Analysis of enzyme kinetics using electrospray ionization mass spectrometry and multiple reaction monitoring: fucosyltransferase V

Mechanistic insights on anserine hydrolyzing activities of human carnosinases

Anserine and carnosine represent histidine-containing dipeptides that exert a pluripotent protective effect on human physiology. Anserine is known to protect against oxidative stress in diabetes and cardiovascular diseases. Human carnosinases (CN1 and CN2) are dipeptidases involved in the homeostasis of carnosine. In poikilothermic vertebrates, the anserinase enzyme is responsible for hydrolyzing anserine. However, there is no specific anserine hydrolyzing enzyme present in humans. In this study, we have systematically investigated the anserine hydrolyzing activity of human CN1 and CN2. A targeted multiple reaction monitoring (MRM) based approach was employed for studying the enzyme kinetics of CN1 and CN2 using carnosine and anserine as substrates. Surprisingly, both CN1 and CN2 can hydrolyze anserine effectively. The observed catalytic turnover rate (V_max/[E]_t) was 21.6 s^-1 and 2.8 s^-1 for CN1 and CN2, respectively. CN1 is almost eight-fold more efficient in hydrolyzing anserine compared to CN2, which is comparable to the efficiency of the carnosine hydrolyzing activity of CN2. The Michaelis constant (K_m) value for CN1 (1.96 mM) is almost three-fold lower compared to CN2 (6.33 mM), representing higher substrate affinity for anserine-CN1 interactions. Molecular docking studies showed that anserine binds at the catalytic site of the carnosinases with an affinity similar to carnosine. Overall, the present study elucidated the inherent promiscuity of human carnosinases in hydrolyzing anserine using a sensitive LC-MS/MS approach.

Kinetic Profiling of Homogeneous and Heterogeneous Biocatalysts in Continuous Flow by Online Mass Spectrometry

Enzyme kinetics is normally assessed by performing individual kinetic measurements using batch-type reactors (test tubes, microtiter plates), in which enzymes are mixed with different substrates. Some drawbacks of conventional methods are the large amounts of experimental materials, long analysis times, and limitations of spectrophotometry. Therefore, we have developed a method for facile determination of enzyme kinetics using online flow-based mass spectrometry. A concentration ramp of substrate or product was created by dynamically adjusting flow rates of pumps delivering stock solution of substrate and diluent. Precise kinetic measurements were performed by reaction product quantification and initial rate calculation. In the presence of ascending substrate concentrations, the rate of a target enzyme (penicillinase)-catalyzed hydrolysis was varied. By measuring the reaction product continuously, Michaelis constants (K_M) could be calculated. The enzyme kinetic measurements for hydrolysis of penicillins were conducted based on this simple, rapid, and low sample consumption online flow device. In the homogeneous reaction, the K_M values for amoxicillin, ampicillin, penicillin G, and penicillin V were 254.9 ± 14.5, 29.2 ± 0.3, 2.6 ± 0.1, and 5.4 ± 0.1 μM, respectively. In the heterogeneous reaction, the K_M values for amoxicillin, ampicillin, penicillin G, and penicillin V were 408.9 ± 75.1, 114.4 ± 8.0, 21.8 ± 0.7, and 83.3 ± 4.8 μM, respectively. Apart from enzyme assay, the showcased method for the generation of temporal concentration ramps can be utilized to perform rapid quantity calibrations for mass spectrometric analyses.

Quantifying Carbohydrate-Active Enzyme Activity with Glycoprotein Substrates Using Electrospray Ionization Mass Spectrometry and Center-of-Mass Monitoring

Carbohydrate-active enzymes (CAZymes) play critical roles in diverse physiological and pathophysiological processes and are important for a wide range of biotechnology applications. Kinetic measurements offer insight into the activity and substrate specificity of CAZymes, information that is of fundamental interest and supports diverse applications. However, robust and versatile kinetic assays for monitoring the kinetics of intact glycoprotein and glycolipid substrates are lacking. Here, we introduce a simple but quantitative electrospray ionization mass spectrometry (ESI-MS) method for measuring the kinetics of CAZyme reactions involving glycoprotein substrates. The assay, referred to as center-of-mass (CoM) monitoring (CoMMon), relies on continuous (real-time) monitoring of the CoM of an ensemble of glycoprotein substrates and their corresponding CAZyme products. Notably, there is no requirement for calibration curves, internal standards, labeling, or mass spectrum deconvolution. To demonstrate the reliability of CoMMon, we applied the method to the neuraminidase-catalyzed cleavage of N-acetylneuraminic acid (Neu5Ac) residues from a series of glycoproteins of varying molecular weights and degrees of glycosylation. Reaction progress curves and initial rates determined with CoMMon are in good agreement (initial rates within ≤5%) with results obtained, simultaneously, using an isotopically labeled Neu5Ac internal standard, which enabled the time-dependent concentration of released Neu5Ac to be precisely measured. To illustrate the applicability of CoMMon to glycosyltransferase reactions, the assay was used to measure the kinetics of sialylation of a series of asialo-glycoproteins by a human sialyltransferase. Finally, we show how combining CoMMon and the competitive universal proxy receptor assay enables the relative reactivity of glycoprotein substrates to be quantitatively established.

