Transition-state structure for a conformation change of ribonuclease

The rate constants k₁₂ⁿ for isomerization of the E₁H isomer (pK_a 8 in H₂O) of ribonuclease-A to the E₂H isomer (pK_a = 6.1 in H₂O), determined from proton-uptake measurements by the temperature-jump technique, in mixtures of protium and deuterium oxides (atom fraction of deuterium n), are described by the equation k₁₂ⁿ = (733 ± 16)(1 − n + [0.46 ± 0.04]n)(1 − n + 0.69n)²sec⁻¹ at 25°C. On the basis of the absolute magnitude of the rate constant, the magnitude of the solvent isotope effect and the proton inventory, it appears that the rate-determining step is proton transfer to a water molecule from the imidazolium form of a histidine residue, with a product-like activated complex resembling a hydronium ion. The subsequent motion of the protein structure to generate the new isomer (conformation change) must then occur in a time approaching a vibrational period. Alternative but less likely mechanisms include rate-limiting protein reorganization concerted with proton transfer to water, rate-limiting diffusion of hydronium ion away from the enzyme, or “solvation catalysis” of protein reorganization.     

Determination of chemical biodegradation by direct and indirect methods

Summary Degradation of 10 organic chemicals by pre-acclimated microorganisms in BOD dilution water was determined directly by UV spectrophotometry and indirectly by a modified BOD method. Residual chemical concentrations were periodically measured and pseudo-first-order biodegradation rate constants (k ₁) were calculated. Thek ₁ spectrophotometry values ranged from 0.006/h to 0.077/h andk ₁-BOD values from 0.002/h to 0.043/h for 1-methylnaphthalene and indole, respectively. The ratios ofk spectrophotometry to k₁-BOD were between 1.5 for salicylic acid and 3.0 for 1-methylnaphthalene with a mean of 2.7. A significant (=0.001) linear correlation (r ²=0.854,F=46.630) existed between the two sets of rate constants. Results from this study suggest that the modified BOD method may be used to estimate chemical biodegradation rates in synthetic media.     

Cation binding to β-casein. a comparison of electrostatic models

The binding of cations of β-casein at pH 6.6 was considered previously. Available for three sodium concentiations, I = 0.04, 0.08, or 0.16 M are: [1] proton releases between I and [2] for each I, as calcium activity is increased, correlated sequences of monomer net charge, proton release, site bound calcium and protein Solvation- Models for ion binding are examined. Critical considerations are the intrinsic binding constants between hydrogen[H], calcium[Ca] and sodium[Na] ions and phosphate[P] and caiboxyIate[C] sites, and the effects of electrostatic interaction between sites as influenced by spatial fixed charge distribution, ionic strength and dielectric constant [D]. Anticipated intrinsic binding constants are k_H,P^o = 3 × 10⁶, k_Ca,P^o = 120, k_Na,P^o = 1, k_H,C^o = 7 × 10⁴ and k_Ca,C^o = 5.6Distributed charge models, either surface or volume, are inadequate since any reasonable monomer size yields fixed charge densities requiring k_H,P^o and k_Ca,C^o which are too low when the maximum in D is 75. Also, with increasing calcium binding, calculated proton release is only 0.4 to 0.5 of that observed.Discrete charge models accept anticipated k^o and yield calculated sequences of calcium binding and proton release which are in good agreement with those observed provided that: (1) using the known amino acid sequence of the phosphate-containing acidic peptide portion of the molecule, pep tide fixed charge is distributed at the lowest I so as to minimize electrostatic free energy; (2) in the region of fixed charge, D is approximately 5; (3) the distances between peptide fixed charges decrease with increasing ionic strength or calcium binding and (4) while protein is in solution, the acidic peptide and the remainder of the molecule are essentially electrostatically independent.     

