions with tetranitromethane and the nitroxyls, TMPN and NPPN. The deoxynucleoside radicals (dG, dA and dC) do not interact with oxygen (k less than 10(6) dm3 mol-1 s-1) in contrast to the interaction observed with the thymidine radical (k = 2.5 X 10(7) dm3 mol-1 s-1). The implications of these findings are presented in terms of the properties of the discussed radicals as relating to those of potential DNA base radicals (positive centres) produced by direct energy deposition within DNA. The use of SO4.- to mimic, to some extent, the effects of direct energy deposition in DNA may assist in our understanding of the resulting molecular processes relevant to radiobiological studies.     

Lifetime of peroxyl radicals of poly(U), poly(A) and single-and double-stranded DNA and the rate of their reaction with thiols

Peroxyl radicals of poly(U), poly(A), and single- and double-stranded DNA have been produced by photolysing H2O2 in oxygenated aqueous solution in presence of the substrates. The peroxyl radicals are formed by the reaction of OH radicals with the polynucleotides followed by addition of oxygen. The lifetime of the peroxyl radicals and the rate constant of their reactions with the thiols cysteamine, glutathione and dithiothreithol have been measured by time-resolved e.s.r. spectroscopy. The unusually long lifetimes range from 0.2 to 3.3 s. The activation energy for the decay for all four substrates is 10.3 +/- 1 kcal/mol (43 kJ mol-1). The reaction rate constants with the thiols range from k = 0.8 X 10(4) to 1.3 X 10(5) dm3 mol-1 s-1. The reactions of the thiols with the peroxyl radical of poly(U) are known to prevent strand break formation. This shows that the peroxyl radicals of poly(U) observed by e.s.r. are intermediates in the pathway leading to strand break formation.     

Equilibrium and kinetic studies on the binding of gluconolactone to almond beta-glucosidase in the absence and presence of glucose

The binding of glucono-1,5-lactone (gluconolactone) with almond beta-glucosidase was studied at pH 5.0 and 25 degrees C, in the absence and presence of glucose, by monitoring the enzyme fluorescence as a probe. From the results of fluorometric titration, the dissociation constant Kd and the maximum fluorescence intensity increase (percent) of the enzyme-gluconolactone complex relative to the enzyme alone, delta Fmax, were determined to be 12.7 microM and 14.7%, respectively. From the study of the temperature dependence of Kd, delta G degrees, delta H degrees and delta S degrees for the binding were evaluated to be -6.7 kcal mol-1, -3.5 kcal mol-1, and 10.8 e.u. (cal mol-1 deg-1), respectively, at 25 degrees C. The analysis of the fluorometric titration data in the presence of glucose revealed that these ligands bind competitively to the enzyme, probably at the same site. The results of a stopped-flow kinetic study are consistent with the following two-step mechanism: (formula; see text) which indicates that gluconolactone (L) and the enzyme (E) transiently form a loosely bound complex, ELtr (k-1/k+1 = 4.5 mM), in the first rapid bimolecular association step, and ELtr is converted into a more tightly bound complex EL (k+2 = 94 s-1, k-2 = 0.36 s-1) in the subsequent slow unimolecular process. The fluorescence intensity increase occurs solely in the latter step.     

Photoactive yellow protein from the purple phototrophic bacterium, Ectothiorhodospira halophila. Quantum yield of photobleaching and effects of temperature, alcohols, glycerol, and sucrose on kinetics of photobleaching and recovery.

A water-soluble yellow protein from E. halophila was previously shown to be photoactive (Meyer, T. E., E. Yakali, M. A. Cusanovich, and G. Tollin. 1987. Biochemistry. 26:418-423). Pulsed laser excitation in the protein visible absorption band (maximum at 445 nm) causes a rapid bleach of color (k = 7.5 x 10(3) s-1) followed by a slower dark recovery (k = 2.6 s-1). This is analogous to the photocycle of sensory rhodopsin II from Halobacterium (which also has k = 2.6 s-1 for recovery). We have now determined the quantum yield of the photobleaching process to be 0.64, which is comparable with that of bacteriorhodopsin (0.25), and is thus large enough to be biologically significant. Although the photoreactions of yellow protein were previously shown to be relatively insensitive to pH, ionic strength and the osmoregulator betaine, the present experiments demonstrate that temperature, glycerol, sucrose, and various alcohol-water mixtures strongly influence the kinetics of photobleaching and recovery. The effect of temperature follows normal Arrhenius behavior for the bleach reaction (Ea = 15.5 kcal/mol). The rate constant for the recovery reaction increases with temperature between 5 degrees C and 35 degrees C, but decreases above 35 degrees C indicating alternate conformations with differing kinetics. There is an order of magnitude decrease in the rate constant for photobleaching in both glycerol and sucrose solutions that can be correlated with the changes in viscosity. We conclude from this that the protein undergoes a conformational change as a consequence of the photoinduced bleach. Recovery kinetics are affected by glycerol and sucrose to a much smaller extent and in a more complicated manner.(ABSTRACT TRUNCATED AT 250 WORDS)     