Active site characterization and activity of the human aspartyl (asparaginyl) β-hydroxylase

Human aspartyl/asparaginyl beta-hydroxylase (HAAH) is a member of the superfamily of nonheme Fe2+/α-ketoglutarate (αKG) dependent oxygenase enzymes with a noncanonical active site. HAAH hydroxylates epidermal growth factor (EGF) like domains to form the β-hydroxylated product from substrate asparagine or aspartic acid and has been suggested to have a negative impact in a variety of cancers. In addition to iron, HAAH also binds divalent calcium, although the role of the latter is not understood. Herein, the metal binding chemistry and influence on enzyme stability and activity have been evaluated by a combined biochemical and biophysical approach. Metal binding parameters for the HAAH active site were determined by use of isothermal titration calorimetry, demonstrating a high-affinity regulatory binding site for Ca2+ in the catalytic domain in addition to the catalytic Fe2+ cofactor. We have analyzed various active site derivatives, utilizing LC-MS and a new HPLC technique to determine the role of metal binding and the second coordination sphere in enzyme activity, discovering a previously unreported residue as vital for HAAH turnover. This analysis of the in vitro biochemical function of HAAH furthers the understanding of its importance to cellular biochemistry and metabolic pathways.

A mechanistic investigation of the Suzuki polycondensation reaction using MS/MS methods

The Suzuki polycondensation can be studied in real time using MS/MS methods, even with the molecular weight of the reaction components changing with every turnover.

CUPRA-ZYME: An Assay for Measuring Carbohydrate-Active Enzyme Activities, Pathways, and Substrate Specificities

Carbohydrate-Active enZymes (CAZymes) are involved in the synthesis, degradation, and modification of carbohydrates. They play critical roles in diverse physiological and pathophysiological processes, have important industrial and biotechnological applications, are important drug targets, and represent promising biomarkers for the diagnosis of a variety of diseases. Measurements of their activities, catalytic pathway, and substrate specificities are essential to a comprehensive understanding of the biological functions of CAZymes and exploiting these enzymes for industrial and biomedical applications. For glycosyl hydrolases a variety of sensitive and quantitative spectrophotometric techniques are available. However, measuring the activity of glycosyltransferases is considerably more challenging. Here, we introduce CUPRA-ZYME, a versatile and quantitative electrospray ionization mass spectrometry (ESI-MS) assay for measuring the kinetic parameters of CAZymes, monitoring reaction pathways, and profiling substrate specificities. The method employs the recently developed competitive universal proxy receptor assay (CUPRA), implemented in a time-resolved manner. Measurements of the hydrolysis kinetics of CUPRA substrates containing ganglioside oligosaccharides by the glycosyl hydrolase human neuraminidase 3 served to validate the reliability of kinetic parameters measured by CUPRA-ZYME and highlight its use in establishing catalytic pathways. Applications to libraries of substrates demonstrate the potential of the assay for quantitative profiling of the substrate specificities glycosidases and glycosyltransferases. Finally, we show how the comparison of the reactivity of CUPRA substrates and glycan substrates present on glycoproteins, measured simultaneously, affords a unique opportunity to quantitatively study how the structure and protein environment of natural glycoconjugate substrates influences CAZyme activity.

Development of multiple reaction monitoring assay for quantification of carnosine in human plasma

Carnosine, a histidine containing dipeptide, exerts beneficial effects by scavenging reactive carbonyl compounds (RCCs) that are implicated in pathogenesis of diabetes. However, the reduced carnosine levels may aggravate the severity of diabetes. The precise quantification of carnosine levels may serve as an indicator of pathophysiological state of diabetes. Therefore, we have developed a highly sensitive targeted multiple reaction monitoring (MRM) method for quantification of carnosine in human plasma samples. Various mass spectrometry parameters such as ionization of precursor, fragment abundance and stability, collision energy, tube lens offset voltage were optimized to develop a sensitive and robust assay. Using the optimized MRM assay, the lower limit of detection (LOD) and limit of quantification (LOQ) for carnosine were found to be 0.4 nM and 1.0 nM respectively. Standard curves were constructed ranging from 1.0 nM to 15.0 μM and the levels of carnosine in mice and human plasma were determined. Further, the MRM assay was extended to study carnosine hydrolyzing activity of human carnosinases, the serum carnosinase (CN1) and the cytosolic carnosinase (CN2). CN1 showed three folds higher activity than CN2. The MRM assay developed in this study is highly sensitive and can be used for basal plasma carnosine quantification, which can be developed as a novel marker for scavenging of RCCs in diabetes.

Human plasma carnosine quantification by developing a sensitive multiple reaction monitoring method.

Step-by-step real time monitoring of a catalytic amination reaction

The multiple reaction monitoring mode of a triple quadrupole mass spectrometer is used to examine the Buchwald-Hartwig amination reaction at 0.1% catalyst loading in real-time using sequential addition of reagents to probe the individual steps in the cycle. This is a powerful new method for probing reactions under realistic conditions.