Detection of dynamic water molecules in a microcrystalline sample of the SH3 domain of α-spectrin by MAS solid-state NMR

Water molecules are a major determinant of protein stability and are important for understanding protein–protein interactions. We present two experiments which allow to measure first the effective T₂ decay rate of individual amide proton, and second the magnetization build-up rates for a selective transfer from H₂O to H^N using spin diffusion as a mixing element. The experiments are demonstrated for a uniformly ²H, ¹⁵N labeled sample of a microcrystalline SH3 domain in which exchangeable deuterons were back-substituted with protons. In order to evaluate the NMR experimental data, as X-ray structure of the protein was determined using the same crystallization protocol as for the solid-state NMR sample. The NMR experimental data are correlated with the dipolar couplings calculated from H₂O–H^N distances which were extracted from the X-ray structure of the protein. We find that the H^N T₂ decay rates and H₂O–H^N build-up rates are sensitive to distance and dynamics of the detected water molecules with respect to the protein. We show that qualitative information about localization and dynamics of internal water molecules can be obtained in the solid-state by interpretation of the spin dynamics of a reporter amide proton.     

Tryptophansynthase in Phycomyces blakesleeanus Teil I: Eigenschaften des Enzyms

Tryptophan synthase in Phycomyces blakesleeanus. Part I: Characterization of the enzyme. Tryptophan synthase was tested in light grown 5 days old cultures of Phycomyces blakesleeanus. The test was carried out only by reaction 3 (indole + serine → tryptophan + water) of the tryptophan synthase. The K_m values for the substrates indole and serine were found to be 1.3 × 10^-4M and 1.0 × 10^-2M. Two K_m values (1.5 × 10^-8M and 1.0 × 10^-6M) for pyridoxal 5′-phosphate could be calculated from a Lineweaver-Burk plot. The transformation of the Lineweaver-Burk plot into the Hill plot resulted in a straight line with a rise of 0.35 for pyridoxal 5′-phosphate. At higher concentrations the end product tryptophan and indole-3-acetic acid inhibit the tryptophan synthase in vitro.     

Thermodynamic analysis of the physical state of water during freezing in plant tissue, based on the temperature dependence of proton spin-spin relaxation

Multi-proton spin-echo images were collected from cold-acclimated winter wheat crowns (Triticum aestivum L.) cv. Cappelle Desprez at 400 MHz between 4 and ?4 °C. Water proton relaxation by the spin-spin (T2) mechanism from individual voxels in image slices was found to be mono-exponential. The temperature dependence of these relaxation rates was found to obey Arrhenius or absolute rate theory expressions relating temperature, activation energies and relaxation rates, Images whose contrast is proportional to the Arrhenius activation energy (E_a), Gibb's free energy of activation (ΔG^?), and the entropy of activation (ΔS^?) for water relaxation on a voxel basis were constructed by post-image processing. These new images exhibit contrast based on activation energies rather than rules of proton relaxation. The temperature dependence of water proton T₂ relaxation rates permits prediction of changes in the physical state of water in this tissue over modest temperature ranges. A simple model is proposed to predict the freezing temperature kof various tissue in wheat crowns. The average E_a and ΔH^? for water proton T₂ relaxation over the above temperature range in winter wheat tissue were ?6.4 ± 14.8 and ?8.6 ± 14.8kj mol^?1, respectively. This barrier is considerably lower than the E_a for proton translation in ice at 0°C, which is reported to be between 46.0 and 56.5 kj mol^?1     

Amiloride sensitivity of proton-conductive pathways in gastric and intestinal apical membrane vesicles

