pH-rate Profile Research Articles

Kinetics and Mechanism of Mn(II) Catalyzed Periodate Oxidation of p-anisidine: Effect of pH

The stoichiometry for the initial part of the reaction, Mn(II) catalysed periodate oxidation of p-anisidine (PMA), has been found to be 1 mol of PMA consuming 2 mol of periodate ion. The kinetic-mechanistic study of reaction in acetone-water medium was made spectrophotometrically by noting the increase in the absorbance of reaction intermediate. Reaction is first order in reactants and catalyst each. A decrease in dielectric constant of the medium results in decrease in the rate of reaction suggesting an ion-dipole type interaction. Free radical scavengers do not affect the reaction rate. A special type of rate-pH profile shows a maximum at pH = 7.0. This pH effect also suggests the involvement of at least three differently reactive reactant species in the reaction and this fact has been considered by us while deriv-ing the rate law. Under pseudo first order conditions [IO4-] >> [PMA] and in agreement with the derived rate law, the 1/kcat versus [H+] plot passes through the minimum and the results can be fitted to the equation: 1/kcat = (K2 / k K3 K4 [H+]) + {(Kw + Kb K2) / k K3 K4 Kw} + Kb [H+] / k K3 K4 Kw, where kK3K4 is the empirical composite rate constant, Kw is ionic product of water, K2 is acid dissociation constant of H4IO6- and Kb is base dissociation constant of PMA. The experimental value of [H+]min is in good agreement with the value calculated by using the derived rate law equation and is character-istic of the substrate involved relating to the base dissociation constant of PMA. The value of thermo-dynamic parameters have been evaluated. © 2014 by Authors, Published by BCREC Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0)

Allosteric reversion of Haemophilus influenzae β-carbonic anhydrase via a proline shift.

Haemophilus influenzae β-carbonic anhydrase (HICA) has been reverse-engineered in the allosteric site region to resemble the nonallosteric Pisum sativum enzyme in order to identify critical features of allostery and intersusbunit communication. Three variants (W39V/G41A, P48S/A49P, and W39V/G41A/P48S/A49P) were identified, through a comparison with a crystal structure of nonallosteric P. sativum β-carbonic anhydrase (PSCA, PDB 1EKJ ), to potentially revert HICA to a nonallosteric enzyme. The W39V/G41A and P48S/A49P mutations decreased the apparent kcat/Km proton dependence from 4 to 2 and 1, respectively, increasing the overall maximal kcat/Km to 16 ± 2 μM(-1) s(-1) (380% of wild type) and 17 ± 3 μM(-1) s(-1) (405% of wild type). The pKa values of the metal-bound water molecule based on the pH-rate profile kinetics (8.32 ± 0.04 for W39V/G41A and 8.3 ± 0.1 for P48S/A49P) were also slightly higher than that for the wild-type enzyme (7.74 ± 0.04). The P48S/A49P variant has lost all pH-rate cooperativity. The W39V/G41A/P48S/A49P variant's kinetics were unusual and were fit with a log-linear function with a slope 0.9 ± 0.2. The crystal structure of the W39V/G41A variant revealed an active site very similar to the T-state wild-type oligomer with bicarbonate trapped in the escort site. By contrast, the X-ray crystal structure of a proline shift variant (P48S/A49P) reveals that it has adopted an active site conformation nearly identical to that of nonallosteric β-carbonic anhydrase (R-state) for one chain, including a tight association with the dimer-exchanged N-terminal helices; the second chain in the asymmetric unit is associated in a biologically relevant oligomer, but it adopts a T-state conformation that is not capped by dimer-exchanged N-terminal helices. The hybrid R/T nature of HICA P48S/A49P structurally recapitulates the interruption of pH-rate cooperativity observed for this variant. Comparison of the conformations of the R and T chains of P48S/A49P suggests a new hypothesis to explain HICA allosteric communication that is mediated by the N-terminal helices and anion binding at the dimer interface.

A new heavy lanthanide-dependent DNAzyme displaying strong metal cooperativity and unrescuable phosphorothioate effect.

