Temperature effects on the catalytic activity of the D38E mutant of 3-oxo-Delta5-steroid isomerase: favorable enthalpies and entropies of activation relative to the nonenzymatic reaction catalyzed by acetate ion

3-oxo-Delta5-steroid isomerase (ketosteroid isomerase, KSI) catalyzes the isomerization of 5-androstene-3,17-dione (1) to 4-androstene-3,17-dione (3) via a dienolate intermediate (2-). KSI catalyzes this conversion about 13 orders of magnitude faster than the corresponding reaction catalyzed by acetate ion, a difference in activation energy (DeltaG) of approximately 18 kcal/mol. To evaluate whether the decrease in DeltaG by KSI is due to enthalpic or entropic effects, the activation parameters for the isomerization of 1 catalyzed by the D38E mutant of KSI were determined. A linear Arrhenius plot of kcat/KM versus 1/T gives the activation enthalpy (DeltaH = 5.9 kcal/mol) and activation entropy (TDeltaS = -2.6 kcal/mol). Relative to catalysis by acetate, D38E reduces DeltaH by approximately 10 kcal/mol and increases TDeltaS by approximately 5 kcal/mol. The activation parameters for the microscopic rate constants for D38E catalysis were also determined and compared to those for the acetate ion-catalyzed reaction. Enthalpic stabilization of 2- and favorable entropic effects in both chemical transition states by D38E result in an overall energetically more favorable enzymatic reaction relative to that catalyzed by acetate ion.     

Enzymes do what is expected (chalcone isomerase versus chorismate mutase)

Madicago sativa chalcone isomerase (CI) catalyzes the isomerization of chalcone to flavanone, whereas E. coli chorismate mutase (CM) catalyzes the pericyclic rearrangement of chorismate to prephenate. Covalent intermediates are not formed in either of the enzyme-catalyzed reactions, K(M) and k(cat) are virtually the same for both enzymes, and the rate constants (k(o)) for the noncatalyzed reactions in water are also the same. This kinetic identity of both the enzymatic and the nonenzymatic reactions is not shared by a similarity in driving forces. The efficiency (DeltaG(o)() - DeltaG(cat)()) for the CI mechanism involves transition-state stabilization through general-acid catalysis and freeing of three water molecules trapped in the E.S species. The contribution to lowering DeltaG(cat)() by an increase in near attack conformer (NAC) formation in E.S as compared to S in water is not so important. In the CM reaction, the standard free energy for NAC formation in water is 8.4 kcal/mol as compared to 0.6 kcal/mol in E.S. Because the value of (DeltaG(o)() - DeltaG(cat)()) is 9 kcal/mol, the greater percentage of NACs accounts for approximately 90% of the kinetic advantage of the CM reaction. There is no discernible transition-state stabilization in the CM reaction. These results are discussed. In anthropomorphic terms, each enzyme has had to do what it must to have a biologically relevant rate of reaction.     

The mechanism of base-promoted HF elimination from 4-fluoro-4-(4-nitrophenyl)butan-2-one is E1cB. evidence from double isotopic fractionation experiments

Leaving-group fluorine and secondary deuterium multiple kinetic isotope effects (KIEs) have been determined for the base-promoted HF elimination from the 4-fluoro-4-(4'-nitrophenyl)-(1,1,1,3,3-(2)H(5))butan-2-one. The fluorine KIE was determined by using the accelerator-produced short-lived radionuclide (18)F in combination with the naturally abundant (19)F. The (19)F substrate was labeled with (14)C in a remote position to enable radioactivity measurements of both substrates. The size of the determined fluorine KIE is 1.0009 +/- 0.0010 when acetate is used as base. The secondary deuterium KIEs are 1.009 +/- 0.017, 1.000 +/- 0.018, and 1.010 +/- 0.023 for formate, acetate, and imidazole, respectively. The magnitudes of these KIEs are significantly smaller compared to the corresponding KIEs that we recently reported for the protic substrate. This new data clearly demonstrates that the elimination proceeds via an E1cB mechanism.     

Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta5-3-ketosteroid isomerase: the catalytic diad versus the cooperative hydrogen bond mechanism

To further understand Delta(5)-3-ketosteroid isomerase (KSI) catalysis, we carried out molecular dynamics (MD) simulations of the KSI dimer ligated with a substrate and reaction intermediate analogue and high level ab initio calculations on relevant enzymatic reaction models. Simulation of the enzyme-substrate complex dimer systems showed asymmetric dynamics between the two monomers, in which the hydrogen bond pattern between the substrate and active site residues in the first and the second subunits supported the cooperative hydrogen bond (CH) and the catalytic diad (CD) mechanisms, respectively. On the other hand, only the CH mechanism was supported in the MD simulation of the enzyme-intermediate complex dimer. From MP2/6-31+G**//RHF/6-31G** calculations, we found the kinetic barriers for the two reaction mechanisms were similar. The CH route afforded a greater stabilization to the enolate intermediate than did the CD counterpart. Thus, the present computational studies indicate that the CH mechanism would be favored over the CD one in the catalytic action of KSI. However, the latter could not be ruled out conclusively because of the explicit appearance of a CD configuration in the MD trajectories of the enzyme-substrate complex and because of the similar intrinsic activation barrier for the CH and CD mechanisms. The appearance of configurations that favor the CD pathway is rationalized in terms of a model in which the KSI-substrate complex does not have a strong preference for one hydrogen bonding pattern over another, while the KSI-intermediate complex favors a cooperative hydrogen bond pattern in order to stabilize the reaction intermediate. This hypothesis is supported by the ab initio calculations which indicate that the CH intermediate is more stable than the CD one by approximately 6.3 kcal/mol.     

Gamma-linolenic acid biosynthesis: cryptoregiochemistry of delta6 desaturation

The valuable nutraceutical gamma-linolenic acid (GLA, (6Z,9Z,12Z)-octadecatrienoic acid) is biosynthesized by a series of regio- and stereoselective dehydrogenation reactions that are catalyzed by a set of enzymes known as fatty acid desaturases. As part of ongoing research into the mechanism of these remarkable catalysts, we have examined the cryptoregiochemistry (site of initial oxidation) of Delta6 desaturation as it occurs in the protozoan Tetrahymena thermophila. Two complementary approaches that address this issue are described. In the first set of experiments, we measured the individual primary deuterium kinetic isotope effects associated with the C-H bond cleavages at C-6 and C-7. Competition experiments using appropriately deuterium-labeled 4-thiasubstrates revealed that a large KIE (kH/kD = 7.1 +/- 0.5) was observed for the C-H bond-breaking step at C-6, whereas the C-H bond cleavage at C-7 was insensitive to deuterium substitution (kH/kD = 1.04 +/- 0.05). These results point to C-6 as the site of initial oxidation in Delta6 desaturation since the first chemical step in this type of reaction is rupture of a strong, unactivated C-H bond, an energetically difficult process that typically exhibits a large KIE. This conclusion was supported by the results of our second approach, which involved locating the position of the putative diiron oxo oxidant with respect to substrate by monitoring the efficiency of oxo transfer to a series of thia fatty acid probes. Thus only a 6-thia-analogue is converted to significant amounts of the corresponding sulfoxide (9% yield). The absolute configuration of this product was determined to be S using (S)-MPAA as a chiral shift reagent. Taken together, these results point to the abstraction of the C-6 pro S hydrogen as the initial event in Delta6 desaturation as it occurs in T. thermophila.     

Turnover is rate-limited by deglycosylation for Micromonospora viridifaciens sialidase-catalyzed hydrolyses: conformational implications for the Michaelis complex

