Immobilized enzymes – valuable tools for the indication of temperature events

Abstract

The enzymes trypsin and urease were covalently tethered to cellulose to utilize their ability to produce colored products as a consequence of enzymatic activity. Therefore, cellulose had to be chemically modified first in order to generate appropriate chemical functionalities. Different approaches including periodate supported oxidation followed by immobilization via reductive amination, insertion of a reactive polymer interface, and cross-linking inside the cellulose matrix were utilized for the immobilization. The success of immobilization was assessed by the quantification of surface-bound protein as well as by recording of enzymatic activities under different conditions. The enzymatic activity of trypsin and urease was maintained best when a hydrophilic intermediate polymer layer was used for immobilization. The applicability of immobilized enzymes as temperature indicators was demonstrated using cross-linked urease.     

Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics

Protein-protein ligand is one of the most detection methods used in Nano biosensors. Based on the advantage of specific docking between two special 3D structures, they have become a potent candidate in bioanalysis and Nanodiagnostic tools. These tools lease users to do a simple, fast, cost-effective, sensitive, and specific detection of molecular biomarkers in real samples. Recent advantages of using protein-protein ligand Nano-biosensors application is remarkable due to its special docking that refers to each protein unique 3D conformation. However, it challenges different problems such as low rate of docking and hard process for fixation on the basic layer. These challenges make developers to optimize the structure and functions of proteins. The process has different Nano scale calculation that could be done with algorithms and solutions are available as bioinformatics tools. This article aimed to have a short overview of the abilities of bioinformatics tools for modeling and optimization of physiochemical features of proteins in Nano scale.     

A new yeast metabolon involving at least the two first enzymes of arginine biosynthesis: acetylglutamate synthase activity requires complex formation with acetylglutamate kinase.

Open reading frame YJL071W of Saccharomyces cerevisiae was shown to be ARG2 and identified as the structural gene for acetylglutamate synthase, first step in arginine biosynthesis. The three Ascomycete acetylglutamate synthases characterized to date appear homologous, but unlike the other enzymes of the yeast arginine biosynthesis pathway, they showed no significant similarity to their prokaryotic equivalents. The measured synthase activity did not increase with the number of ARG2 gene copies unless the number of ARG5,6 gene copies was increased similarly. ARG5,6 encodes a precursor that is maturated in the mitochondria into acetylglutamate kinase and acetylglutamyl-phosphate reductase, catalyzing the second and third steps in the pathway. The results imply that the synthase must interact stoichiometrically in vivo with the kinase, the reductase, or both to be active. Results obtained with synthetic ARG5 and ARG6 genes suggested that both the kinase and the reductase could be needed. This situation, which has completely escaped notice in yeast until now, is reminiscent of the observation in Neurospora crassa that nonsense arg-6 kinase/reductase mutants lack synthase activity (Hinde, R. W., Jacobson, J. A., Weiss, R. L., and Davis, R. H. (1986) J. Biol. Chem. 261, 5848-5852). In immunoprecipitation experiments, hemagglutinin-tagged synthase coprecipitated with a protein proven by microsequencing to be the kinase. Western blot analyses showed that the synthase has reduced stability in the absence of the kinase/reductase. Our data demonstrate the existence of a new yeast arginine metabolon involving at least the first two, and possibly the first three, enzymes of the pathway. Hypotheses regarding the biological significance of this interaction are discussed.     

DNA aptamers for as analytical tools for the quantitative analysis of DNA-dealkylating enzymes

The AlkB family of oxygenases catalyze the removal of alkyl groups from nucleic acid substrates in an iron and 2-oxoglutarate-dependent manner and have roles including in DNA repair. To understand the biological functions of these DNA-dealkylating enzymes it is desirable to measure their expression levels in vitro and in vivo in complex biological matrixes. Quantitative analyses of the enzymes require affinity probes capable of binding AlkB family members selectively and with high affinity. Here we report that DNA aptamers can serve as efficient affinity probes for quantitative detection of such enzymes in vitro. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was applied as a general tool for: (i) selection of DNA aptamers, (ii) characterization of binding parameters for the aptamers, and (iii) quantitative detection of the target in an aptamer-based affinity analysis. The selected aptamers have a range of K_d values between 20 and 240 nM. The aptamers enabled accurate quantitative analysis of AlkB even in the presence of the Escherichia coli cell lysate. Aptamers can likely be developed for other nucleic acid repair enzymes. They may also be developed for use in in vitro and potentially in vivo studies of known nucleic acid-modifying enzymes including for functional analysis.     

Biotransformation enzymes in fish as tools for biomonitoring aquatic environment

Biotransformation in fish--as in mammals--is catalyzed by several enzymes. These convert liposoluble endogenous and exogenous substrates to more water-soluble compounds prior to excretion. The biotransformation enzymes are induced by environmental pollutants. The induction can be expected to precede the onset of more serious changes at higher organization levels. We have studied the effect of petroleum from a ship spill and bleached kraft mill effluent on hepatic biotransformation enzyme activities of local fish species perch (Perca fluviatilis) and vedace (Coregonus albula) in Finland. Four months after the petroleum spill an elevated level of monoxygenase as well as glutathione S-transferase enzyme activities was seen in perch. Afterwards the difference between the control perch and the exposed ones disappeared. Bleached kraft mill effluent had effect on hepatic biotransformation in vendace. Increasing exposure time and effluent concentration elevated the activities.     