Summary Passive proton permeability of gastrointestinal apical membrane vesicles was determined. The nature of the pathways for proton permeation was investigated using amiloride. The rate of proton permeation (k _H ⁺ was determined by addition of vesicles (pH _i = 6.5) to a pH 8.0 solution containing acridine orange. The rate of recovery of acridine orange fluorescence after quenching by the acidic vesicles ranged from 4 × 10^–3 (gastric parietal cell stimulation-associated vesicles; SAV) and 5 × 10^–3 (duodenal brush-border membrane vesicles; dBBMV) to 11 × 10+^–3 sec^–1 (ileal BBMV; iBBMV). Amiloride, 0.03 and 0.1 mm, significantly reduced the rate of proton permeation in dBBMV and iBBMV, but not gastric SAV. The decreases in k _H ⁺ were proportionately greater in iBBMV as compared with dBBMV. The presence of Na⁺/H⁺ exchange was demonstrated in both dBBMV and iBBMV by proton-driven (pH _i < pH _o ) ²²Na⁺ uptake. Evidence was also sought for the conductive nature of pathways for proton permeation. Intravesicular acidification, again determined by quenching of acridine orange fluorescence, was observed during imposition of K⁺-diffusion potential ([K⁺] _i [K⁺ _o ). In dBBMV and iBBMV, intravesicular acidification was enhanced in the presence of the K⁺-ionophore valinomycin, indicating that the native K⁺ permeability is rate limiting. In the presence of valinomycin, the K⁺-diffusion potential drove BBMV intravesicular acidification to levels close to the electrochemical potential. In gastric SAV, acidification was not limited by the K⁺ permeability. Valinomycin was without effect, but the K⁺/H⁺ ionophore nigericin enhanced acidification in gastric SAV, illustrating the low proton permeability of these membranes. Amiloride, 0.03–1 mm, resulted in concentration-dependent reductions of K⁺-diffusion potential-driven acidification in dBBMV and iBBMV but not in gastric SAV. These data demonstrate that proton permeation in the three membrane types is rheogenic. The sensitivity of the proton-conductive pathways in intestinal BBMV to high concentrations of amiloride correlated with the presence of the Na⁺/H⁺ antiport and indicates that this transmembrane protein may represent a pathway for proton permeation.We thank Ruth Briggs for assistance with the Na/H exchange experiments. This work was supported by a grant from the Medical Research Council (G8418056CA).     

Synthesis and physicochemical characterization of a novel precursor for covalently bound macromolecular MRI contrast agents

 The ligand DOTASA was designed and synthesized in the aim of obtaining a kinetically and thermodynamically stable Gd(III) chelate which, through its uncoordinated carboxylate function, will provide an efficient pathway to couple the complex to bio- or macromolecules without affecting the coordination pattern of DOTA. Furthermore, it allows us to study the influence of an extra carboxylate arm on the parameters determining proton relaxivity in comparison to the commercial agent [Gd(DOTA)(H₂O)]^–. A combined variable-temperature ¹⁷O NMR, EPR and nuclear magnetic relaxation dispersion study on the Gd(III) chelate resulted in k ²⁹⁸ _ex=(6.3±0.2)×10⁶ s^–1 for the water exchange rate and τ²⁹⁸ _R=125±2 ps for the rotational correlation time. The slight increase in both k ²⁹⁸ _ex and τ²⁹⁸ _R, as compared to those for [Gd(DOTA)(H₂O)]^–, is attributed to the presence of the extra negative charge. The longer rotational correlation time results in a proton relaxivity of 5.03 mM^–1 s^–1 for [Gd(DOTASA)(H₂O)]^2–, which is approximately 30% higher than that for [Gd(DOTA)(H₂O)]^–. The increased water exchange rate of [Gd(DOTASA)(H₂O)]^2– has no consequence for proton relaxivity since this latter is exclusively limited by fast rotation for both complexes. However, for slowly rotating macromolecular agents, which contain a covalently coupled DOTASA unit instead of a coupled DOTA, this increased exchange rate will have a significant positive effect. Received: 31 December 1998 / Accepted: 4 March 1999     

Proton transfer and polarizability of hydrogen bonds in proteins coupled with conformational changes. I. Infrared investigation of poly(glutamic acid) with various N Bases