A panel of seven isotopically substituted sialoside natural substrate analogues based on the core structure 7-(5-acetamido-3,5-dideoxy-d-glycero-α-d-galacto-non-2-ulopyranosylonic acid)-(2→6)-β-D-galactopyranosyloxy)-8-fluoro-4-methylcoumarin (1, Neu5Acα2,6GalβFMU) have been synthesized and used to probe the rate-limiting step for turnover by the M. viridifaciens sialidase. The derived kinetic isotope effects (KIEs) on k(cat) for the ring oxygen ((18)V), leaving group oxygen ((18)V), anomeric carbon ((13)V), C3-carbon ((13)V), C3-R deuterium ((D)V(R)), C3-S deuterium ((D)V(S)), and C3-dideuterium ((D)(2)V) are 0.986 ± 0.003, 1.003 ± 0.005, 1.021 ± 0.006, 1.001 ± 0.008, 1.029 ± 0.007, 0.891 ± 0.008, and 0.890 ± 0.006, respectively. The solvent deuterium KIE ((D(2)O)V) for the sialidase-catalyzed hydrolysis of 1 is 1.585 ± 0.004. In addition, a linear proton inventory was measured for the rate of hydrolysis, under saturating condition, as a function of n, the fraction of deuterium in the solvent. These KIEs are compatible with rate-determining cleavage of the enzymatic tyrosinyl β-sialoside intermediate. Moreover, the secondary deuterium KIEs are consistent with the accumulating Michaelis complex in which the sialosyl ring of the carbohydrate substrate is in a (6)S(2) skew boat conformation. These KIE measurements are also consistent with the rate-determining deglycosylation reaction occurring via an exploded transition state in which synchronous charge delocalization is occurring onto the ring oxygen atom. Finally, the proton inventory and the magnitude of the solvent KIE are consistent with deglycosylation involving general acid-catalyzed protonation of the departing tyrosine residue rather than general base-assisted attack of the nucleophilic water.     

Quantum dynamics of hydride transfer catalyzed by bimetallic electrophilic catalysis: synchronous motion of Mg(2+) and H(-) in xylose isomerase

Xylose isomerase exhibits a bridged-bimetallic active-site motif in which the substrate is bound to two metals connected by a glutamate bridge, and X-ray crystallographic studies suggest that metal movement is involved in the hydride transfer rate-controlling catalytic step. Here we report classical/quantal dynamical simulations of this step that provide new insight into the metal motion. The potential energy surface is calculated by treating xylose with semiempirical molecular orbital theory augmented by a simple valence bond potential and the rest of the system by molecular mechanics. The rate constant for the hydride-transfer step was calculated by ensemble-averaged dynamical simulations including both variational transition-state theory for determination of the statistically averaged dynamical bottleneck and optimized multidimensional tunneling calculations. The dynamics calculations include 25 317 atoms, with quantized vibrational free energy in 89 active-site degrees of freedom, and with 32 atoms moving through static secondary zone transition-state configurations in the quantum tunneling simulation. Our simulations show that the average Mg-Mg distance R increases monotonically as a function of the hydride-transfer progress variable z. The range of the average R along the reaction path is consistent with the X-ray structure, thus providing a dynamical demonstration of the postulated role of Mg in catalysis. We also predicted the primary deuterium kinetic isotope effect (KIE) for the chemical step. We calculated a KIE of 3.8 for xylose at 298 K, which is consistent with somewhat smaller experimentally observed KIEs for glucose substrate at higher temperatures. More than half of our KIE is due to tunneling; neglecting quantum effects on the reaction coordinate reduces the calculated KIE to 1.8.     

Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase

Prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (KSI) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to KSI catalysis. But these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potentially exaggerating the apparent energetic benefit of the hydrogen bonds relative to water-mediated hydrogen bonds in solution. We determined the functional and structural consequences of substituting the oxyanion hole hydrogen bond donors and several residues surrounding the oxyanion hole with smaller residues in an attempt to create a local site that would provide interactions more analogous to those in aqueous solution. These more drastic mutations created an active-site cavity estimated to be ~650 ?(3) and sufficient for occupancy by 15-17 water molecules and led to a rate decrease of only ~10(3)-fold for KSI from two different species, a much smaller effect than that observed from more traditional conservative mutations. The results underscore the strong context dependence of hydrogen bond energetics and suggest that the oxyanion hole provides an important, but moderate, catalytic contribution relative to the interactions in the corresponding solution reaction.     