Monitoring proteolytic processing events by quantitative mass spectrometry

INTRODUCTION

Protease activity plays a key role in a wide variety of biological processes including gene expression, protein turnover and development. misregulation of these proteins has been associated with many cancer types such as prostate, breast, and skin cancer. thus, the identification of protease substrates will provide key information to understand proteolysis-related pathologies. Areas covered: Proteomics-based methods to investigate proteolysis activity, focusing on substrate identification, protease specificity and their applications in systems biology are reviewed. Their quantification strategies, challenges and pitfalls are underlined and the biological implications of protease malfunction are highlighted. Expert commentary: Dysregulated protease activity is a hallmark for some disease pathologies such as cancer. Current biochemical approaches are low throughput and some are limited by the amount of sample required to obtain reliable results. Mass spectrometry based proteomics provides a suitable platform to investigate protease activity, providing information about substrate specificity and mapping cleavage sites.

Bacterial Glycosyltransferases: Challenges and Opportunities of a Highly Diverse Enzyme Class Toward Tailoring Natural Products

The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition GTs also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial GTs show a higher sequence similarity in comparison to mammalian ones. Even when most GTs are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial GTs, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.

Position of Proline Mediates the Reactivity of S-Palmitoylation

Palmitoylation, a post-translational modification in which a saturated 16-carbon chain is added predominantly to a cysteine residue, participates in various biological functions. The position of proline relative to other residues being post-translationally modified has been previously reported as being important. We determined that proline is statistically enriched around cysteines known to be S-palmitoylated. The goal of this work was to determine how the position of proline influences the palmitoylation of the cysteine residue. We established a mass spectrometry-based approach to investigate time- and temperature-dependent kinetics of autopalmitoylation in vitro and to derive the thermodynamic parameters of the transition state associated with palmitoylation; to the best of our knowledge, our work is the first to study the kinetics and activation properties of the palmitoylation process. We then used these thermochemical parameters to determine if the position of proline relative to the modified cysteine is important for palmitoylation. Our results show that peptides with proline at the -1 position of cysteine in their sequence (PC) have lower enthalpic barriers and higher entropic barriers in comparison to the same peptides with proline at the +1 position of cysteine (CP); interestingly, the free-energy barriers for both pairs are almost identical. Molecular dynamics studies demonstrate that the flexibility of the cysteine backbone in the PC-containing peptide when compared to the CP-containing peptide explains the increased entropic barrier and decreased enthalpic barrier observed experimentally.

Utilization of real-time electrospray ionization mass spectrometry to gain further insight into the course of nucleotide degradation by intestinal alkaline phosphatase

RATIONALE

Related with its ability to degrade nucleotides, intestinal alkaline phosphatase (iAP) is an important participant in intestinal pH regulation and inflammatory processes. However, its activity has been investigated mainly by using artificial non-nucleotide substrates to enable the utilization of conventional colorimetric methods. To capture the degradation of the physiological nucleotide substrate of the enzyme along with arising intermediates and the final product, the enzymatic assay was adapted to mass spectrometric detection. Therewith, the drawbacks associated with colorimetric methods could be overcome.

METHODS

Enzymatic activity was comparatively investigated with a conventional colorimetric malachite green method and a single quadrupole mass spectrometer with an electrospray ionization source using the physiological nucleotide substrates ATP, ADP or AMP and three different pH-values in either methodological approach. By this means the enzymatic activity was assessed on the one hand by detecting the phosphate release spectrometrically at defined time points of enzymatic reaction or on the other by continuous monitoring with mass spectrometric detection.

RESULTS

Adaption of the enzymatic assay to mass spectrometric detection disclosed the entire course of all reaction components--substrate, intermediates and product--resulting from the degradation of substrate, thereby pointing out a stepwise removal of phosphate groups. By calculating enzymatic substrate conversion rates a distinctively slower degradation of AMP compared to ADP or ATP was revealed together with the finding of a substrate competition between ATP and ADP at alkaline pH.

CONCLUSIONS

The comparison of colorimetric and mass spectrometric methods to elucidate enzyme kinetics and specificity clearly underlines the advantages of mass spectrometric detection for the investigation of complex multi-component enzymatic assays. The entire course of enzymatic substrate degradation was revealed with different nucleotide substrates, thus allowing a specific monitoring of intestinal alkaline phosphatase activity.

Purification and characterization of a betanidin glucosyltransferase from Amaranthus tricolor L catalyzing non-specific biotransformation of flavonoids

Betacyanins are the major pigments present in Amaranthus tricolor, a leafy vegetable consumed globally. The terminal glycosylation of the aglycone betanidin is an important step in the biosynthesis of this natural red antioxidant pigment. A betanidin 5-O-glucosyltransferase (BGT) was fully purified to 134 folds (specific activity, 265.2 nkat mg(-1)) from the red amaranth by ammonium sulfate precipitation followed by hydrophobic interaction, anion exchange and size exclusion chromatography. Homogeneity of the purified protein was confirmed by 2-dimensional polyacrylamide gel electrophoresis (2D PAGE). The molecular weight of the enzyme determined by liquid chromatography-mass spectrometry (LC-MS) was found to be 62.8 kDa. Furthermore, the enzyme glycosylated flavonoids (kaempferol and quercetin) but not anthocyanidins, presence of which is mutually exclusive to betacyanin accumulating plants. The apparent Km (344±2.34 μM) and Vmax (17.24 μM min(-1)) of the enzyme were determined by LC-MS/MS. Peptide mass fingerprinting of the purified protein showed 38.4% coverage of peptide masses with anthocyanidin 3-O-glucosyltransferase from Zea mays. Study on this purified enzyme, for the first time, revealed its role of glycosylation in biosynthesis of betacyanin in A. tricolor and indicates promiscuous substrate-specificity.