The nature of hydrogen bonds formed between carboxylic acid residues and histidine residues in proteins is studied by ir spectroscopy. Poly(glutamic acid) [(Glu)_n] is investigated with various monomer N bases. The position of the proton transfer equilibrium OH…?N ? O^?…?H⁺N is determined considering the bands of the carboxylic group. It is shown that largely symmetrical double minimum energy surfaces are present in the OH…?N ? O^?…?H⁺N bonds when the pK_a of the protonated N base is two values larger than that of the carboxylic groups of (Glu)_n. Hence OH…?N ? O^?…?H⁺N bonds between glutamic and aspartic acid residues and histidine residues in proteins may be easily polarizable proton transfer hydrogen bonds. The polarizability of these bonds is one to two orders of magnitude larger than usual electron polarizabilities; therefore, these bonds strongly interact with their environment. It is demonstrated that water molecules shift these proton transfer equilibria in favor of the polar proton boundary structure. The access of water molecules to such bonds in proteins and therefore the position of this proton transfer equilibrium is dependent on conformation. The amide bands show that (Glu)_n is α-helical with all systems. The only exception is the (Glu)_n-n-propylamine system. When this system is hydrated (Glu)_n is α-helical, too. When it is dried, however, (Glu)_n forms antiparallel β-structure. This conformational transition, dependent on degree of hydration, is reversible. An excess of n-propylamine has the same effect on conformation as hydration.     

Reversible addition of bisulfite buffer to the cytidine ring system

The rate constants for the reversible addition of protons and sulfite to the 5,6 double bond of cytidine and 3-methylcytidine have been spectrophotometrically measured under conditions (25°C, μ = 1.0 ) where the deamination of 5,6-dihydrocytidine-6-sulfonate is minimal. Both the addition and the elimination of sulfite from the ring system are subject to general catalysis of proton transfer. For the reaction in either direction, plots of the pseudo-firstorder rate constants against increasing buffer concentration are biphasic and indicative of at least a two-step reaction pathway with both steps being subject to general acid-base catalysis. Kinetic hydrogen-deuterium isotope effects were measured for both buffer-catalyzed steps of sulfite elimination from 3-methyl-5,6-dihydrocytidine-6-sulfonate and sulfite addition to 3-methylcytidine. Both H₂O and D₂O were used as solvent. For both the addition and the elimination of SO₃²⁻ values of k₂^H/k₂^D were 6.3–7.1 and 2.3–2.6 at low and high imidazole buffer concentration, respectively. The large isotope effects values in the range of 6–7 can be attributed to rate-determining proton transfer to carbon-5 of the cytidine ring system. The smaller values are more likely caused by proton transfer to a electronegative atom such as the oxygen on carbon-2 of the cytidine ring. The equilibrium constants for bisulfite buffer addition to 3-methylcytidine and cytidine at 25°C, μ = 1.0 , pH 7.2, are 10.2 and 1.3 ⁻¹, respectively.     

Kinetic study of aroxyl radical-scavenging action of vitamin E in membranes of egg yolk phosphatidylcholine vesicles

