Subnanoliter enzymatic assays on microarrays

Many areas of research today are based on enzymatic assays most of which are still performed as enzyme-linked immunosorbent assays in microtiter plates. The demand for highly parallel screening of thousands of samples eventually led to a miniaturization and automation of these assays. However, the final transfer of enzymatic assays from a microtiter-based technology to microarrays has proven to be difficult for various reasons, such as the inability to maintain unbound reaction products on the spot of reaction or the missing capability of multiplexing. Here, we have conducted multiplex enzymatic assays in subnanoliter volumes on a single microarray using the multiple spotting technology. We were able to measure enzymatic activity with a sensitivity down to 35 enzyme molecules, applying only conventional flat microarray surfaces and standard microarray hardware. We have performed assays of inhibition and applied this format for the detection of prognostic markers, such as cathepsin D. The new approach allows the rapid and multiplex screening of thousands of samples on a single microarray with applications in drug screening, metagenomics, and high-throughput enzyme assays.     

Sequential enzymatic reactions and stability of biomolecules immobilized onto phospholipid polymer nanoparticles

Polymer nanoparticles for sequential enzymatic reactions were prepared by combining a phospholipid polymer shell with a polystyrene core. The active ester groups for the bioconjugation and phospholipid polar groups were incorporated into the phospholipid polymer backbone using a novel active ester monomer and 2-methacryloyloxyethyl phosphorylcholine. For the sequential enzymatic reactions, acetylcholinesterase, choline oxidase, and horseradish peroxidase-labeled IgG were immobilized onto the nanoparticles. As substrates, acetylcholine chloride, choline chloride, and tetramethylbenzidine were added to the nanoparticle suspension, the acetylcholine chloride was converted to choline chloride, the choline chloride was oxidized by choline oxidase, and hydrogen peroxide was then formed as an enzymatic degradation product. The hydrogen peroxide was used for the next enzymatic reaction (oxidized by peroxidase) with tetramethylbenzidine. The sequential enzymatic reactions on the nanoparticles via degradation products (hydrogen peroxide) were significantly higher than that of the enzyme mixture. This result indicated that the diffusion pathway of the enzymatic products and the localization of the immobilized enzyme were important for these reactions. These nanoparticles were capable of facilitating sequential enzymatic reactions.     

海洋贝类蛋白资源酶解利用研究进展

海洋贝类蛋白资源的高效利用是我国海洋生物资源可持续利用中重要研究方向,酶解技术已经成为海洋贝类蛋白资源高值化、资源化、生态化开发的重要手段,具有重要的理论意义和实践意义。贝类酶解采用的主要商品酶为中性蛋白酶、风味酶、木瓜蛋白酶、菠萝蛋白酶、胃蛋白酶等,酶解效果评价的主要参数为蛋白水解率以及抗氧化、清除自由基等生理功能指标,酶解产物主要用途为调味品、营养功能制品、饲料蛋白产品、医药品等。从商品工具酶的选择,酶解优选工艺、酶解产物应用等角度,综合论述了海洋贝类蛋白资源酶解利用的发展现状,展望了其发展趋势,为我国商品酶制剂在海洋贝类乃至整个海洋生物蛋白资源的高值化开发中的利用提供参考。     

Relations between biochemical thermodynamics and biochemical kinetics

The parameters in steady-state or rapid-equilibrium rate equations for enzyme-catalyzed reactions depend on the temperature, pH, and ionic strength, and may depend on the concentrations of specific species in the buffer. When the complete rate equation (i.e. the equation with parameters for the reverse reaction as well as the forward reaction) is determined, there are one or more Haldane relations between some of the kinetic parameters and the apparent equilibrium constant for the reaction that is catalyzed. When the apparent equilibrium constant can be calculated from the kinetic parameters, the equilibrium composition can be calculated. This is remarkable because the kinetic parameters all depend on the properties of the enzymatic site, but the apparent equilibrium constant and the equilibrium composition do not. The effects of ionic strength and pH on the unoccupied enzymatic site and the occupied enzymatic site have to cancel in the Haldane relation or in the calculation of the apparent equilibrium constant using the rate constants for the steps in the mechanism. Several simple enzymatic mechanisms and their complete rate equations are discussed.     

Evolutionary analysis of enzymes using Chisel

MOTIVATION: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes. RESULTS: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, 'binning' of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.     

Isolation of bovine retinal pigment epithelial cells using adhesion to agarose: demonstration of cellular and regional heterogeneity.