Recruitment of both uniform and differential binding energy in enzymatic catalysis: xylanases from families 10 and 11

The contributions of enzyme-substrate hydrogen-binding interactions to catalysis by two different families of xylanases were evaluated through kinetic studies with two representative wild-type enzymes, Cellulomonas fimi xylanase (Cex) and Bacillus circulans xylanase (Bcx), on a series of monodeoxygenated and monodeoxyfluorinated p-nitrophenyl xylobioside substrates. Effects of substitution in the distal (-2 subsite) sugar on kcat/Km for Cex were moderately large (up to 2.9 kcal mol-1), with no effect seen on kcat. By contrast, substantial effects upon both kcat and kcat/Km were seen for substrates modified in the proximal (-1 subsite) sugar. Very similar results were obtained with Bcx. Kinetic analyses with a series of eight mutants of Cex in which active site residues interacting with the substrate were mutated yielded complementary insights. Again, interactions with the distal (-2) sugar were seen to contribute substantially to kcat/Km (up to 3.7 kcal mol-1), thus to the formation of the glycosyl-enzyme intermediate, but not to kcat, thus to the hydrolysis of the glycosyl-enzyme. Interactions with the proximal (-1) sugar are much more significant, contributing up to 6.7 kcal mol-1 to both kcat/Km and kcat. These results together indicate that interactions with the distal sugar maintain similar magnitudes in the transition states for glycosylation and deglycosylation as well as in the glycosyl-enzyme intermediate and can be referred to as "uniform binding interactions" in the parlance of Albery and Knowles (Albery, W. J., and Knowles, J. R. (1976) Biochemistry 15, 5631-5640). Interactions with the proximal sugar are considerably stronger at the deglycosylation transition state than in the intermediate, and fall into the category of differential binding interactions. This behavior likely has its origins in the changes in ring conformation of the proximal sugar but not of the distal sugar between the ground state and the reaction transition state. Correlation of these individual interaction energies with the hydrogen-bonding pattern seen in the glycosyl-enzyme intermediate allows for the assignment of hydrogen-bond strengths to each interaction, with good correlation between the two approaches. These findings are relevant to the discussion of remote binding effects upon enzymatic catalysis.     

Model studies for the direct effect of high-energy irradiation on DNA. Mechanism of strand break formation induced by laser photoionization of poly U in aqueous solution

Laser flash photolysis of polyuridylic acid (poly U) in anoxic aqueous solutions leads to biphotonic photoionization of the uracil moiety followed by the formation of single strand breaks (ssb). The rate constant for ssb formation (1.0 s-1, obtained from the slow component of conductivity increase at 23 degrees C and pH 6.8) increases with decreasing pH to 235 s-1 at pH 3.5. The activation energy (pre-exponential factor) was measured to be 66 kJ mol-1 (5 X 10(11) s-1) at pH 6.8. Addition of dithiothreitol (DTT) or glutathione (GSH) prevents ssb formation by reacting with a poly U intermediate (rate constant = 1.2 X 10(6) and 0.16 X 10(6) dm3 mol-1 s-1, respectively). Since with OH radicals as initiators very similar data have been obtained for the kinetics of ssb formation and for the reaction with DTT, we conclude that photoionization of the uracil moiety in poly U leads eventually to the same chemical pathway for ssb formation as that induced by OH radicals. Furthermore, we propose that protection by DTT and GSH occurs via H donation to the C-4' radicals of the sugar moiety of DNA and to the C-4' and the C-2' radicals of poly U.