Vitamin E is localized in membranes and functions as an efficient inhibitor of lipid peroxidation in biological systems. In this study, we measured the reaction rates of vitamin E (α-, β-, γ-, δ-tocopherols, TocH) and tocol with aroxyl radical (ArO) as model lipid peroxyl radicals in membranes by stopped-flow spectrophotometry. Egg yolk phosphatidylcholine (EYPC) vesicles were used as a membrane model. EYPC vesicles were prepared in the aqueous methanol solution (MeOH:H₂O = 7:3, v/v) that gave the lowest turbidity in samples. The second-order rate constants (k_s) for α-TocH in MeOH/H₂O solution with EYPC vesicles were apparently 3.45 × 10⁵ M⁻¹ s⁻¹, which was about 8 times higher than that (4.50 × 10⁴ M⁻¹ s⁻¹) in MeOH/H₂O solution without EYPC vesicles. The corrected k_s of α-TocH in vesicles, which was calculated assuming that the concentration of α-TocH was 133 times higher in membranes of 10 mM EYPC vesicles than in the bulk MeOH/H₂O solution, was 2.60 × 10³ M⁻¹ s⁻¹, which was one-seventeenth that in MeOH/H₂O solution because of the lower mobility of α-TocH in membranes. Similar analyses were performed for other vitamin E analogues. The k_s of vitamin E in membranes increased in the order of tocol < δ-TocH < γ-TocH ∼ β-TocH < α-TocH. There was not much difference in the ratios of reaction rates in vesicles and MeOH/H₂O solution among vitamin E analogues [k_s(vesicle)/k_s (MeOH/H₂O) = 7.7, 10.0, 9.5, 7.4, and 5.1 for α-, β-, γ-, δ-TocH, and tocol, respectively], but their reported ratios in solutions of micelles and ethanol were quite different [k_s(micelle)/k_s(EtOH) = 100, 47, 41, 15, and 6.3 for α-, β-, γ-, δ-TocH, and tocol, respectively]. These results indicate that the reaction sites of vitamin E analogues were similar in vesicle membranes but depended on hydrophobicity in micelle membranes, which increased in the order of tocol < δ-TocH < γ-TocH ∼ β-TocH < α-TocH.     

Kinetics and mechanism of catalase action. Formation of the intermediate complex

The kinetics of formation of the intermediate complex between catalase and H₂O₂ has been reexamined. It has been shown that the kinetics consists of a rapid and of a subsequent slow phase. At the maximum of the transient decrement of the optical absorption, the system was found to be in a terminal state with regard to the rapid phase. On this basis, the formation curve of the intermediate complex was calculated. From the parameters of the curve the maximal saturation of catalase hematins (from horse erythrocytes) by H₂O₂ is 35%. The absolute spectrum of the intermediate complex was established. The variation of the previously calculated rate constant of formation of the intermediate complex was shown to be due to the inapplicability of the pre-steady-state approximation to the rate data. By applying a more general approach and by the use of a computer, the individual rate constants of the peroxidatic scheme were calculated (relevant to micromolar solutions of catalase) k₁ = (3.0 ± 0.2) × 10⁶ M^?1 sec^?1k₄ = (5.6 ± 0.3) × 10⁶ M^?1 sec^?1 These values are 2.2 times higher in a nanomolar solution.     

Efficient isotopic tryptophan labeling of membrane proteins by an indole controlled process conduct

A protocol for the efficient isotopic labeling of large G protein‐coupled receptors with tryptophan in Escherichia coli as expression host was developed that sufficiently suppressed the naturally occurring L‐tryptophan indole lyase, which cleaves tryptophan into indole, pyruvate, and ammonia resulting in scrambling of the isotopic label in the protein. Indole produced by the tryptophanase is naturally used as messenger for cell–cell communication. Detailed analysis of different process conducts led to the optimal expression strategy, which mimicked cell–cell communication by the addition of indole during expression. Discrete concentrations of indole and ¹⁵N₂‐L‐tryptophan at dedicated time points in the fermentation drastically increased the isotopic labeling efficiency. Isotope scrambling was only observed in glutamine, asparagine, and arginine side chains but not in the backbone. This strategy allows producing specifically tryptophan labeled membrane proteins at high concentrations avoiding the disadvantages of the often low yields of auxotrophic E. coli strains. In the fermentation process carried out according to this protocol, we produced ～15 mg of tryptophan labeled neuropeptide Y receptor type 2 per liter medium. Biotechnol. Bioeng. 2013; 110: 1681–1690. © 2013 Wiley Periodicals, Inc.     