A mechanistic study of the alkaline hydrolysis of diaryl sulfate diesters

Nearly all of the reported studies of reactions of sulfate diesters are for dialkyl or alkyl aryl diesters, which undergo reaction by carbon-oxygen bond fission. Sulfuryl transfer reactions of sulfate diesters (RO-SO(2)-OR') proceeding by attack at sulfur have been little explored. When both ester groups are aryl groups the hydrolysis reaction (sulfuryl transfer to water) occurs by way of attack at sulfur. The alkaline hydrolysis of diaryl sulfate diesters was shown to obey first-order kinetics with respect to [(-)OH] and proceed through S-O bond fission, in a mechanism that is most likely concerted. Activation parameters for 4-chloro-3-nitrophenyl phenyl sulfate and 4-nitrophenyl phenyl sulfate gave the following respective values: Delta H(++) = 88.0 +/- 0.1 and 84.83 +/- 0.06 kJ mol(-)(1) and Delta S(++) = -37 +/- 1 and -50.2 +/- 0.5 J mol(-)(1) deg(-)(1). The dependence of the second-order rate constant for hydrolysis on leaving group pK(a) was analyzed giving a beta(lg) slope of -0.7 +/- 0.2 and a Leffler alpha parameter value of 0.36. A (15)k kinetic isotope effect (KIE) for the hydroxide attack on 4-nitrophenyl phenyl sulfate of 1.0000 +/-0.0005 and an (18)k(lg) KIE value of 1.003+/-0.002 were obtained.     

Comparison of enzymatic and non-enzymatic nitroethane anion formation: thermodynamics and contribution of tunneling

In the reaction of nitroalkane oxidase (NAO), the oxidation of nitroalkanes to the corresponding aldehydes or ketones is initiated by the deprotonation of the neutral nitroalkane. The energetics of nitroethane ionization for both the enzymatic and non-enzymatic reactions have been determined by measuring rate constants as a function of temperature. At 25 degrees C, the rate constant for the acetate-catalyzed reaction is a billionfold smaller than the kcat/Km value for NAO. This corresponds to a difference of 12.3 kcal/mol in the free energy of activation that is largely due to a difference in the activation enthalpy. Analysis of the temperature dependence of the deuterium kinetic isotope effects on the reactions yields similar DeltaEa and AH/AD values for the acetate, phosphate, and NAO-catalyzed reactions that fall within the semiclassical limits, consistent with similar contributions of tunneling to the enzymatic and non-enzymatic reactions.     

Activation enthalpies and entropies for the microscopic rate constants of acetate-catalyzed isomerization of 5-androstene-3,17-dione

Both acetic acid and acetate catalyze the isomerization of 5-androstene-3,17-dione (1) to its conjugated isomer, 4-androstene-3,17-dione (3), through a dienol(ate) intermediate. The temperature dependence of the overall isomerization rate constants and of the microscopic rate constants for this isomerization was determined, and the Arrhenius plots give the activation enthalpy and entropy for each step. The source of the activation energy for the overall isomerization and for each of the individual steps is predominantly enthalpic, with a moderate to low entropic penalty. Additionally, the entropy and enthalpy for the keto-enol equilibrium of 1 and dienol were determined; this equilibrium is entirely controlled by enthalpy with no entropic contribution. The relevance of these results to the mechanism of the isomerization of 1 catalyzed by the enzyme 3-oxo-Delta(5)-steroid isomerase is discussed.     

Milieux hyperacides—XXIII: Isomerisation dienone-phenol et phenol-phenol en serie steroide. mise en evidence d'un intermediaire reactionnel

In the hyperacid medium HF-SbF₅, 3,17-dione androst-1,4-diene leads first to the expected 1-methyl estrone and 1-hydroxy 4-methyl estra-1,3,5(10)-triene-17-one in a 9:1 ratio. In a second step, 1-methyl estrone isomerises to the more stable 1-methyl(8α, 14β)estrone. Kinetic studies show the influence of anion structure on the rate of the Al step. The mechanism of the phenol-phenol isomerisation is substantiated through trapping the short-lived species involved in the reaction by hydrogen (or deuterium) donor. This reduction gives 1-methyl (5βH or D) estr-1-en-3,17-dione setting up a mechanism involving C-para (C-10) and C-ortho (C-4) diprotonation of the aromatic ring.     