In vitro selection of RNA-cleaving DNAzymes was performed using three heavy lanthanide ions (Ln3+): Ho3+, Er3+ and Tm3+. The resulting sequences were aligned together and about half of the library contained a new family of DNAzyme. These DNAzymes have a simple loop structure, and they are active only with the seven heavy Ln3+. Among the tested non-lanthanide ions, only Y3+ induced cleavage and even Pb2+ failed to cleave, suggesting a very high specificity. A representative DNAzyme, Tm7, has a sigmoidal metal binding curve with a Hill coefficient of 3, indicating that three metal ions are involved in the catalytic step. Its pH-rate profile has a slope of 1, suggesting a single deprotonation step is involved in the rate-limiting step. Tm7 has a cleavage rate of 1.6 min−1 at pH 7.8 with 10 μM Er3+. Phosphorothioate substitution at the cleavage junction completely inhibits the activity, which cannot be rescued by Cd2+ alone, or by a mixture of Er3+ and Cd2+, suggesting that two interacting metal ions are involved in direct bonding to both non-bridging oxygen atoms. A new model involving three lanthanide ions is proposed based on this study. A biosensor is engineered using Tm7 to detect Dy3+ down to 14 nM.

Stability-Indicating Methods for Determination of Flubendazole and Its Degradants.

The resolution of flubendazole (FLB) and its degradants has been accomplished by using liquid chromatography (LC) using an octadecylsilane column and a mobile phase that consists of methanol and (0.1%) formic acid (75:25, v/v). Identification of FLB degradants was achieved with positive electron spray spectrometry detection. Furthermore, high-performance thin layer chromatography (HPTLC) separation was carried out using ethyl acetate:formic acid:acetic acid:water (9.5:0.11:0.11:0.28, v/v/v/v) as a mobile phase. Quantitation was achieved using densitometry at 254 nm. FLB was subjected to conditions of hydrolysis, photolysis, oxidation and thermal degradation. The proposed LC method determined that the kinetics of acidic and basic degradation followed a first-order kinetics, with an activation energy of 17.80 and 13.93 kcal mol(-1) for acidic and alkaline degradation processes, respectively. The pH-rate profiles of degradation of FLB in Britton-Robinson buffer solutions within the pH range (2-12) were studied. The developed methods were validated within the corresponding linear ranges of 3-30 µg mL(-1) with detection limits of 0.11 and 0.13 µg mL(-1) for FLB and DG1, respectively, for the high-performance liquid chromatography method and 10-65 and 5-30 µg band(-1) with detection limits of 0.22 and 0.30 µg band(-1) for FLB and DG1, respectively, for the HPTLC method.

Catalytic mechanism of bacteriophage T4 Rad50 ATP hydrolysis.

Spontaneous double-strand breaks (DSBs) are one of the most deleterious forms of DNA damage, and their improper repair can lead to cellular dysfunction. The Mre11 and Rad50 proteins, a nuclease and an ATPase, respectively, form a well-conserved complex that is involved in the initial processing of DSBs. Here we examine the kinetic and catalytic mechanism of ATP hydrolysis by T4 Rad50 (gp46) in the presence and absence of Mre11 (gp47) and DNA. Single-turnover and pre-steady state kinetics on the wild-type protein indicate that the rate-limiting step for Rad50, the MR complex, and the MR-DNA complex is either chemistry or a conformational change prior to catalysis. Pre-steady state product release kinetics, coupled with viscosity steady state kinetics, also supports that the binding of DNA to the MR complex does not alter the rate-limiting step. The lack of a positive deuterium solvent isotope effect for the wild type and several active site mutants, combined with pH-rate profiles, implies that chemistry is rate-limiting and the ATPase mechanism proceeds via an asymmetric, dissociative-like transition state. Mutation of the Walker A/B and H-loop residues also affects the allosteric communication between Rad50 active sites, suggesting possible routes for cooperativity between the ATP active sites.

Oxidation of bromophenols and formation of brominated polymeric products of concern during water treatment with potassium permanganate.