Physicochemical and MRI characterization of Gd<Superscript>3+</Superscript>-loaded polyamidoamine and hyperbranched dendrimers

Generation 4 polyamidoamine (PAMAM) and, for the first time, hyperbranched poly(ethylene imine) or polyglycerol dendrimers have been loaded with Gd³⁺ chelates, and the macromolecular adducts have been studied in vitro and in vivo with regard to MRI contrast agent applications. The Gd³⁺ chelator was either a tetraazatetracarboxylate DOTA-pBn⁴⁻ or a tetraazatricarboxylate monoamide DO3A-MA³⁻ unit. The water exchange rate was determined from a ¹⁷O NMR and ¹H Nuclear Magnetic Relaxation Dispersion study for the corresponding monomer analogues [Gd(DO3A-AEM)(H₂O)] and [Gd(DOTA-pBn-NH₂)(H₂O)]⁻ (k _ex²⁹⁸ = 3.4 and 6.6 × 10⁶ s⁻¹, respectively), where H₃DO3A-AEM is {4-[(2-acetylaminoethylcarbamoyl)methyl]-7,10-bis(carboxymethyl-1,4,7,10-tetraazacyclododec-1-yl)}-acetic acid and H₄DOTA-pBn-NH₂ is 2-(4-aminobenzyl)-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid. For the macromolecular complexes, variable-field proton relaxivities have been measured and analyzed in terms of local and global motional dynamics by using the Lipari–Szabo approach. At frequencies below 100 MHz, the proton relaxivities are twice as high for the dendrimers loaded with the negatively charged Gd(DOTA-pBn)⁻ in comparison with the analogous molecule bearing the neutral Gd(DO3A-MA). We explained this difference by the different rotational dynamics: the much slower motion of Gd(DOTA-pBn)⁻-loaded dendrimers is likely related to the negative charge of the chelate which creates more rigidity and increases the overall size of the macromolecule compared with dendrimers loaded with the neutral Gd(DO3A-MA). Attachment of poly(ethylene glycol) chains to the dendrimers does not influence relaxivity. Both hyperbranched structures were found to be as good scaffolds as regular PAMAM dendrimers in terms of the proton relaxivity of the Gd³⁺ complexes. The in vivo MRI studies on tumor-bearing mice at 4.7 T proved that all dendrimeric complexes are suitable for angiography and for the study of vasculature parameters like blood volume and permeability of tumor vessels. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Intramolecular general base catalyzed transesterification: The cyclization of ethyl 2-hydroxymethylbenzoate and ethyl 2-hydroxymethyl 4-nitrobenzoate to phthalide and 5-nitrophthalide

The rates of cyclization of ethyl 2-hydroxymethylbenzoate to phthalide have been measured in H₂O at 30°C with μ = 0.5. There is pronounced general base catalysis in the reaction with β = 0.87. The second-order rate constant for imidazole general base catalysis is decreased in D₂O as compared with H₂O by a factor of 3.46. The pH-rate constant profile obtained by extrapolation to zero buffer concentration shows hydronium ion and apparent hydroxide ion catalysis. The value of the second-order rate constant k_OH is 10⁵ greater than k_OH for hydrolysis of ethyl benzoate. Ethyl 2-hydroxymethyl 4-nitrobenzoate cyclizes to 5-nitrophthalide in a similar manner. The Brönsted coefficient β for general base catalysis is 0.97, within error of unity. Thus, it is probable that general base catalysis involves rate-determining proton transfer.     