Combining chemical labeling, bottom-up and top-down ion-mobility mass spectrometry to identify metal-binding sites of partially metalated metallothionein

Metalation and demetalation of human metallothionein-2A (MT) with Cd(2+) is investigated by using chemical labeling and "bottom-up" and "top-down" proteomics approaches. Both metalation and demetalation of MT-2A by Cd(2+) are shown to be domain specific and occur as two distinct processes. Metalation involves sequential addition of Cd(2+) to the α-domain resulting in formation of an intermediate, Cd4MT. Chemical labeling with N-ethylmaleimide (NEM) and tandem mass spectrometry experiments clearly show that the four metal ions are located in the α-domain. In the presence of excess Cd(2+), the Cd4MT intermediate reacts to add Cd(2+) to the β-domain to yield the fully metalated Cd7MT. Demetalation occurs in the reverse order, i.e., Cd(2+) is removed (by EDTA) first from the β-domain followed by Cd(2+) removal from the α-domain. Metalation of human MT-2A is shown to be metal ion specific by comparing relative metal ion binding constants for Cd(2+) and Zn(2+).

Online electrospray ionization mass spectrometric monitoring of protease-catalyzed reactions in real time

Although there are a lot of well established methods for monitoring enzyme-catalyzed reactions, most of them are based on changes in spectroscopic properties during the conversion of substrates to products. However, reactions without optical changes are common, which are inapplicable to these spectroscopic methods. As an alternative technique for enzymologic research, mass spectrometry (MS) is favored due to its specificity, sensitivity, and the ability to obtain stoichiometric information. In this work, probe electrospray ionization (PESI) source coupled with a time of flight mass spectrometer was employed to monitor some typical protease-catalyzed reactions, including pepsinolysis and trypsinolysis of cytochrome c in real time. Due to the high electrical conductivity of each reaction system, corona discharges are likely to occur, which would decrease intensities of mass spectrometric signals. An ultra-fine sampling probe and an auxiliary vapor spray were adopted to prevent corona discharges. Experimental results from peptic and tryptic digestions of cytochrome c showed different and characteristic catalytic pathways. With the data presented in this study, PESI-MS can be considered as a potential tool for real-time monitoring of enzymatic reactions because of its simplicity in instrumental configuration, wide applicability under harsh conditions, and flexibility in combination with other techniques.

Enabling Lead Discovery for Histone Lysine Demethylases by High-Throughput RapidFire Mass Spectrometry

A high-throughput RapidFire mass spectrometry assay is described for the JMJD2 family of Fe2+, O2, and α-ketoglutarate-dependent histone lysine demethylases. The assay employs a short amino acid peptide substrate, corresponding to the first 15 amino acid residues of histone H3, but mutated at two positions to increase assay sensitivity. The assay monitors the direct formation of the dimethylated-Lys9 product from the trimethylated-Lys9 peptide substrate. Monitoring the formation of the monomethylated and des-methylated peptide products is also possible. The assay was validated using known inhibitors of the histone lysine demethylases, including 2,4-pyridinedicarboxylic acid and an α-ketoglutarate analogue. With a sampling rate of 7 s per well, the RapidFire technology permitted the single-concentration screening of 101 226 compounds against JMJD2C in 10 days using two instruments, typically giving Z′ values of 0.75 to 0.85. Several compounds were identified of the 8-hydroxyquinoline chemotype, a known series of inhibitors of the Lys9-specific histone demethylases. The peptide also functions as a substrate for JMJD2A, JMJD2D, and JMJD2E, thus enabling the development of assays for all 3 enzymes to monitor progress in compound selectivity. The assay represents the first report of a RapidFire mass spectrometry assay for an epigenetics target.

Determination of steady-state kinetic parameters for a xylanase-catalyzed hydrolysis of neutral underivatized xylooligosaccharides by mass spectrometry

A direct mass spectrometric approach was used for the determination of steady-state kinetic parameters, the turnover number (k(cat)), the Michaelis constant (K(M)), and the specificity constant (k(cat)/K(M)) for an enzyme-catalyzed hydrolysis of xylooligosaccharides. Electrospray ionization mass spectrometry was performed to observe product distributions and to determine k(cat), K(M), and k(cat)/K(M) values for Trichoderma reesei endo-1,4-beta-xylanase II (TRX II) with xylohexaose (Xyl(6)), xylopentaose (Xyl(5)), xylotetraose (Xyl(4)), and xylotriose (Xyl(3)) as substrates. The determined k(cat)/K(M) values (0.93, 0.37, 0.027, and 0.00015 microM(-1) s(-1), respectively) indicated that Xyl(6) was the most preferred substrate of TRX II. In addition, the obtained K(M) value for Xyl(5) (136 microM) was roughly twice as high as that for Xyl(6) (73 microM), suggesting that at least six putative subsites contribute to the substrate binding in the active site of TRX II. Previous mass spectrometric assays for enzyme kinetics have been used mostly in the case of reactions that result in a transfer of acidic groups (e.g., phosphate) into neutral oligosaccharides giving rise to negatively charged products. Here we demonstrate that such analysis is also feasible in the case of neutral underivatized oligosaccharides. Implications of the results for the catalytic mechanism of TRX II in particular are discussed.