The extensive use of bromophenols (BrPs) in industrial products leads to their occurrence in freshwater environments. This study explored the oxidation kinetics of several BrPs (i.e., 2-BrP, 3-BrP, 4-BrP, 2,4-diBrP, and 2,6-diBrP) and potential formation of brominated polymeric products of concern during water treatment with potassium permanganate [Mn(VII)]. These BrPs exhibited appreciable reactivity toward Mn(VII) with the maxima of second-order rate constants (kMn(VII)) at pH near their pKa values, producing bell-shaped pH-rate profiles. The unusual pH-dependency of kMn(VII) was reasonably explained by a tentative reaction model, where the formation of an intermediate between Mn(VII) and dissociated BrP was likely involved. A novel and powerful precursor ion scan (PIS) approach was used for selective detection of brominated oxidation products by liquid chromatography/electrospray ionization-triple quadrupole mass spectrometry. Results showed that brominated dimeric products such as hydroxylated polybrominated diphenyl ethers (OH-PBDEs) and hydroxylated polybrominated biphenyls (OH-PBBs) were readily produced. For instance, 2'-OH-BDE-68, one of the most naturally abundant OH-PBDEs, could be formed at a relatively high yield possibly via the coupling between bromophenoxyl radicals generated from the one-electron oxidation of 2,4-diBrP by Mn(VII). Given the altered or enhanced toxicological effects of these brominated polymeric products compared to the BrP precursors, it is important to better understand their reactivity and fate before Mn(VII) is applied by water utilities for the oxidative treatment of BrP-containing waters.

Kinetics and Mechanism of the Base-Catalyzed Rearrangement and Hydrolysis of Ezetimibe

The pH-rate profile of the pseudo-first-order rate constants for the rearrangement and hydrolysis of Ezetimibe giving (2R,3R,6S)-N,6-bis(4-fluorophenyl)-2-(4-hydroxyphenyl)-3,4,5,6-tetrahydro-2H-pyran-3-carboxamide (2) as the main product at pH of less than 12.5 and the mixture of 2 and 5-(4-fluorophenyl)-5-hydroxy-2-[(4-fluorophenylamino)-(4-hydroxyphenyl)methyl]-pentanoic acid (3) at pH of more than 12.5 in aqueous tertiary amine buffers and in sodium hydroxide solutions at ionic strength I = 0.1 mol L(-1) (KCl) and at 39 °C is reported. No buffer catalysis was observed and only specific base catalysis is involved. The pH-rate profile is more complex than the pH-rate profiles for the hydrolysis of simple β-lactams and it contains several breaks. Up to pH 9, the log k(obs) linearly increases with pH, but between pH 9 and 11 a distinct break downwards occurs and the values of log k(obs) slightly decrease with increasing pH of the medium. At pH of approximately 13, another break upwards occurs that corresponds to the formation of compound 3 that is slowly converted to (2R,3R,6S)-6-(4-fluorophenyl)-2-(4-hydroxyphenyl)-3,4,5,6-tetrahydro-2H-pyran-3-carboxylic acid (4). The kinetics of base-catalyzed hydrolysis of structurally similar azetidinone is also discussed.

Degradation kinetics study of cabozantinib by a novel stability-indicating LC method and identification of its major degradation products by LC/TOF-MS and LC–MS/MS

The chemical stability of cabozantinib (CBZ) was investigated using a novel stability-indicating LC method. Forced degradation of CBZ was carried out under acidic, basic, thermal, oxidative and photolytic stress conditions. Hydrolysis and oxidation were the primary pathways for this compound and three major unknown degradation products were characterized by LC/TOF-MS and LC–MS/MS. The major oxidative degradation product was isolated by preparative LC and identified by UV, HRMS and NMR techniques to be N-{4-[(N-oxide-6,7-dimethoxyquinolin-4-yl)oxy]phenyl}-N′-(4-fluorophenyl)-cyclopropane-1,1-dicarboxamide. The developed method was validated as per ICH guidelines and then successfully applied to investigate the degradation kinetics of CBZ. Degradation of CBZ followed first-order kinetics under all experimental conditions. A V-shaped pH-rate profile over the pH range 2–10 was observed with maximum stability at pH 6. The effect of temperature on the rate of CBZ degradation was characterized using the Arrhenius equation. The activation energy for hydrolysis was 57.31kJmol−1 in alkaline solution.

