Determination of enzyme activity by high-performance liquid chromatography

Enzymatic cell disruption followed by application of imposed potential for enhanced lipid extraction from wet algal biomass employing photosynthetic microbial fuel cell

Solvent-free algal cell lysis using fungal enzyme for enhanced lipid recovery diminishes per unit production cost of algal biodiesel. In this investigation, a triple chamber photosynthetic microbial fuel cell (PMFC) was fabricated, where positive potential was imposed in the extraction chamber to draw the negatively charged lipid ions from the cathodic chamber. Under optimum imposed potential of + 3.0 V (vs standard hydrogen electrode) and with 3.5% (v/v) dosage of fungal enzyme in to the algal consortium of cathodic chamber, a maximum of 79.0% of lipid was recovered. Additionally, enzyme-assisted de-oiled algal biomass was applied in the anodic chamber to function as substrate and mediator for exo-electrogens, and the maximum power density of 10.0 W/m³ with 82.4% removal of chemical oxygen demand was achieved while treating synthetic wastewater. Therefore, this cost-effective exploration demonstrated successful bioelectricity production and concomitant wastewater treatment with solvent-free direct lipid recovery from wet algal biomass through PMFC.

Acquisition of enzymatic progress curves in real time by quenching-free ion exchange chromatography

We describe a quenching-free, 'online' ion exchange chromatography (oIEC) method for the quantitative analysis of enzymatic reactions in real-time. We show that separate quenching of the ongoing reaction performed conventionally is not required, since enzymatic reactions are interrupted upon immobilization of the reaction compounds by binding to the stationary phase of the ion exchange column. The reaction mix samples are directly injected into the column, thereby improving data consistency and allowing automation of the process. The method allows reliable and efficient acquisition of enzymatic progress curves by automatic loading of aliquots of an ongoing reaction at predefined timepoints. We demonstrate the applicability of this method for a variety of enzymatic reactions. SUBJECT: Enzymatic assays and analysis.

Workflow for Data Analysis in Experimental and Computational Systems Biology: Using Python as ‘Glue’

Bottom-up systems biology entails the construction of kinetic models of cellular pathways by collecting kinetic information on the pathway components (e.g., enzymes) and collating this into a kinetic model, based for example on ordinary differential equations. This requires integration and data transfer between a variety of tools, ranging from data acquisition in kinetics experiments, to fitting and parameter estimation, to model construction, evaluation and validation. Here, we present a workflow that uses the Python programming language, specifically the modules from the SciPy stack, to facilitate this task. Starting from raw kinetics data, acquired either from spectrophotometric assays with microtitre plates or from Nuclear Magnetic Resonance (NMR) spectroscopy time-courses, we demonstrate the fitting and construction of a kinetic model using scientific Python tools. The analysis takes place in a Jupyter notebook, which keeps all information related to a particular experiment together in one place and thus serves as an e-labbook, enhancing reproducibility and traceability. The Python programming language serves as an ideal foundation for this framework because it is powerful yet relatively easy to learn for the non-programmer, has a large library of scientific routines and active user community, is open-source and extensible, and many computational systems biology software tools are written in Python or have a Python Application Programming Interface (API). Our workflow thus enables investigators to focus on the scientific problem at hand rather than worrying about data integration between disparate platforms.

Generic HPLC platform for automated enzyme reaction monitoring: Advancing the assay toolbox for transaminases and other PLP-dependent enzymes

Methods for rapid and direct quantification of enzyme kinetics independent of the substrate stand in high demand for both fundamental research and bioprocess development. This study addresses the need for a generic method by developing an automated, standardizable HPLC platform monitoring reaction progress in near real-time. The method was applied to amine transaminase (ATA) catalyzed reactions intensifying process development for chiral amine synthesis. Autosampler-assisted pipetting facilitates integrated mixing and sampling under controlled temperature. Crude enzyme formulations in high and low substrate concentrations can be employed. Sequential, small (1 µL) sample injections and immediate detection after separation permits fast reaction monitoring with excellent sensitivity, accuracy and reproducibility. Due to its modular design, different chromatographic techniques, e.g. reverse phase and size exclusion chromatography (SEC) can be employed. A novel assay for pyridoxal 5'-phosphate-dependent enzymes is presented using SEC for direct monitoring of enzyme-bound and free reaction intermediates. Time-resolved changes of the different cofactor states, e.g. pyridoxal 5'-phosphate, pyridoxamine 5'-phosphate and the internal aldimine were traced in both half reactions. The combination of the automated HPLC platform with SEC offers a method for substrate-independent screening, which renders a missing piece in the assay and screening toolbox for ATAs and other PLP-dependent enzymes.