Polyacrylamide gel technique for the histochemical demonstration of soluble enzymes.

Soluble enzymes were immobilized and visualized by polyacrylamide gel slabs, impregnated with the incubation medium including auxiliary enzymes. The method has several advantages over existing techniques which make use of gel films or a semipermeable membrane. The diffusion of tissue compounds is effectively limited, while auxiliary enzymes may be operative. Moreover the viscosity of the medium is temperature-independent so that the incubation temperature can be varied. To demonstrate the suitability of the method glycerol-3-phosphate dehydrogenase, lactate dehydrogenase, glucose-6-phosphate dehydrogenase, hexokinase, phosphoglucomutase and aldolase were visulaized in human or rat skeletal muscle. Cytosolic and mitochondrial glycerol-3-phosphate dehydrogenase were both visualized in the absence of added NAD+ and menadione. For the visualization of ATP producint enzymes, like creatine kinase and pyruvate kinase, the method is not suitable.     

Developing inhibitors of glycan processing enzymes as tools for enabling glycobiology

Glycoconjugates are ubiquitous biomolecules found in all kingdoms of life. These diverse structures are metabolically responsive and occur in a cell line- and protein-specific manner, conferring tissue type-specific properties. Glycans have essential roles in diverse processes, including, for example, intercellular signaling, inflammation, protein quality control, glucohomeostasis and cellular adhesion as well as cell differentiation and proliferation. Many mysteries remain in the field, however, and uncovering the physiological roles of various glycans remains a key pursuit. Realizing this aim necessitates the ability to subtly and selectively manipulate the series of different glycoconjugates both in cells and in vivo. Selective small-molecule inhibitors of glycan processing enzymes hold great potential for such manipulation as well as for determining the function of 'orphan' carbohydrate-processing enzymes. In this review, we discuss recent advances and existing inhibitors, the prospects for small-molecule inhibitors and the challenges associated with generating high-quality chemical probes for these families of enzymes. The coordinated efforts of chemists, biochemists and biologists will be crucial for creating and characterizing inhibitors that are useful tools both for advancing a basic understanding of glycobiology in mammals as well as for validating new potential therapeutic targets within this burgeoning field.     

A genomic overview of pyridoxal-phosphate-dependent enzymes

Enzymes that use the cofactor pyridoxal phosphate (PLP) constitute a ubiquitous class of biocatalysts. Here, we analyse their variety and genomic distribution as an example of the current opportunities and challenges for the study of protein families. In many free-living prokaryotes, almost 1.5% of all genes code for PLP-dependent enzymes, but in higher eukaryotes the percentage is substantially lower, consistent with these catalysts being involved mainly in basic metabolism. Assigning the function of PLP-dependent enzymes simply on the basis of sequence criteria is not straightforward because, as a consequence of their common mechanistic features, these enzymes have intricate evolutionary relationships. Thus, many genes for PLP-dependent enzymes remain functionally unclassified, and several of them might encode undescribed catalytic activities. In addition, PLP-dependent enzymes often show catalytic promiscuity (that is, a single enzyme catalyses different reactions), implying that an organism can have more PLP-dependent activities than it has genes for PLP-dependent enzymes. This observation presumably applies to many other classes of protein-encoding genes.     

A device for the retrenchment of coupling enzymes for demonstration of creatine kinase on polyacrylamide gel.

We have established several optimal conditions for qualitative and quantitative allantoin determination by applying Ehrlich's reagent. The limit of detection for allantoin determination amounts to 5 × 10^?6 mm. Allantoin is determined quantitatively by measuring the absorbance at 440 nm (from 300 to 1000 μg/ml). The color of the complex becomes stable by standing for 10 min at room temperature. We have used these conditions for allantoin determination in Agrostemma githago seed.     

A short overview of chlorophyll biosynthesis in algae

Chlorophylls are the most abundant classes of natural pigments and their biosynthesis is therefore a major metabolic activity in the ecosphere. Two pathways exist for chlorophyll biosynthesis, one taking place in darkness and the other requiring continuous light as a precondition. The key process for Chl synthesis is the reduction of protochlorophyllide (Pchlide). This enzymatic reaction is catalysed by two different enzymes — DPOR (dark-operative Pchlide oxidoreductase) or the structurally distinct LPOR (light-dependent Pchlide oxidoreductase). DPOR which consists of three subunits encoded by three plastid genes in eukaryotes was subject of our study. A short overview of our present knowledge of chlorophyll biosynthesis in Chlamydomonas reinhardtii in comparison with other plants is presented. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

HPLC techniques for proteomics analysis--a short overview of latest developments.