A computational study of the effect of bending on secondary kinetic isotope effects in SN2 transition states

Using conventional transition state theory, the secondary deuterium kinetic isotope effect (KIE) in the inversion SN2 reaction of CH3F and F- is calculated to be small, 0.98 (T = 298 K). This is shown to be the result of a balance among opposing entropy and enthalpy terms. By contrast, KIE in the retention SN2 mechanism is calculated to be large (1.5). Accordingly, KIE is a potential observable for discriminating between the two mechanisms. Large KIE's are also found for the inversion and retention mechanisms of the ion pair reactions between CH3F and LiF. All of the transition structures leading to large KIE's have a bent FCF angle and an imaginary frequency that is sensitive to deuterium labeling.     

Secondary kinetic isotope effect on the photoenolization of triplet o-methylanthrones. A microcanonical transition state theory calculation

The energy profile for the tautomerization reaction of 1,4-dimethylanthrone in the first triplet electronic state obtained through electronic calculations (B3LYP/ 6-31G(d)) is used to calculate the rate constants for the process at a wide range of energies using a modified RRKM microcanonical statistical formalism that takes into account tunneling. Through partial or total substitution of the hydrogen atoms of the methyl groups by deuterium atoms, it is possible to evaluate different primary and secondary kinetic isotope effects (KIE). These results can be compared with experimental data for these processes taking place in solid matrix at extremely low temperatures (4-50 K). Such a comparison allows us to conclude that the reaction is taking place at energies just slightly below (around 0.5 kcal/mol) the adiabatic potential energy barrier, a result that was previously found for other related molecules so that this mechanism may be extended to the photoenolization of other o-aryl methyl ketones. Analysis of the different factors contributing to the primary and secondary KIEs discloses that at energies not far below the adiabatic barrier, the tunneling effect is not the only factor that accounts for the large KIE but the differences in the energy level distribution upon isotopic substitution may be the predominant factor at a certain range of negative energies (this is especially so for the case of primary KIE). At positive energies (above the barrier) the levels factor is always the dominant factor in the total KIE.     

Probing the transition states of four glucoside hydrolyses with 13C kinetic isotope effects measured at natural abundance by NMR spectroscopy

Kinetic isotope effects (KIEs) were measured for methyl glucoside (4) hydrolysis on unlabeled material by NMR. Twenty-eight (13)C KIEs were measured on the acid-catalyzed hydrolysis of alpha-4 and beta-4, as well as enzymatic hydrolyses with yeast alpha-glucosidase and almond beta-glucosidase. The 1-(13)C KIEs on the acid-catalyzed reactions of alpha-4 and beta-4, 1.007(2) and 1.010(6), respectively, were in excellent agreement with the previously reported values (1.007(1), 1.011(2): Bennet and Sinnott, J. Am. Chem. Soc. 1986, 108, 7287). Transition state analysis of the acid-catalyzed reactions using the (13)C KIEs, along with the previously reported (2)H KIEs, confirmed that both reactions proceed with a stepwise D(N)A(N) mechanism and showed that the glucosyl oxocarbenium ion intermediate exists in an E(3) sofa or (4)H(3) half-chair conformation. (13)C KIEs showed that the alpha-glucosidase reaction also proceeded through a D(N)*A(N) mechanism, with a 1-(13)C KIE of 1.010(4). The secondary (13)C KIEs showed evidence of distortions in the glucosyl ring at the transition state. For the beta-glucosidase-catalyzed reaction, the 1-(13)C KIE of 1.032(1) demonstrated a concerted A(N)D(N) mechanism. The pattern of secondary (13)C KIEs was similar to the acid-catalyzed reaction, showing no signs of distortion. KIE measurement at natural abundance makes it possible to determine KIEs much more quickly than previously, both by increasing the speed of KIE measurement and by obviating the need for synthesis of isotopically labeled compounds.     