Stability of an anti-stroke peptide: Driving forces and kinetics in chemical degradation

NR2B9c (Lys-Leu-Ser-Ser-Ile-Glu-Ser-Asp-Val) is a 9-amino acid peptide that has been illustrated to be a potential anti-stroke drug. For more effective treatment, suitable drug delivery systems should be developed. However, little is known about the stability of NR2B9c which is essential to its formulation. In this study, a reversed-phase high-performance liquid chromatography (HPLC) was applied to study the forced degradation behavior and stability of NR2B9c. HPLC studies were performed with an C8 column using a mobile phase consisting of acetonitrile (14.5:85.5, v/v) and aqueous solution (0.1% trifluoroacetic acid (TFA) and 0.05M KH2PO4). The flow rate and the wavelength set during HPLC detection were 1.0mL/min and 205nm, respectively. The degradation pattern of NR2B9c aqueous solution followed pseudo first-order kinetics. The degradation rate at pH 7.5 was the slowest according to the plotting V-shaped pH-rate profile. The influence of temperature on the rate of reactions was interpreted in terms of Arrhenius equation (r2>0.98). Thermodynamic parameters were calculated based on Eyring equation (r2>0.98). The concentrations of drug, buffer species, buffer concentrations, oxidation and organic solvents have noticeable effects on the degradation of NR2B9c while ultrasound shows little impact under the experimental conditions. In a word, this study may give a detailed description of stability of NR2B9c.

Unprecedented reactivity of alkoxo/hydroxide-bridged dinuclear copper(II) complexes as artificial carboxylesterase: Effects of Gemini 16-6-16 micelles and bimetallic synergistic effect

One μ-alkoxo/hydroxide-bridged dinuclear copper(II) complex (Cu2L) and a mononuclear analogue (CuL) with symmetric Schiff base compound were employed as carboxylesterase models to promote the hydrolysis of a carboxylic acid ester, p-nitrophenyl picolinate (PNPP). Also the introducing of a Gemini surfactant, bis(hexadecyldimethylammonium)hexane bromide (16-6-16, 2Br−), gave interested observations relative to those controlled trials preformed in buffer and a micellar solution of traditional single-chain surfactant, CTAB (cetyltrimethylammonium bromide). The results indicated that the dinuclear Cu2L efficiently accelerated PNPP hydrolysis with 18,096- and 49,569.6-fold rate enhancement under moderate conditions (pH 7.00, 25°C) in buffer and 16-6-16 micellar solution, respectively. Much greater rate enhancement was observed in 16-6-16 micelles in contrast with CTAB micelles, launching 1.6–2.6 folds difference in hydrolysis rate of PNPP at pH 7.00. Additionally, the Cu2L-induced PNPP hydrolysis showed a bell-shaped rate-pH profile, which is an enzyme-like behaviour. Interestingly, rate–pH curves could provide the direct evidence for the interfacial effects of Gemini 16-6-16 micelles on the deprotonation of coordinated water, indicating about 0.2 unit pKa1 difference of the Cu2L-bound H2O between in micellar phase and bulk phase. Cu2L was found to be approximately 199.3- and 288.7-fold reactive than CuL in buffer and 16-6-16 micellar solution, respectively. Significant activity difference between both complexes probably results from the bimetallic coorperation of the two catalytic copper sites and more open binding site of Cu2L.

PH‐dependent studies on the reductive half‐reaction of E. coli methylenetetrahydrofolate reductase (769.13)

Methylenetetrahydrofolate reductase (MTHFR) is a flavoprotein that utilizes two substrates, NADH and 5,10‐methylenetetrahydrofolate (CH2‐H4folate), in a ping pong bi‐bi mechanism. In the reaction, bound FAD is reduced by NADH and then oxidized by CH2‐H4folate. The pH dependence of the reductive half‐reaction was studied with steady‐state kinetics using the NADH‐menadione oxidoreductase assay. In this assay the reductive half‐reaction is rate‐limiting, and menadione is used to reoxidize the flavin. The wild‐type MTHFR reaction was found to be pH‐dependent with an inflection point (pKa) at 4.9. We have hypothesized that this pKa belongs to the active‐site amino acid glutamate 28 (Glu28). When Glu28 is deprotonated, the negatively‐charged side chain can stabilize the positively‐charged nicotinamide ring of NADH during the reductive half‐reaction. To determine whether Glu28 is responsible for the pKa of 4.9, we have examined a mutant enzyme with Glu28 replaced by a glutamine. Kinetic parameters were obtained for the NADH‐menadione reaction catalyzed by the Glu28Gln mutant at pH values 4.5 to 8. Our results suggest that a pKa ~5 still exists in the pH rate profile of the Glu28Gln mutant. However, instability and denaturation have plagued our studies. In current work, we are testing alternate buffers conditions to stabilize the mutant enzyme.