Quantitative analysis of flux regulation through hierarchical regulation analysis

Regulation analysis is a methodology that quantifies to what extent a change in the flux through a metabolic pathway is regulated by either gene expression or metabolism. Two extensions to regulation analysis were developed over the past years: (i) the regulation of V(max) can be dissected into the various levels of the gene-expression cascade, such as transcription, translation, protein degradation, etc. and (ii) a time-dependent version allows following flux regulation when cells adapt to changes in their environment. The methodology of the original form of regulation analysis as well as of the two extensions will be described in detail. In addition, we will show what is needed to apply regulation analysis in practice. Studies in which the different versions of regulation analysis were applied revealed that flux regulation was distributed over various processes and depended on time, enzyme, and condition of interest. In the case of the regulation of glycolysis in baker's yeast, it appeared, however, that cells that remain under respirofermentative conditions during a physiological challenge tend to invoke more gene-expression regulation, while a shift between respirofermentative and respiratory conditions invokes an important contribution of metabolic regulation. The complexity of the regulation observed in these studies raises the question what is the advantage of this highly distributed and condition-dependent flux regulation.

Proenkephalin A-derived peptides in invertebrate innate immune processes

Lipopolysaccharides (LPS) injection into the coelomic fluid of the leech Theromyzon tessulatum stimulates release of proenkephalin A (PEA)-derived peptides as determined by immunoprecipitation and Western blot analyses. This release occurs in the first 15 min after LPS exposure and yields a 5.3-kDa peptide fragment corresponding to the C-terminal part of the precursor. This fragment is then cleaved to free an antibacterial peptide related to mammals arginine phenylalanine extended enkelytin: the peptide B. These PEA processing peptides were characterized using a combination of techniques including reversed-phase HPLC, microsequencing and mass spectrometry. The isolated invertebrate peptide B presents a high sequence homology with the bovine's and the same activity against Gram+bacteria. Titrations revealed the simultaneous appearance of Methionine-enkephalin (ME) and peptide B in invertebrates after stimulation by LPS (in a dose-dependent manner), surgical trauma or electrical stimulations to neural tissues of the mussel. Furthermore, peptide B processing in vitro yields Methionine-enkephalin arginine phenylalanine (MERF), which exhibits via the delta receptors, immunocyte excitatory properties, i.e., movement and conformational changes, but no antibacterial activity. We surmise that this unified response to the various stimuli is a survival strategy for organism by providing immediate antibacterial activity and immunocyte stimulation, thereby reducing any immune latency period needed for an adequate immune response.

Biochemical identification and ganglionic localization of leech angiotensin-converting enzymes

We demonstrate the presence of a membrane and soluble form of leech Theromyzon tessulatum angiotensin-converting enzyme (ACE). Four steps in the purification of this enzyme include gel-permeation, captopril-sepharose affinity and anion-exchange chromatography followed by a reverse-phase HPLC. The peptidyl dipeptidases (of approximately 120 and approximately 100 kDa) are glycosylated enzymes hydrolysing the Phe8-His9 bond of angiotensin I, exhibiting the same specific activity and Km whereas the soluble ACE exhibits a higher catalytic efficiency. This hydrolysis is inhibited by the ACE-specific antagonist captopril. Western blot analysis of a polyclonal antiserum raised against the first 11 amino-acid residues of the membrane ACE and the N-terminal sequence of the soluble molecule also demonstrates the presence of two ACE enzymes. Anti-ACE immunocytochemistry also supports the presence of two forms of ACE. This material is found in neurons and glia. We demonstrate for the first time the cellular localization and biochemical characterization of ACEs in the central nervous system of an invertebrate. Thus, the leech brain may represent a simple model for the study of these enzymes.

A renin-like enzyme in the leech Theromyzon tessulatum

We report on the biochemical isolation and characterization of a 32 kDa aspartyl protease from the leech Theromyzon tessulatum. Following a three step purification (gel permeation chromatography, pepstatin A-sepharose affinity column separation followed by reversed-phase HPLC) a renin-like enzyme was purified to homogeneity. The first 124 amino acid residues of the N-terminal part of the purified S-pyridylethylated leech renin exhibits a 26.5-35.5% sequence identity with that of mammals. The 20-81 region of leech renin exhibits a 80% sequence homology with the 175-232 region in mammals. This highly conserved region, which is also found in all aspartic proteases, possesses the aspartyl catalytic residue (D11TGSS). Leech renin hydrolyses at neutral pH and at 37 degrees C the Leu10-Leu11 bond of synthetic porcine angiotensinogen tetradecapeptide yielding the angiotensin I and the Leu11-Val12-Tyr13-Ser14 peptides, with a specific activity of 115 microg AI/min/mg (K[M] 22 microM; K[cat], 2.7). This hydrolysis is inhibited by pepstatin A (IC50: 4.6 microM). Moreover, this enzyme is found on a multiple hormone precursor of 19 kDa which exhibits a specific activity of 850 pmol AI/min/mg of renin. This is the first biochemical characterization of a renin-like enzyme in invertebrates and non-mammalian vertebrates.