Hydride reduction of NAD+ analogues by isopropyl alcohol: kinetics, deuterium isotope effects and mechanism

Observed pseudo-first-order rate constants (k(obs)) of the hydride-transfer reactions from isopropyl alcohol (i-PrOH) to two NAD(+) analogues, 9-phenylxanthylium ion (PhXn(+)) and 10-methylacridinium ion (MA(+)), were determined at temperatures ranging from 49 to 82 degrees C in i-PrOH containing various amounts of AN or water. Formations of the alcohol-cation ether adducts (ROPr-i) were observed as side equilibria. The equilibrium constants for the conversion of PhXn(+) to PhXnOPr-i in i-PrOH/AN (v/v = 1) were determined, and the equilibrium isotope effect (EIE = K(i-PrOH)/K(i-PrOD)) at 62 degrees C was calculated to be 2.67. The k(H) of the hydride-transfer step for both reactions were calculated on the basis of the k(obs) and K. The corresponding deuterium kinetic isotope effects (e.g., KIE(OD)(H) = k(H)(i-PrOH)/k(H)(i-PrOD) and KIE(beta-D6)(H) = k(obs)(i-PrOH)/k(obs)((CD3)2CHOH)), as well as the activation parameters, were derived. For the reaction of PhXn(+) (62 degrees C) and MA(+) (67 degrees C), primary KIE(alpha-D)(H) (4.4 and 2.1, respectively) as well as secondary KIE(OD)(H) (1.07 and 1.18) and KIE(beta-D6)(H) (1.1 and 1.5) were observed. The observed EIE and KIE(OD)(H) were explained in terms of the fractionation factors for deuterium between OH and OH(+)(OH(delta+)) sites. The observed inverse kinetic solvent isotope effect for the reaction of PhXn(+) (k(obs)(i-PrOH)/k(obs)(i-PrOD) = 0.39) is consistent with the intermolecular hydride-transfer mechanism. The dramatic reduction of the reaction rate for MA(+), when the water or i-PrOH cosolvent was replaced by AN, suggests that the hydride-transfer T.S. is stabilized by H-bonding between O of the solvent OH and the substrate alcohol OH(delta+). This result suggests an H-bonding stabilization effect on the T.S. of the alcohol dehydrogenase reactions.     

Transition state analysis of Vibrio cholerae sialidase-catalyzed hydrolyses of natural substrate analogues

A series of isotopically labeled natural substrate analogues (phenyl 5-N-acetyl-α-d-neuraminyl-(2→3)-β-d-galactopyranosyl-(1→4)-1-thio-β-d-glucopyranoside; Neu5Acα2,3LacβSPh, and the corresponding 2→6 isomer) were prepared chemoenzymatically in order to characterize, by use of multiple kinetic isotope effect (KIE) measurements, the glycosylation transition states for Vibrio cholerae sialidase-catalyzed hydrolysis reactions. The derived KIEs for Neu5Acα2,3LacβSPh for the ring oxygen ((18)V/K), leaving group oxygen ((18)V/K), C3-S deuterium ((D)V/K(S)) and C3-R deuterium ((D)V/K(R)) are 1.029 ± 0.002, 0.983 ± 0.001, 1.034 ± 0.002, and 1.043 ± 0.002, respectively. In addition, the KIEs for Neu5Acα2,6βSPh for C3-S deuterium ((D)V/K(S)) and C3-R deuterium ((D)V/K(R)) are 1.021 ± 0.001 and 1.049 ± 0.001, respectively. The glycosylation transition state structures for both Neu5Acα2,3LacβSPh and Neu5Acα2,6LacβSPh were modeled computationally using the experimental KIE values as goodness of fit criteria. Both transition states are late with largely cleaved glycosidic bonds coupled to pyranosyl ring flattening ((4)H(5) half-chair conformation) with little or no nucleophilic involvement of the enzymatic tyrosine residue. Notably, the transition state for the catalyzed hydrolysis of Neu5Acα2,6βSPh appears to incorporate a lesser degree of general-acid catalysis, relative to the 2,3-isomer.     