Applications of mass spectrometry in early stages of target based drug discovery

Mass spectrometry (MS) has been applied to drug discovery for many years. With the advent of new ionization techniques, MS has emerged as an important analytical tool in identification and characterization of protein targets, structure elucidation of synthetic compounds, and early drug metabolism and pharmacokinetics studies. Two MS-based strategies, function-based and affinity-based, have been employed in recent years for screening and evaluation of compounds. In the function-based approach, the effects of compounds on the biological activity of a target molecule are measured. In the affinity-based approach, compounds are screened based on their binding affinities to target molecules. The interaction between targets and compounds can be directly evaluated by monitoring the formation of non-covalent target-ligand complexes (direct detection) or indirectly evaluated by detecting the compounds after separating bound compounds from unbound (indirect detection). Various techniques including high performance liquid chromatography (HPLC)-MS, size exclusion chromatography (SEC)-MS, frontal affinity chromatography (FAC)-MS and desorption/ionization on silicon (DIOS)-MS can be applied. The recent advances, relative advantages, and limitations of each MS-based method as a tool in compound screening and compound evaluation in the early stages of drug discovery are discussed in this review.

Probing the role of tightly bound phosphoenolpyruvate in Escherichia coli 3-deoxy-d-manno-octulosonate 8-phosphate synthase catalysis using quantitative time-resolved electrospray ionization mass spectrometry in the millisecond time range

Escherichia coli 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of phosphoenolpyruvate (PEP) and D-arabinose 5-phosphate (A5P) to produce KDO8P and inorganic phosphate. The enzyme is often isolated with varying amounts of tightly bound PEP substrate. To better understand the role of tightly bound PEP in E. coli KDO8P synthase catalysis, a combination of transient kinetic methodologies including rapid chemical quench and mass spectrometry techniques such as time-resolved electrospray ionization mass spectrometry (ESI-TOF MS) were used to study the enzyme purified both in the PEP-bound state and in the unbound state. Pre-steady state burst and single-turnover experiments using radiolabeled [1-(14)C] and [(32)P]A5P revealed significant kinetic differences between these enzyme preparations. The active sites concentrations for the bound and unbound states of the enzyme were almost the same (approximately 100%) and the product release for both states of the enzyme was rate limiting. However, the rate constant of product formation for the PEP-bound enzyme (125 s(-1)) was higher than that of the unbound enzyme (46 s(-1)). This was further confirmed by single-turnover experiments using radiolabeled [(32)P]A5P. Interestingly, when PEP was removed from the PEP-bound enzyme and external PEP was added before the kinetic experiments, both the pre-steady state burst and the single-turnover kinetic parameters were similar to those of the enzyme purified in the unbound state. The rate constants of product formation were determined as 44 s(-1) (burst experiment) and 48 s(-1) (single-turnover experiment). The reaction kinetics of the E. coli KDO8P synthase was also followed by time-resolved ESI mass spectrometry. To validate the suitability of this technique for conducting enzyme kinetics, the standard reaction of p-nitrophenyl acetate hydrolysis by chymotrypsin was analyzed by stopped-flow and time-resolved ESI-TOF MS. The rate constant of p-nitrophenol formation followed by stopped-flow spectrophotometry matched perfectly the rate constant of acetyl-chymotrypsin intermediate formation followed by time-resolved ESI-TOF MS (0.1 s(-1)). The catalytic properties of the PEP-bound and unbound states of the E. coli KDO8P synthase were then studied on a millisecond time scale. The changes in the intensity of E*PEP, E*KDO8P, and E*intermediate complexes as a function of time were quantified and the reaction kinetics were modeled using KinTekSim simulation software. An analysis of the reaction kinetics established the kinetic competence of the intermediate based upon the rate constants for substrate decay and product formation. The ability of time-resolved ESI-TOF MS to detect and monitor the kinetics for the reaction intermediate constitutes a significant advantage over the traditional rapid chemical quench technique. For all three states of the enzyme (PEP-bound, unbound, and PEP removed from the PEP-bound state) the rate constants obtained by time-resolved ESI-TOF MS matched the pre-steady state rates determined by rapid chemical quench. A comparison of reaction time courses for each state of the enzyme revealed that, in the case of PEP-bound enzyme, the enzymatic reaction reached completion faster than that for the unbound state. In summary, these studies led to the conclusion that bound PEP has an important role in catalysis, maintaining the enzyme in a conformational state optimal for catalytic activity, and established the kinetic competence of the reaction intermediate. This technique has broad applicability for the kinetic analysis of any enzyme system where the substrates, products, or intermediates are eluding the common detection techniques or as a method alternative to the widely used radioactivity assays.