Molecular Recognition of Fluorine Impacts Substrate Selectivity in the Fluoroacetyl-CoA Thioesterase FlK

The fluoroacetate-producing bacterium Streptomyces cattleya has evolved a fluoroacetyl-CoA thioesterase (FlK) that exhibits a remarkably high level of discrimination for its cognate substrate compared to the cellularly abundant analogue acetyl-CoA, which differs only by the absence of the fluorine substitution. A major determinant of FlK specificity derives from its ability to take advantage of the unique properties of fluorine to enhance the reaction rate, allowing fluorine discrimination under physiological conditions where both substrates are likely to be present at saturating concentrations. Using a combination of pH–rate profiles, pre-steady-state kinetic experiments, and Taft analysis of wild-type and mutant FlKs with a set of substrate analogues, we explore the role of fluorine in controlling the enzyme acylation and deacylation steps. Further analysis of chiral (R)- and (S)-[2H1]fluoroacetyl-CoA substrates demonstrates that a kinetic isotope effect (1.7 ± 0.2) is observed for only the (R)-2H1 isomer, indicating that deacylation requires recognition of the prochiral fluoromethyl group to position the α-carbon for proton abstraction. Taken together, the selectivity for the fluoroacetyl-CoA substrate appears to rely not only on the enhanced polarization provided by the electronegative fluorine substitution but also on molecular recognition of fluorine in both formation and breakdown of the acyl-enzyme intermediate to control active site reactivity. These studies provide insights into the basis of fluorine selectivity in a naturally occurring enzyme–substrate pair, with implications for drug design and the development of fluorine-selective biocatalysts.

Loop‐loop interactions govern multiple steps in indole‐3‐glycerol phosphate synthase catalysis

Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent interactions with nearby structural elements.

STABILITY-INDICATING HPLC METHOD FOR SIMULTANEOUS DETERMINATION OF CAPTOPRIL, INDAPAMIDE, AND THEIR RELATED COMPOUNDS

A validated stability-indicating HPLC method was developed for simultaneous determination of Captopril (CP), Indapamide (ID), and their related compounds in tablets using a 250 × 4.6 mm Xterra RP8 column, 5 µm particle size with UV detection at 210 nm. Isocratic elution was employed using mobile phase consisting of a mixture of 26 mM pentane-1-sulfonic acid sodium salt in 30 mM potassium dihydrogen phosphate (pH 2.8, adjusted by phosphoric acid):methanol:acetonitril (6:2:2) v/v/v. The described method was linear over the range of 0.25–150 µg/mL with (r = 0.9999) for CP and 0.2–100 µg/mL with (r = 0.9999) for ID. The stability of CP and ID was studied under accelerated acidic, alkaline, and oxidative conditions. The proposed method was used to investigate the kinetics of acidic and alkaline degradation process of CP and ID at different temperatures and the apparent pseudo first-order rate constant, half-life, and activation energy were calculated. The pH rate profiles of degradation of CP and ID in Britton-Robinson buffer solutions within the pH range 1.8–12.0 were studied. The developed method was validated with respect to linearity, accuracy, precision, selectivity, and robustness. The forced degradation studies prove the stability indicating power of the developed method.