The retinal pigment epithelium (RPE) shows cell heterogeneity in morphology and enzymatic activity. Routine isolation procedures for RPE cells may reduce enzymatic activity and prevent the quantification of regional enzymatic differences in vivo. We developed a new technique for the isolation of RPE cells based on adhesion of the cells to agarose. The morphology of the isolated cells resembled that of RPE cells in vivo. The cells were viable in the dye exclusion test and showed a histochemical staining pattern as RPE cells in vivo. With this technique, quantitative regional differences in the enzymatic activities were detected.     

Application of high throughput pretreatment and co‐hydrolysis system to thermochemical pretreatment. Part 1: Dilute acid

Because conventional approaches for evaluating sugar release from the coupled operations of pretreatment and enzymatic hydrolysis are extremely time and material intensive, high throughput (HT) pretreatment and enzymatic hydrolysis systems have become vital for screening large numbers of lignocellulosic biomass samples to identify feedstocks and/or processing conditions that significantly improve performance and lower costs. Because dilute acid pretreatment offers many important advantages in rendering biomass highly susceptible to subsequent enzymatic hydrolysis, a high throughput pretreatment and co‐hydrolysis (HTPH) approach was extended to employ dilute acid as a tool to screen for enhanced performance. First, a single‐step neutralization and buffering method was developed to allow effective enzymatic hydrolysis of the whole pretreated slurry. Switchgrass and poplar were then pretreated with 0.5% and 1% acid loadings at a 5% solids concentration, the resulting slurry conditioned with the buffering approach, and the entire mixture enzymatically hydrolyzed. The resulting sugar yields demonstrated that single‐step neutralizing and buffering was capable of adjusting the pH as needed for enzymatic saccharification, as well as overcoming enzyme inhibition by compounds released in pretreatment. In addition, the effects of pretreatment conditions and biomass types on susceptibility of pretreated substrates to enzymatic conversion were clearly discernible, demonstrating the method to be a useful extension of HTPH systems. Biotechnol. Bioeng. 2013; 110: 754–762. © 2012 Wiley Periodicals, Inc.     

Production of cellulases and xylanase by Trichoderma reesei F-522 on pretreated wheat straw

Autohydrolyzed and ethanol-alkali pulped wheat straw was examined as a candidate feedstock for both cellulase and xylanase production and enzymatic hydrolysis. Submerged cultures of Trichoderma reesei F-522 grown on hydrothermally modified straw provided culture supernatants of the highest enzymatic activities, whereas the maximal efficiency of enzymatic hydrolysis was recorded in straw treated with ethanol-NaOH mixture. Some culture conditions were optimized to improve the growth and cellulase production by T. reesei on autohydrolyzed wheat straw.     

Some notes on the theory of reaction rates: Enzymatic reactions

A generalized model of an enzymatic reaction in a biological system is used for the construction of a possible model of the “concentrating mechanism” after the introduction of a tracer, and for the formulation of an excretion rate of substances reabsorbed or actively secreted into the urine by the kidneys. In considering this generalized model of the enzymatic reaction, the term “tracer” is used in a limited sense, and it is concluded that a linear system is suitable for the study of the kinetics of the tracer—even in the case when the transport of the tracer between compartments is due to an enzymatic reaction. The rate coefficients of the linear differential systems, which are dependent on the state of the enzymatic system, are functions of the amount of the substrates, as well as of the amounts of activators and inhibitors of the enzymatic reaction and of the amount of the substances, which are responsible for the enzyme production.     

Effect of ionic liquid on activity, stability, and structure of enzymes: A review

Ionic liquids have shown their potential as a solvent media for many enzymatic reactions as well as protein preservation, because of their unusual characteristics. It is also observed that change in cation or anion alters the physiochemical properties of the ionic liquids, which in turn influence the enzymatic reactions by altering the structure, activity, enatioselectivity, and stability of the enzymes. Thus, it is utmost need of the researchers to have full understanding of these influences created by ionic liquids before choosing or developing an ionic liquid to serve as solvent media for enzymatic reaction or protein preservation. So, in the present review, we try to shed light on effects of ionic liquids chemistry on structure, stability, and activity of enzymes, which will be helpful for the researchers in various biocatalytic applications.     