High-throughput mass-spectrometry monitoring for multisubstrate enzymes: determining the kinetic parameters and catalytic activities of glycosyltransferases

A novel high-throughput screening (HTS) method with electrospray time-of-flight (ESI-TOF) mass spectrometry allows i) rapid and broad screening of multisubstrate enzyme catalytic activity towards a range of donor and acceptor substrates; ii) determination of full multisubstrate kinetic parameters and the binding order of substrates. Two representative glycosyltransferases (GTs, one common, one recently isolated, one O-glycosyltransferase (O-GT), one N-glycosyltransferase (N-GT)) have been used to validate this system: the widely used bovine beta-1,4-galactosyltransferase (EC 2.4.1.22), and the recently isolated Arabidopsis thaliana GT UGT72B1 (EC 2.4.1.-). The GAR (green/amber/red) broad-substrate-specificity screen, which is based on the mass ion abundance of product, provides a fast, high-throughput method for finding potential donors and acceptors from substrate libraries. This was evaluated by using six natural and non-natural donors (alpha-UDP-D-Glucose (UDPGlc), alpha-UDP-N-Acetyl-D-glucosamine (UDPGlcNAc), alpha-UDP-D-5-thioglucose (UDP5SGlc), alpha-GDP-L-fucose (GDPFuc), alpha-GDP-D-mannose (GDPMan), alpha,beta-UDP-D-mannose (UDPMan)) and 32 broad-ranging acceptors (sugars, plant hormones, antibiotics, flavonoids, coumarins, phenylpropanoids and benzoic acids). By using the fast-equilibrium assumption, KM, kcat and KIA were determined for representative substrates, and these values were used to determine substrate binding orders. These screening methods applied to the two very different enzymes revealed some unusual substrate specificities, thus highlighting the utility of broad-ranging substrate screening. For UGT72B1, it was shown that the donor specificity is determined largely by the nucleotide moiety. The method is therefore capable of identifying GT enzymes with usefully broad carbohydrate-transfer ability.

Monitoring enzymatic conversions by mass spectrometry: a critical review

This review highlights recent advances in the application of electrospray ionisation and matrix-assisted laser desorption/ionisation mass spectrometry (MS) to study enzymatic reactions. Several assay schemes for different fields of application are presented. The employment of MS as a means of detection in pre-steady-state kinetic studies by rapid-mixing direct analysis and rapid-mixing quench flow techniques is discussed. Several steady-state kinetic studies of a broad range of different enzymatic systems are presented as well as enzyme inhibition studies for various target enzymes. As a promising new development multiplex assays, which monitor the conversion of several substrates simultaneously in one experiment, are described. This assay type has been used for competition studies, enzymatic activity screenings and for diagnostic purposes in clinical chemistry. Generally, it can be concluded that mass spectrometry offers an intriguing alternative as detection methodology in enzymatic bioassays. Its applicability for the monitoring the conversion of naturally occurring substrates and its overall versatility make MS an especially promising tool for the study of enzyme-catalysed processes.

Mechanistic studies on enzymatic reactions by electrospray ionization MS using a capillary mixer with adjustable reaction chamber volume for time-resolved measurements

Mass spectrometry (MS)-based techniques have enormous potential for kinetic studies on enzyme-catalyzed processes. In particular, the use of electrospray ionization (ESI) MS for steady-state measurements is well established. However, there are very few reports of MS-based studies in the pre-steady-state regime, because it is difficult to achieve the time resolution required for this type of experiment. We have recently developed a capillary mixer with adjustable reaction chamber volume for kinetic studies by ESI-MS with millisecond time resolution (Wilson, D. J.; Konermann, L. Anal. Chem. 2003, 75, 6408-6414). Data can be acquired in kinetic mode, where the concentrations of selected reactive species are monitored as a function of time, or in spectral mode, where entire mass spectra are obtained for selected reaction times. Here, we describe the application of this technique to study the kinetics of enzyme reactions. The hydrolysis of p-nitrophenyl acetate by chymotrypsin was chosen as a simple chromophoric model system. On-line addition of a "makeup solvent" immediately prior to ionization allowed the pre-steady-state accumulation of acetylated chymotrypsin to be monitored. The rate constant for acetylation, as well as the dissociation constant of the enzyme-substrate complex obtained from these data, is in excellent agreement with results obtained by conventional stopped-flow methods. Bradykinin was chosen to illustrate the performance of the ESI-MS-based method with a nonchromophoric substrate. In this case, the unfavorable rate constant ratio for acylation and deacylation of the enzyme precluded measurements in the pre-steady-state regime. Steady-state experiments were carried out to determine the turnover number and the Michaelis constant for bradykinin. The methodologies used in this work open a wide range of possibilities for future ESI-MS-based kinetic assays in enzymology.

General assay for sugar nucleotidyltransferases using electrospray ionization mass spectrometry

An electrospray ionization mass spectrometry-based assay has been developed to study the class of enzymes called sugar nucleotidyltransferases that couple sugar-1-phosphates and nucleotide triphosphates to form Leloir pathway glycosyl donors. The recombinant Escherichia coli and the commercially available yeast uridine-diphosphoglucose pyrophosphorylases were used as model systems. This technique allows the simultaneous and direct detection of the substrates and products without separation and, as described, is as sensitive as traditional coupled techniques. More importantly, the assay is capable of easily measuring kinetic values and inhibition constants for a range of natural and nonnatural substrates. This new assay was used to show for the first time that the reaction of the commercially available yeast uridine-diphosphoglucose pyrophosphorylase preparation is competitively inhibited by adenosine 5'-triphosphate (ATP), an observation that indicates a single active site that accepts both uridine 5'-triphosphate and ATP substrates.