Cysteine Is the General Base That Serves in Catalysis by Isocitrate Lyase and in Mechanism-Based Inhibition by 3-Nitropropionate

Isocitrate lyase (ICL) catalyzes the reversible cleavage of isocitrate into succinate and glyoxylate. It is the first committed step in the glyoxylate cycle used by some organisms, including Mycobacterium tuberculosis, where it has been shown to be essential for cell survival during chronic infection. The pH-rate and pD-rate profiles measured in the direction of isocitrate synthesis revealed solvent kinetic isotope effects (KIEs) of 1.7 ± 0.4 for (D2O)V and 0.56 ± 0.07 for (D2O)(V/Ksuccinate). Whereas the (D2O)V is consistent with partially rate-limiting proton transfer during formation of the hydroxyl group of isocitrate, the large inverse (D2O)(V/Ksuccinate) indicates that substantially different kinetic parameters exist when the enzyme is saturated with succinate. Inhibition by 3-nitropropionate (3-NP), a succinate analogue, was found to proceed through an unusual double slow-onset process featuring formation of a complex with a Ki of 3.3 ± 0.2 μM during the first minute, followed by formation of a final complex with a Ki* of 44 ± 10 nM over the course of several minutes to hours. Stopped-flow measurements during the first minute revealed an apparent solvent KIE of 0.40 ± 0.03 for association and unity for dissociation. In contrast, itaconate, a succinate analogue lacking an acidic α-proton, did not display slow-binding behavior and yielded a (D2O)Ki of 1.0 ± 0.2. These results support a common mechanism for catalysis with succinate and inhibition by 3-NP featuring (1) an unfavorable prebinding isomerization of the active site Cys191-His193 pair to the thiolate-imidazolium form, a process that is favored in D2O, and (2) the transfer of a proton from succinate or 3-NP to Cys191. These findings also indicate that propionate-3-nitronate, which is the conjugate base of 3-NP and the "true inhibitor" of ICL, does not bind directly and must be generated enzymatically.

Prediction of the pH-rate profile for dimethyl sulfide oxidation by hydrogen peroxide: The role of elusive H3 O2 + Ion

Experimental kinetics of sulfide oxidation by hydrogen peroxide presents a pH-dependent profile. In this article, it was carried out a detailed study of the mechanism and kinetics of dimethyl sulfide (DMS) oxidation by H2O2 in neutral, acid, and basic aqueous medium using ab initio calculations. The results point out that DMS oxidation in neutral aqueous medium occurs through its direct reaction with H2O2. In acid medium, cluster-continuum model calculations shows that cluster is the best representation of the very reactive species. In basic medium, there is formation of the species. However, the pathway involving this species has high free energy barrier, making this pathway unfeasible. The theoretical pH-rate profile is in good agreement with the experimental observations. © 2013 Wiley Periodicals, Inc.

PH-rate profiles of l-arabinitol 4-dehydrogenase from Hypocrea jecorina and its application in l-xylulose production

l-Arabinitol 4-dehydrogenase (LAD) from Hypocrea jecorina (HjLAD) was cloned and overexpressed in Escherichia coli BL21 (DE3). The kinetics of l-arabinitol oxidation by NAD+, catalyzed by HjLAD, was studied within the pH range of 7.0–9.5 at 25°C. The turnover number (kcat) and the catalytic efficiency (kcat/Km) were 4200min−1 and 290mM−1min−1, respectively. HjLAD showed the highest turnover number and catalytic efficiency among all previously characterized LADs. In further application of HjLAD, rare l-sugar l-xylulose was produced by the enzymatic oxidation of arabinitol to give a yield of approximately 86%.

Acid–Base Catalysis and Crystal Structures of a Least Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion

In green-to-red photoconvertible fluorescent proteins, a three-ring chromophore is generated by the light-activated incorporation of a histidine residue into the conjugated π-system. We have determined the pH-rate profile and high- and low-pH X-ray structures of a least evolved ancestor (LEA) protein constructed in the laboratory based on statistical sequence analysis. LEA incorporates the minimal number of substitutions necessary and sufficient for facile color conversion and exhibits a maximal photoconversion quantum yield of 0.0015 at pH 6.1. The rate measurements provide a bell-shaped curve, indicating that the reaction is controlled by the two apparent pKa values, 4.5 ± 0.2 and 7.5 ± 0.2, flanking the chromophore pKa of 6.3 ± 0.1. These data demonstrate that the photoconversion rate of LEA is not proportional to the A-form of the GFP-like chromophore, as previously reported for Kaede-type proteins. We propose that the observed proton dissociation constants arise from the internal quadrupolar charge network consisting of Glu222, His203, Glu148, and Arg69. Increased active site flexibility may facilitate twisting of the chromophore upon photoexcitation, thereby disrupting the charge network and activating the Glu222 carboxylate for the abstraction of a proton from a carbon acid. Subsequently, the proton may be delivered to the Phe64 carbonyl by a hydrogen-bonded network involving Gln42 or by means of His65 side chain rotations promoted by protein breathing motions. A structural comparison of LEA with the nonphotoconvertible LEA-Q42A variant supports a role for Gln42 either in catalysis or in the coplanar preorganization of the green chromophore with the His65 imidazole ring.