Rapid near infrared spectroscopy for prediction of enzymatic hydrolysis of corn bran after various pretreatments

Efficient generation of a fermentable hydrolysate is a primary requirement in the utilization of fibrous plant biomass as feedstocks in bioethanol processes. The first biomass conversion step usually involves a hydrothermal pretreatment before enzymatic hydrolysis. The purpose of the pretreatment step is to increase the responsivity of the substrate to enzymatic attack and the type of pretreatment affects the enzymatic conversion efficiency. Destarched corn bran is a fibrous, heteroxylan-rich side-stream from the starch industry which may be used as a feedstock for bioethanol production or as a source of xylose for other purposes. In the present study we demonstrate the use of diffuse reflectance near infrared spectroscopy (NIR) as a rapid and non-destructive analytical tool for evaluation of pretreatment effects on destarched corn bran. NIR was used to achieve classification between 43 differently pretreated corn bran samples using principal component analysis (PCA) and hierarchal clustering algorithms. Quantification of the enzymatically released monosaccharides by HPLC was used to design multivariate calibration models (biPLS) on the NIR spectra. The models could predict the enzymatic release of different levels of arabinose, xylose and glucose from all the differently pretreated destarched corn bran samples. The present study also demonstrates a generic, non-destructive solution to determine the enzymatic monosaccharide release from polymers in biomass side-streams, thereby potentially replacing the cumbersome HPLC analysis.     

Low temperature alkali pretreatment for improving enzymatic digestibility of sweet sorghum bagasse for ethanol production

A low temperature alkali pretreatment method was proposed for improving the enzymatic hydrolysis efficiency of lignocellulosic biomass for ethanol production. The effects of the pretreatment on the composition, structure and enzymatic digestibility of sweet sorghum bagasse were investigated. The mechanisms involved in the digestibility improvement were discussed with regard to the major factors contributing to the biomass recalcitrance. The pretreatment caused slight glucan loss but significantly reduced the lignin and xylan contents of the bagasse. Changes in cellulose crystal structure occurred under certain treatment conditions. The pretreated bagasse exhibited greatly improved enzymatic digestibility, with 24-h glucan saccharification yield reaching as high as 98% using commercially available cellulase and β-glucosidase. The digestibility improvement was largely attributed to the disruption of the lignin-carbohydrate matrix. The bagasse from a brown midrib (BMR) mutant was more susceptible to the pretreatment than a non-BMR variety tested, and consequently gave higher efficiency of enzymatic hydrolysis.     

Energy requirements and process design considerations in compression-milling pretreatment of cellulosic wastes for enzymatic hydrolysis

The effectiveness of compression-milling pretreatment of lignocellulosics for enzymatic hydrolysis has been demonstrated for a wide variety of substrate sources. Reductions in the degree of crystallinity and the degree of polymerization of cellulose and partial destruction of the structural integrity of lignocellulosics brought about by compression milling significantly increase the susceptibility of cellulose to enzymatic hydrolysis. The enzymatic hydrolysis yield was found to be directly related to the specific energy input to the cellulosic substrate (kWh/1b substrate) by compression milling, and the energy input can be controlled by the milling time. The enzymatic hydrolysis yeilds from cellulosic materials pretreated by compression milling also vary significantly depending on the source and kind, the composition milling also vary significantly depending on the source and kind, the composition (contents of lignin and other components), and the structure. The power requirements for compression milling which renders equivalent hydrolysis yields also depend on the source and kind of lignocellulosics to be pretreated. For newspaper, the specific energy input required for 55% sugar yield is estimated as 0.3 kWh/lb substrate including 15% power loss. The additional sugar yield gained from the enzymatic hydrolysis of compression-milled newspaper (over and above the sugar yield of untreated substrate) is determined as 453 g sugar/kWh energy input.     

Deriving enzymatic and taxonomic signatures of metagenomes from short read data

Background  

We propose a method for deriving enzymatic signatures from short read metagenomic data of unknown species. The short read data are converted to six pseudo-peptide candidates. We search for occurrences of Specific Peptides (SPs) on the latter. SPs are peptides that are indicative of enzymatic function as defined by the Enzyme Commission (EC) nomenclature. The number of SP hits on an ensemble of short reads is counted and then converted to estimates of numbers of enzymatic genes associated with different EC categories in the studied metagenome. Relative amounts of different EC categories define the enzymatic spectrum, without the need to perform genomic assemblies of short reads.     

Assay of apical membrane enzymes based on fluorogenic substrates.