Cation binding to beta-casein. A comparison of electrostatic models

The binding of cations of β-casein at pH 6.6 was considered previously. Available for three sodium concentiations, I = 0.04, 0.08, or 0.16 M are: [1] proton releases between I and [2] for each I, as calcium activity is increased, correlated sequences of monomer net charge, proton release, site bound calcium and protein Solvation- Models for ion binding are examined. Critical considerations are the intrinsic binding constants between hydrogen[H], calcium[Ca] and sodium[Na] ions and phosphate[P] and caiboxyIate[C] sites, and the effects of electrostatic interaction between sites as influenced by spatial fixed charge distribution, ionic strength and dielectric constant [D]. Anticipated intrinsic binding constants are k_H,P^o = 3 × 10⁶, k_Ca,P^o = 120, k_Na,P^o = 1, k_H,C^o = 7 × 10⁴ and k_Ca,C^o = 5.6Distributed charge models, either surface or volume, are inadequate since any reasonable monomer size yields fixed charge densities requiring k_H,P^o and k_Ca,C^o which are too low when the maximum in D is 75. Also, with increasing calcium binding, calculated proton release is only 0.4 to 0.5 of that observed.Discrete charge models accept anticipated k^o and yield calculated sequences of calcium binding and proton release which are in good agreement with those observed provided that: (1) using the known amino acid sequence of the phosphate-containing acidic peptide portion of the molecule, pep tide fixed charge is distributed at the lowest I so as to minimize electrostatic free energy; (2) in the region of fixed charge, D is approximately 5; (3) the distances between peptide fixed charges decrease with increasing ionic strength or calcium binding and (4) while protein is in solution, the acidic peptide and the remainder of the molecule are essentially electrostatically independent.     

Substrate promiscuity of secondary metabolite enzymes: prenylation of hydroxynaphthalenes by fungal indole prenyltransferases

Fungal prenyltransferases of the dimethylallyltryptophan synthase (DMATS) superfamily share no sequence, but structure similarity with the prenyltransferases of the CloQ/NphB group. The members of the DMATS superfamily have been reported to catalyze different prenylations of diverse indole or tyrosine derivatives, while some members of the CloQ/NphB group used hydroxynaphthalenes as prenylation substrates. In this study, we report for the first time the prenylation of hydroxynaphthalenes by the members of the DMATS superfamily. Three tryptophan-containing cyclic dipeptide prenyltransferases (AnaPT, CdpNPT and CdpC3PT), one tryptophan C7-prenyltransferase and one tyrosine O-prenyltransferase (SirD) were incubated with naphthalene and 11 derivatives. The enzyme activity and preference of the tested prenyltransferases towards hydroxynaphthalenes differed clearly from each other. For an accepted substrate, however, different enzymes produced usually the same major prenylation product, i.e. with a regular C-prenyl moiety at para- or ortho-position to a hydroxyl group. Regularly, O-prenylated and diprenylated derivatives were also identified as enzyme products of substrates with low conversion rates and regioselectivity. This was unequivocally proven by mass spectrometry and nuclear magnetic resonance analyses. The K _M values and turnover numbers (k _cat) of the enzymes towards selected hydroxynaphthalenes were determined to be in the range of 0.064–2.8 mM and 0.038–1.30 s⁻¹, respectively. These data are comparable to those obtained using indole derivatives. The results presented in this study expanded the potential usage of the members of the DMATS superfamily for production of prenylated derivatives including hydroxynaphthalenes.     

Kinetic and thermodynamic study of the substituent effect on the amino-Claisen rearrangement of para-substituted N-allyl-N-arylamine: a Hammett study via DFT

In order to find the susceptibility of the amino-Claisen rearrangement and the next proton shift reaction of N-allyl-N-arylamine to the substituent effects in the para position, the kinetic and thermodynamic parameters were calculated at the B3LYP level using the 6-31G^** basis set. The calculated activation energies for the rearrangements and proton shift reactions are close to 44.4 and 49.5 kcal mol^? 1, respectively. The transition states of the rearrangement with electron-donor substituents are more stable than those with electron-withdrawing substituent groups, but for the proton shift reaction, this situation is reversed (with the exception of fluorine atom for the rearrangement and fluorine and chlorine atoms for the proton shift reaction). Negative values for the activation entropy confirm the concerted mechanism for the amino-Claisen rearrangement and proton shift reaction. The Hammett ρ values of ? 2.4172 and ? 1.7791 are obtained for σ_p and σ^?  (enhanced sigma) in the amino-Claisen rearrangement, respectively. The correlation between log(k _X/k _H) and σ_p is weaker than that with σ^?  (enhanced sigma). A negative Hammett ρ value indicates that the electron-donating groups slightly increase the rate of amino-Claisen rearrangement. A positive Hammett ρ value (2.4921) for the proton shift reaction indicates that electron-withdrawing groups increase the rate of reaction.     