Mass spectrometric approaches for the investigation of dynamic processes in condensed phase

Mass spectrometry (MS) offers many advantages over other established spectroscopic techniques employed for the investigation of processes in condensed phase. The sensitivity, specificity, and speed afforded by MS-based methods enable to obtain very valuable insights into the mechanism of complex dynamic processes. Off-line methods rely on quenching to halt the progress of the reaction of interest and allow for the implementation of a broad range of analytical procedures for sample fractionation, isolation, or desalting. On the contrary, on-line methods are designed to carry out the real-time monitoring of dynamic processes through a continuous uninterrupted analysis of reaction mixtures, with the only caveat that the sample solutions be directly amenable to the available ionization technique. The utilization of rapid mixing devices in direct connection with a mass spectrometer or included in off-line schemes provides access to the initial moments of a reaction, which can offer very important information about the reaction mechanism. This report summarizes the different off- and on-line strategies developed to study chemical and biochemical reactions in solution and obtain kinetic/mechanistic information. The merits of the various experimental designs, the characteristics of the different instrumental setups, and the factors affecting time resolution are discussed with the aid of specific examples, which highlight the contributions of MS to the different facets of the investigation of dynamic processes in condensed phase.

Kinetic and substrate binding analysis of phosphorylase b via electrospray ionization mass spectrometry: a model for chemical proteomics of sugar phosphorylases

As a general strategy for determining the chemical function of the class of enzymes that cleaves glycosidic linkages with phosphate, the first mass spectrometry and direct detection assay for sugar phosphorylases has been developed and used to study the inhibition and minimal binding requirements of rabbit muscle phosphorylase b. In contrast to the currently employed assays for these enzymes that measure the nonphysiologically relevant reverse reaction of glycosidic bond synthesis and thereby require prior knowledge of not just one but two sugar components, this new method has the potential to greatly reduce the complexity in discovering the substrate specificity of a new enzyme. Certain phosphorylases can catalyze the degradation of glycogen into alpha-D-glucose-1-phosphate and are targets for the development of antidiabetic therapeutics. By electrospray ionization mass spectrometry analysis, the kinetic parameters K(m), V(max), and K(i) (for alpha/beta-D-glucose) have been determined for the rabbit muscle phosphorylase b. This enzyme accepts maltoheptaose, maltohexaose, and maltopentaose as substrates in the direction of glycogen degradation, but the tetrasaccharide maltotetraose cannot serve as a substrate for this phosphorylysis reaction.

Inhibition kinetics of carba- and C-fucosyl analogues of GDP-fucose against fucosyltransferase V: implication for the reaction mechanism

Inhibition kinetics of two isosteric analogues of GDP-fucose (GDP-Fuc) were investigated against fucosyltransferase V using electrospray ionization mass spectrometry coupled to multiple reaction monitoring. The carba-Fuc analogue was found to be a competitive inhibitor with a K(i) value of 67.1+/-9.8 microM, similar to the K(m) value for GDP-Fuc (50.4+/-5.5 microM), while the C-Fuc analogue exhibited significantly weak competitive inhibition with a K(i) value of 889+/-93 microM.

Quantitative matrix-assisted laser desorption/ionization mass spectrometry for the determination of enzyme activities

Quantitative matrix-assisted laser desorption/ionization (MALDI) time-of-flight (ToF) mass spectrometry (MS) was applied for the determination of concentrations of low-molecular-weight (< 400Da) substrates and products of enzyme-catalyzed reactions. Isotope-labeled and fluorinated internal standards were used for the quantification. Automated quantitative MALDI-ToF MS analysis of quenched samples allowed the direct and simultaneous observation of time-dependent decrease of substrate concentration and increase of product concentration without any need for prepurification or desalting steps. The results showed good agreement with established but more elaborate analytical methods. MALDI-ToF MS thus is an interesting alternative tool for the determination of enzyme activities. Due to automated and miniaturized measurement it is especially suitable for the screening of biocatalysts.

Discovery of the archaeal chemical link between glycogen (starch) synthase families using a new mass spectrometry assay

Starch and its analogue glycogen are biosynthesized by enzymes that have been classified by sequence similarities into two families that have no significant sequence overlap: the animal/fungal glycogen synthases and the plant/bacterial glycogen (starch) synthases. Recent gene sequence analysis of putative archaea enzymes implicates them as a third family that links the structural and functional features of the other two classes. Herein, we present the first rapid electrospray ionization mass spectrometry-based assay to quantify any carbohydrate-polymerizing activity, the first cloning and recombinant expression as well as verification of the putative function of a glycogen synthase from the hyperthermophilic archaea Pyrococcus furiosus, and the characterization of a variety of glycogen synthases with the new assay. The new assay allowed the determination of Km and Vmax values for the rabbit, yeast, and P. furiosus glycogen synthases. Most surprisingly, unlike the synthases from rabbit or yeast and in contradiction to what would be expected from structural studies of other nucleotide-sugar binding proteins, the synthase from the archaea source accepts both uridine- and adenine-diphosphate activated glucose competitively and with comparable affinities to form a glucose polymer. This loose substrate specificity implicates this protein as the chemical link between the two branches of glycogen synthases that have evolved to accept primarily one or the other nucleotide as well as a good source enzyme for polymer bioengineering efforts.