A series of enzymatic rate assays are described. The assays are based on coumarin derivatives that are fluorogenic substrates for the enzymes dipeptidase IV, aminopeptidase N, alkaline phosphatase, and gamma-glutamyltransferase. These simple assays are rapid and offer improved sensitivity over established colorimetric methods. The substrates have apparent affinities for the enzymes of 5-250 microM. L-Glutamic acid gamma-(7-amido-4-methylcoumarin) is characterized as a substrate of gamma-glutamyltransferase on the basis of inhibition of enzymatic cleavage when the glycylglycine acceptor molecule is omitted and inhibition of the enzymatic reaction by addition of glycine. Assay conditions for the four enzymes are established such that less than 0.6% of the substrate is consumed, fluorescence is proportional to enzymatic product, and results may be directly compared to established colorimetric assays. Intestinal epithelial cells are used both to establish appropriate assay conditions and to demonstrate the utility of the assays.     

Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis: I. Significance and mechanism of cellobiose and glucose inhibition on cellulolytic enzymes

Achievement of efficient enzymatic degradation of cellulose to glucose is one of the main prerequisites and one of the main challenges in the biological conversion of lignocellulosic biomass to liquid fuels and other valuable products. The specific inhibitory interferences by cellobiose and glucose on enzyme-catalyzed cellulose hydrolysis reactions impose significant limitations on the efficiency of lignocellulose conversion — especially at high-biomass dry matter conditions. To provide the base for selecting the optimal reactor conditions, this paper reviews the reaction kinetics, mechanisms, and significance of this product inhibition, notably the cellobiose and glucose inhibition, on enzymatic cellulose hydrolysis. Particular emphasis is put on the distinct complexity of cellulose as a substrate, the multi-enzymatic nature of the cellulolytic degradation, and the particular features of cellulase inhibition mechanisms and kinetics. The data show that new strategies that place the bioreactor design at the center stage are required to alleviate the product inhibition and in turn to enhance the efficiency of enzymatic cellulose hydrolysis. Accomplishment of the enzymatic hydrolysis at medium substrate concentration in separate hydrolysis reactors that allow continuous glucose removal is proposed to be the way forward for obtaining feasible enzymatic degradation in lignocellulose processing.     

Effect of organic sulfur compounds on the chemical and enzymatic transformations of prostaglandin endoperoxide H2.

The effects of several sulfur organic compounds on the enzymatic and non-enzymatic transformations of prostaglandin endoperoxide H2 to prostaglandins were studied. Mercaptoethanol, methional alpha-lipoic acid and dimercaptopropanol increased the chemical (i.e. non-enzymatic) reduction of prostaglandin H2 to prostaglandin F2alpha but except for alpha-lipoic acid, had no effect on the enzymatic conversion of prostaglandin H2 to prostaglandin. In contrast, reduced glutathione showed no effect on the chemical conversion of prostaglandin H2, but exerted a marked and specific stimulation on the enzymatic isomerization of prostaglandin H2 to prostaglandin E2. This specific effect of gluthione may serve to regulate the overall intracellular activity of prostaglandin synthetase as well as the particular ratio of prostaglandins produced.     

Michaelis-Menten kinetics under spatially constrained conditions: application to mibefradil pharmacokinetics

Two different approaches were used to study the kinetics of the enzymatic reaction under heterogeneous conditions to interpret the unusual nonlinear pharmacokinetics of mibefradil. Firstly, a detailed model based on the kinetic differential equations is proposed to study the enzymatic reaction under spatial constraints and in vivo conditions. Secondly, Monte Carlo simulations of the enzyme reaction in a two-dimensional square lattice, placing special emphasis on the input and output of the substrate were applied to mimic in vivo conditions. Both the mathematical model and the Monte Carlo simulations for the enzymatic reaction reproduced the classical Michaelis-Menten (MM) kinetics in homogeneous media and unusual kinetics in fractal media. Based on these findings, a time-dependent version of the classic MM equation was developed for the rate of change of the substrate concentration in disordered media and was successfully used to describe the experimental plasma concentration-time data of mibefradil and derive estimates for the model parameters. The unusual nonlinear pharmacokinetics of mibefradil originates from the heterogeneous conditions in the reaction space of the enzymatic reaction. The modified MM equation can describe the pharmacokinetics of mibefradil as it is able to capture the heterogeneity of the enzymatic reaction in disordered media.     

Enzymatic Reactions inside Biological Condensates

Biological enzymes significantly speed up chemical reactions in living organisms. The complex environment within cells has long been appreciated as a major regulator of enzymatic activities. Recent advances in the rapidly evolving field of biological condensates, which are spontaneously formed by macromolecules through phase separation, suggest new possibilities for how enzymatic reactions may be modulated within cells. Here, we review the latest studies of enzymatic reactions in biological condensates focusing on basic concepts in enzymology and discussing some context-dependent roles of phase separation in regulating biochemical reactions.