15NH/D-SOLEXSY experiment for accurate measurement of amide solvent exchange rates: application to denatured drkN SH3

Amide solvent exchange rates are regarded as a valuable source of information on structure/dynamics of unfolded (disordered) proteins. Proton-based saturation transfer experiments, normally used to measure solvent exchange, are known to meet some serious difficulties. The problems mainly arise from the need to (1) manipulate water magnetization and (2) discriminate between multiple magnetization transfer pathways that occur within the proton pool. Some of these issues are specific to unfolded proteins. For example, the compensation scheme used to cancel the Overhauser effect in the popular CLEANEX experiment is not designed for use with unfolded proteins. In this report we describe an alternative experimental strategy, where amide ¹⁵N is used as a probe of solvent exchange. The experiment is performed in 50% H₂O–50% D₂O solvent and is based on the (HACACO)NH pulse sequence. The resulting spectral map is fully equivalent to the conventional HSQC. To fulfill its purpose, the experiment monitors the conversion of deuterated species, ¹⁵N^D, into protonated species, ¹⁵N^H, as effected by the solvent exchange. Conceptually, this experiment is similar to EXSY which prompted the name of ¹⁵N^H/D-SOLEXSY (SOLvent EXchange SpectroscopY). Of note, our experimental scheme, which relies on nitrogen rather than proton to monitor solvent exchange, is free of the complications described above. The developed pulse sequence was used to measure solvent exchange rates in the chemically denatured state of the drkN SH3 domain. The results were found to correlate well with the CLEANEX-PM data, r = 0.97, thus providing a measure of validation for both techniques. When the experimentally measured exchange rates are converted into protection factors, most of the values fall in the range 0.5–2, consistent with random-coil behavior. However, elevated values, ca. 5, are obtained for residues R38 and A39, as well as the side-chain indole of W36. This is surprising, given that high protection factors imply hydrogen bonding or hydrophobic burial not expected to occur in a chemically denatured state of a protein. We, therefore, hypothesized that elevated protection factors are an artefact arising from the calculation of the reference (random-coil) exchange rates. To confirm this hypothesis, we prepared samples of several short peptides derived from the sequence of the drkN SH3 domain; these samples were used to directly measure the reference exchange rates. The revised protection factors obtained in this manner proved to be close to 1.0. These results also have implications for the more compact unfolded state of drkN SH3, which appears to be fully permeable to water as well, with no manifestations of hydrophobic burial.     

Studies on the reactivity of malondialdehyde. I. Effects of acid concentration and solvent composition on deuterium exchange reactions

The rates of deuterium exchange reactions of malondialdehyde (MDA) and deuterated malondialdehyde (MDAd) have been studied as a function of acidity and the content of dimethyl sulfoxide (DMSO) in binary mixtures with D₂O . MDA incorporates deuterium from D₂O solutions in a first-order reaction with a rate constant (k_obs) that depends on the acid concentration. From this dependence, a catalytic constant, k_cat, can be derived (k_cat^MDA = 2.25 × 10⁵M^?s^?1). Similar kinetic behavior was found for MDAd in H₂O solutions, and in this case, k_cat^MDA = 1.56 × 10⁵M^?1s^?1. Results from reactions of MDA and MDAd in identical H₂OD₂O mixtures show that primary and secondary isotope effects are small (k_H/k_D = 1.13) and that solvent isotope effects cause most of the differences found between reactions in D₂O and H₂O. Reactions in binary DMSOd₆D₂O mixtures show a six-fold rate increase as the proportion of DMSOd₆ increases from 50% to 90%. These results also illustrate the relatively high reactivity of MDA at pH values well above its pK_a and the importance of medium composition on its reaction rate.