Due to the complex nature of the proteome, instrumentation and methods development for sample cleanup, fractionation, preconcentration, chromatographic separation and detection becomes urgent for the identification of peptides and proteins. Newly developed techniques and equipment for separation and detection, such as nano-HPLC and multidimensional HPLC for protein and peptide separation, enabled proteomics to experience dynamic growth during the past few years. In any proteomic analysis the most important and sometimes most difficult task is the separation of the complex mixture of proteins or peptides. This review describes some aspects and limitations of HPLC, both multidimensional and one-dimensional, in proteomics research without attempting to discuss all available HPLC methods, which would need far more space than available here.     

Mixed-function oxygenase enzymes as tools for pollution monitoring: field studies on the French coast of the Mediterranean Sea.

1. MFO enzyme activities were measured in microsomes from whole mussels (Mytilus galloprovincialis) comber livers (Serranus cabrilla), or Posidonia oceanica etiolated tissues, and PAH contents were determined in sediments collected in coastal locations of the French Riviera and Corsica during 3 oceanographic cruises in 1987-1988. 2. BaP activities in mussel and EROD activities measured in fish were strongly correlated to the log of PAH content in sediments. The first results for CA4H in Posidonia showed significant differences related to PAH pollution levels. The increase in MFO activities measured in Corsica in summer 1988 indicated a recent petroleum contamination.     

Polyacrylamide gel technique for the histochemical demonstration of soluble enzymes

Summary Soluble enzymes were immobilized and visualized by polyacrylamide gel slabs, impregnated with the incubation medium including auxiliairy enzymes. The method has several advantages over existing techniques which make use of gel films or a semipermeable membrane. The diffusion of tissue compounds is effectively limited, while auxiliary enzymes may be operative. Moreover the viscosity of the medium is temperature-independent so that the incubation temperature can be varied.To demonstrate the suitability of the method glycerol-3-phosphate dehydrogenase, lactate dehydrogenase, glucose-6-phosphate dehydrogenase, hexokinase, phosphoglucomutase and aldolase were visualized in human or rat skeletal muscle. Cytosolic and mitochondrial glycerol-3-phosphate dehydrogenase were both visualized in the absence of added NAD⁺ and menadione.For the visualization of ATP producing enzymes, like creatine kinase and pyruvate kinase, the method is not suitable.     

An overview of tools for the validation of protein NMR structures

Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11 % of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).     

Site-directed genome modification: derivatives of DNA-modifying enzymes as targeting tools

The modification of mammalian genomes is an important goal in gene therapy and animal transgenesis. To generate stable genetic and biochemical changes, the therapeutic genes or transgenes need to be incorporated into the host genome. Ideally, the integration of the foreign gene should occur at sites that ensure their continual expression in the absence of any unwanted side effects on cellular metabolism. In this article, we discuss the opportunities provided by natural DNA-modifying enzymes, such as transposases, recombinases and integrases, to mediate the stable integration of foreign genes into host genomes. In addition, we discuss the approaches that have been taken to improve the efficiency and to modify the site-specificity of these enzymes.     

Decalcification for histochemical demonstration of hydrolytic and oxidative enzymes

Summary A method for histochemical demonstration of hydrolytic and oxidative enzymes following decalcification was described in mature bone and tooth by neutral EDTA decalcifying solution.The decalcifying solution, 0.5 M EDTA tetrasodium salt was adjusted to neutral pH with 5 M citric acid, obtained the most sufficient results for demonstration of enzymes in decalcified tissue. The hard tissue decalcified in 30 to 40 days at 4° C exhibited a good preservation of hydrolytic and oxidative enzymes histochemically, but a few structural destruction in a long term decalcification was found in soft tissues and certain organs.     

Peptides as tools and drugs for immunotherapies.

Peptides are essential tools for discovery and pre-clinical and pharmaceutical development of viral and cancer vaccines ('active immunotherapies') as well as for therapeutic antibodies ('passive immunotherapies'). They help to trigger and analyze immune responses at a molecular level (B-cell, T-helper and CTL epitopes). They contribute largely to the design of new vaccine candidates and to the generation of monoclonal antibodies. They are also valuable analytical reference compounds for the structural characterisation by liquid chromatography and mass spectrometry of recombinant proteins used as biopharmaceuticals. As for other therapeutic applications, formulation, solubilisation, batch consistency and stability, issues have to be addressed to allow the pre-clinical and clinical development of this class of compounds as immunotherapeutic drugs. In the present review, three case studies dealing with (i) the design and the characterisation of Respiratory Syntycial Virus subunit vaccines, (ii) peptide-based melanoma vaccines, and (iii) therapeutic monoclonal antibodies, all investigated in clinical trials, are reported and discussed.     

Immobilized enzymes at the surface of rat heart muscle mitochondria

Of the three pairs of complementary replicas mentioned in the previous paper (1985, J. Ultrastruct. Res. 91, 38-50) one pair consisted of fracture faces exposing the cytoplasmic surface of the outer surface membrane while the complementary face exposed the cytosol at the membrane surface. The latter face was particulate with randomly distributed particles in the size range of 100 to 200 A. These particles could be shown to be located in the cytosol at the membrane surface. They qualify as particles that are loosely bound to this surface, and it is proposed that at least part of these particles consist of glycolytic enzymes.