Improving cabazitaxel chemical stability in parenteral lipid emulsions using cholesterol

Intravenous lipid emulsions of cabazitaxel (CLEs) with a high stability were prepared by adding cholesterol (CH) to provide a new and more suitable delivery system for its administration. The factors affecting CLEs, such as the solubility of cabazitaxel in various oils, different kinds of lecithin, pH, different types of oil phases, and different concentrations of lipoid E80®, CH and poloxamer 188 were investigated systematically. The degradation of cabazitaxel in aqueous solution and lipid emulsion both followed pseudo first-order kinetics. A degradation mechanism was suggested by the U-shaped pH-rate profile of cabazitaxel. A formulation containing 0.5% (w/v) CH and another formulation without CH were made to investigate the protective influence of CH on the chemical stability of CLEs. The activation energy of the two formulations was calculated to be 65.74±6.88 and 54.24±1.43kJ/mol (n=3), respectively. Compared with the untreated CH, the shelf-life of cabazitaxel with added CH was longer, namely 134.0±23.4days versus 831.4±204.4days (n=3) at 4°C. This indicates that the addition of CH significantly improved the lifetime of cabazitaxel in intravenous lipid emulsions. The hydrogen bonding that takes place between cabazitaxel and CH accounts for the protective effect of CH on the chemical stability of CLEs in two ways: preventing cabazitaxel from leaking and hydrolyzing in aqueous solution and hindering hydrolysis in the oil phase. Finally, the hypothesis was confirmed by LC/TOFMS and Fourier-transform infrared-spectroscopy. As a result, CLEs were obtained successfully by the addition of CH and were stable enough to allow further research.

Enzyme-Dependent Lysine Deprotonation in EZH2 Catalysis

Protein lysine methyltransferases (PKMTs) are key players in epigenetic regulation and have been associated with a variety of diseases, including cancers. The catalytic subunit of Polycomb Repressive Complex 2, EZH2 (EC 2.1.1.43), is a PKMT and a member of a family of SET domain lysine methyltransferases that catalyze the transfer of a methyl group from S-adenosyl-l-methionine to lysine 27 of histone 3 (H3K27). Wild-type (WT) EZH2 primarily catalyzes the mono- and dimethylation of H3K27; however, a clinically relevant active site mutation (Y641F) has been shown to alter the reaction specificity, dominantly catalyzing trimethylation of H3K27, and has been linked to tumor genesis and maintenance. Herein, we explore the chemical mechanism of methyl transfer by EZH2 and its Y641F mutant with pH-rate profiles and solvent kinetic isotope effects (sKIEs) using a short peptide derived from histone H3 [H3(21-44)]. A key component of the chemical reaction is the essential deprotonation of the ε-NH3(+) group of lysine to accommodate subsequent methylation. This deprotonation has been suggested by independent studies (1) to occur prior to binding to the enzyme (by bulk solvent) or (2) to be facilitated within the active site following binding, either (a) by the enzyme itself or (b) by a water molecule with access to the binding pocket. Our pH-rate and sKIE data best support a model in which lysine deprotonation is enzyme-dependent and at least partially rate-limiting. Furthermore, our experimental data are in agreement with prior computational models involving enzyme-dependent solvent deprotonation through a channel providing bulk solvent access to the active site. The mechanism of deprotonation and the rate-limiting catalytic steps appear to be unchanged between the WT and Y641F mutant enzymes, despite their activities being highly dependent on different substrate methylation states, suggesting determinants of substrate and product specificity in EZH2 are independent of catalytic events limiting the steady-state rate.