Unusual observations during steroid analysis

In September 2005, our laboratory detected the presence of 4-androstene-3,17-dione and androsterone in a standard steroid screen of a post-race gelding urine sample received from an overseas authority. All other urine samples from the same batch tested negative. Subsequent gas chromatography/mass spectrometry (GC/MS) confirmatory analyses, however, repeatedly failed to detect any amount of 4-androstene-3,17-dione and androsterone in the suspicious sample. On the other hand, identical results were obtained when the initial GC/MS screening method was repeated on the suspicious sample as well as on the other samples of the same batch, showing the presence of 4-androstene-3,17-dione and androsterone only in the suspicious sample. These unusual and contradictory findings between the screening and confirmatory procedures were investigated, leading to the unequivocal conclusion that the 4-androstene-3,17-dione and androsterone observed during screening were artefacts from the internal standards, [16,16,17-d3]-testosterone and [16,16,17-d3]-5alpha-androstane-3alpha,17beta-diol. The two deuterated internal standards were thought to have undergone first an enzymatic oxidation of the 17beta-hydroxyl group to a 17-keto function by the enzyme 17beta-hydroxysteroid dehydrogenase; complete deuterium-hydrogen exchange at C16 during the methanolysis deconjugation step would then produce the two artefacts. The findings from this study highlight the potential problem of using internal standards in qualitative confirmatory analyses, which may lead to undesirable false positive results.     

Formation of the active species of cytochrome p450 by using iodosylbenzene: a case for spin-selective reactivity

The generation of the active species for the enzyme cytochrome P450 by using the highly versatile oxygen surrogate iodosylbenzene (PhIO) often produces different results compared with the native route, in which the active species is generated through O(2) uptake and reduction by NADPH. One of these differences that is addressed here is the deuterium kinetic isotope effect (KIE) jump observed during N-dealkylation of N,N-dimethylaniline (DMA) by P450, when the reaction conditions change from the native to the PhIO route. The paper presents a theoretical analysis targeted to elucidate the mechanism of the reaction of PhIO with heme, to form the high-valent iron-oxo species Compound I (Cpd I), and define the origins of the KIE jump in the reaction of Cpd I with DMA. It is concluded that the likely origin of the KIE jump is the spin-selective chemistry of the enzyme cytochrome P450 under different preparation procedures. In the native route, the reaction proceeds via the doublet spin state of Cpd I and leads to a low KIE value. PhIO, however, diverts the reaction to the quartet spin state of Cpd I, which leads to the observed high KIE values. The KIE jump is reproduced here experimentally for the dealkylation of N,N-dimethyl-4-(methylthio)aniline, by using intra-molecular KIE measurements that avoid kinetic complexities. The effect of PhIO is compared with N,N-dimethylaniline-N-oxide (DMAO), which acts both as the oxygen donor and the substrate and leads to the same KIE values as the native route.     

Deep tunneling dominates the biologically important hydride transfer reaction from NADH to FMN in morphinone reductase

The temperature dependence of the primary kinetic isotope effect (KIE), combined temperature-pressure studies of the primary KIE, and studies of the alpha-secondary KIE previously led us to infer that hydride transfer from nicotinamide adenine dinucleotide to flavin mononucleotide in morphinone reductase proceeds via environmentally coupled hydride tunneling. We present here a computational analysis of this hydride transfer reaction using QM/MM molecular dynamics simulations and variational transition-state theory calculations. Our calculated primary and secondary KIEs are in good agreement with the corresponding experimental values. Although the experimentally observed KIE lies below the semiclassical limit, our calculations suggest that approximately 99% of the reaction proceeds via tunneling: this is the first "deep tunneling" reaction observed for hydride transfer. We also show that the dominant tunneling mechanism is controlled by the isotope at the primary rather than the secondary position: with protium in the primary position, large-curvature tunneling dominates, whereas with deuterium in this position, small-curvature tunneling dominates. Also, our study is consistent with tunneling being preceded by reorganization: in the reactant, the rings of the nicotinamide and isoalloxazine moieties are stacked roughly parallel to each other, and as the system moves toward a "tunneling-ready" configuration, the nicotinamide ring rotates to become almost perpendicular to the isoalloxazine ring.