A Capillary Mixer with Adjustable Reaction Chamber Volume for Millisecond Time-Resolved Studies by Electrospray Mass Spectrometry

A novel continuous-flow apparatus for on-line kinetic studies of (bio)chemical solution-phase processes by electrospray ionization mass spectrometry (ESI-MS) is described. The device is based on two concentric capillaries. Fluid is released from the inner capillary into the intercapillary space, where it mixes with solution flowing through the outer capillary, thus initiating the reaction of interest. Gas-phase analyte ions are formed near the tip of the outer capillary by pneumatically assisted ESI. This setup allows the mixer to be placed directly within the ion source, thus providing a minimal dead volume of ~8 nL. Time-resolved data can be recorded in both "spectral" and "kinetic" modes. In the former case, the position of the inner capillary is fixed at various points, such that entire mass spectra can be recorded for selected reaction times. For experiments in kinetic mode, the mass spectrometer monitors the signal intensity at selected m/z values, while the inner capillary is continuously pulled back, thus providing intensity-time profiles for specific reactive species. A theoretical framework is developed that allows the measured kinetics to be analyzed by taking into account the effects of laminar flow within the reaction capillary. Failure to take these effects into account results in erroneous rate constants. Studies on the demetalation kinetics of chlorophyll reveal that the apparatus can reliably measure rate constants up to at least 100 s-1. This represents a substantial improvement over previous ESI-MS-based kinetic methods. Spectral mode experiments on the refolding of ubiquitin show the changing proportions of denatured and tightly folded protein subpopulations in solution. When monitored in kinetic mode, the refolding process was found to proceed with a rate constant of 5.2 s-1.

Multiplex inhibitor screening and kinetic constant determinations for yeast hexokinase using mass spectrometry based assays

An electrospray ionization mass spectrometry based assay was developed for kinetic measurements and inhibitor screening of yeast hexokinase. There is considerable discrepancy in the literature as to the accuracy of kinetic data obtained for hexokinase. In the assay described herein, the product, glucose 6-phosphate was directly monitored by ion trap mass spectrometry and quantified using an internal standard, 2 deoxy-glucose 6-phosphate. The kinetic parameters, K(M) and V(max) for the two substrates were determined without using a coupling enzyme as is normally employed in the traditional spectrophotometric assay for systems lacking a chromophore. In addition, hexokinase was successfully immobilized onto an amino-link gel, and a mock library was screened against the immobilized enzyme for the identification of possible inhibitors. After comparing the mass spectra of the library before and after incubation, trehalose 6-phosphate, ADP, and oxidized glutathione were differentiated from other weak or non-inhibitors. Inhibition behavior of ADP with respect to ATP was further evaluated with the ESI-MS assay and the value of K(i) was determined. This ESI-MS assay was demonstrated to be both accurate and precise for determining kinetic constants and for identifying enzyme inhibitors.

ESI-MS in the study of the activity of α-chymotrypsin in aqueous surfactant media

The catalytic activity of alpha-chymotrypsin on a model and a peptide substrate, in the supramolecular system "enzyme-surfactant" in water solution, has been studied by electrospray ionization mass spectrometry. Hydrolysis of N-succinyl-L-phenylalanine p-nitroanilide as the model compound, catalysed by alpha-chymotrypsin in the presence of monomeric cetyltributylammonium bromide, has been followed by UV and ESI-MS detection. Kinetic data, which are essentially identical independent of their determination techniques, show a twelve fold improvement of the enzyme catalytic efficiency when compared with the reaction carried out in the absence of the additive. Once validated, the ESI-MS technique was used to study the hydrolytic activity of the enzyme on a peptide substrate like substance P: it is worth emphasising that the spectrophotometric detection cannot be employed on peptides, where the chromophores are untouched by the hydrolytic process. Substance P hydrolyses in aqueous surfactant following dichotomic kinetics, which are initially rapid but then slow down as the reaction progress. The results presented in this paper are expected to extend studies on biocatalysis in aqueous surfactant media to a wide range of substrates, independent of their spectroscopic properties.

Kinetic characterization of enzyme inhibitors using electrospray-ionization mass spectrometry coupled with multiple reaction monitoring

Electrospray ionization mass spectrometry coupled to multiple reaction monitoring (ESI-MS/MRM) has been applied for the first time to analyze enzyme inhibitor kinetics. Specifically, a known competitive inhibitor, guanosine 5'-monophosphate (GMP), and a synthetic, transition-state analogue inhibitor, guanosine 5'-[1D-(1,3,4/2)-5-methyl-5-cyclohexene-1,2,3,4-tetrol 1-diphosphate] (1) have been characterized against recombinant fucosyltransferase (Fuc-T) V using ESI-MS/MRM. Dixon analysis with GMP yielded a signature plot for competitive inhibition. Nonlinear regression analysis gave a Ki of 211.8+/-24.7 microM. The conventional analysis using GDP-[U-14C]-Fuc yielded a similar Ki value of 235.6+/-59.4 microM, confirming the validity of the MS-based method. The synthetic inhibitor 1 showed potent competitive inhibition with a Ki of 25.6+/-2.8 microM. Although 1 possesses a chemically reactive allyl phosphate group, ESI-MS/MRM showed that there was no reduction in the concentration of 1 and no production of a predicted metabolite GDP during the assay. MS/MS also confirmed the absence of a possible pseudo-trisaccharide product. The results clearly show that 1 is neither a slow-reacting donor nor does it act as a suicide-type inhibitor toward Fuc-T V. ESI-MS/MRM is therefore a powerful tool for the kinetic characterization of enzyme inhibitors, providing complete disclosure of the mechanism of action of 1 as an inhibitor.