Metabolism of enkephalins in head membranes of the leech Theromyzon tessulatum by peptidases: isolation of an enkephalin-degrading aminopeptidase

Metabolism of leucine and methionine enkephalins by enzyme preparations from head parts of the leech Theromyzon tessulatum was investigated. Leech homogenate degraded enkephalins by cleavage of the Tyr1-Gly2 and Gly3-Phe4 bonds. The Tyr1-Gly2-Gly3 was detected as a major metabolite when amastatin (aminopeptidase inhibitor) was present to prevent Tyr1-Gly2 breakdown. Around 50% of enkephalin-degrading activity was isolated in a 20000 x g membrane fraction and was shown to be almost entirely due to an aminopeptidase activity. This enzyme, a homodimer of approx. 70 kDa, has been purified to homogeneity by a combined approach including gel permeation and anion exchange chromatographies followed by reversed-phase HPLC. This enkephalin-degrading aminopeptidase is a typical integral membrane 'zincin' metalloprotein with an apparent k(m) of 30 microM, a specific activity of 12 nmol GGFM min-1 mg protein-1 and a catalytic efficiency (kcat/k(m)) of 46 x 10(6) mol-1 min-1. This enzyme is specifically inhibited by amastatin (IC50 = 0.5 microM), but not by bestatin and actinonin. In leech membranes, the other degrading activities performed at the same time were due to a neuropeptide-endopeptidase (NEP)-like enzyme attack, inhibited by phosphoramidon (IC50 = 0.1 microM) and in the case of the Met-enkephalin by a combined action of an angiotensin-converting-like enzyme, inhibited by captopril (IC50 = 0.2 microM) and the NEP-like enzyme. These two enzymes were previously isolated from head membranes of T. tessulatum and possess towards Met-enkephalin a catalytic efficiency (kcat/k(m)) of, respectively, 12 x 10(6) mol-1 min-1 and 78 x 10(6) mol-1 min-1. These findings constitute the first report in leeches on the nature and the sites of attack of the membrane peptidases involved in the metabolism of enkephalins and also the first biochemical evidence for a novel member of the aminopeptidase family.

Metabolism of angiotensins by head membranes of the leech Theromyzon tessulatum

Angiotensins (angiotensin I, angiotensin II, angiotensin II-amide) have been isolated in leeches and such peptides are involved in diuresis in these animals. To explore possible inactivation mechanisms of these peptides, angiotensins were incubated with head membranes of the leech T. tessulatum. Membranes derived from head parts of this leech are very rich in peptidases. They contain endopeptidase-24.11-like enzyme (NEP-like) associated with a battery of exopeptidase. The way that angiotensins are degraded by the combined attack of these membrane peptidases has been investigated. The contribution of individual peptidases was assessed by adding inhibitors (phosphoramidon, captopril and amastatin) to the membrane fractions, when they were incubated with the peptides. In the case of angiotensin I, the primary attack was performed by a combined action of the NEP-like and the ACE-like enzymes, followed by aminopeptidase attacks. Angiotensin II and III were hydrolyzed by NEP-like enzyme at the same Tyr-Ile bond, whereas the N-terminal arginine residue of angiotensin III was removed by an arginyl aminopeptidase. These results show that angiotensins are efficiently degraded by membranes and that NEP-like enzyme plays a key role in this process.

Biochemical properties of the angiotensin-converting-like enzyme from the leech Theromyzon tessulatum

This article reports the evidence and the biochemical properties of an angiotensin-converting (ACE)-like enzyme from head parts of the leech Theromyzon tessulatum. After solubilization from membranes with Triton X-114, the ACE-like enzyme was purified from the detergent-poor fraction. Four steps of purification including gel permeation and anion exchange chromatographies followed by a reversed-phase HPLC were needed. This poor glycosylated peptidyl dipeptidase (of ca. 120 kDa) hydrolyzes, at pH 8.4 and at 37 degrees C, the Phe8-His9 bond of angiotensin I with a high catalytic activity (i.e., K(m): 830 microM and Kcat/K(m): 153 s-1 mM-1). The hydrolysis of angiotensin I is inhibitable at 80% by captopril (IC50 = 175 nM) and lisinopril (IC50 = 35 nM). This activity is strictly dependent on the presence of NaCl and is increased by Zn2+. This zinc metallopeptidase also attacks peptides that have in their sequence either Gly-His, Gly-Phe, or Phe-His bond [e.g., enkephalins (Kcat/K(m): 12 s-1 mM-1) or bradykinin (Kcat/K(m): 2200 s-1 mM-1]. Taken together, these arguments are consistent with an ACE-like activity implicated in metabolism of angiotensins and bradykinin in leeches.

Isolation of a renin-like enzyme from the leech Theromyzon tessulatum

This article reports the purification of a renin-like enzyme (an aspartyl protease) from head parts of the leech Theromyzon tessulatum. After four steps of purification including gel permeation and anion exchange chromatographies followed by reversed-phase HPLC, this enzyme was purified to homogeneity. The renin-like enzyme (of 32 kDa) hydrolyses at neutral pH and at 37 degrees C, the Leu10-Leu11 bond of synthetic porcine angiotensinogen tetradecapeptide yielding the angiotensin I and the Leu11-Val12-Tyr13-Ser14 peptide as products, with a specific activity of 1.35 pmol AI/min/mg (Km 22 microM; Kcat 2.7). The hydrolysis of angiotensinogen is inhibitable at 90% by pepstatin A (IC50 = 4.6 microM), consistent with a renin activity. This is the first biochemical evidence of renin-like enzyme in invertebrates.