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Enzyme Complex (enzyme + complex)
Selected AbstractsCE-ESI-MS/MS as a rapid screening tool for the comparison of protein,ligand interactionsELECTROPHORESIS, Issue 7 2010Thomas Hoffmann Abstract In drug development, the combinatorial synthesis of drug libraries is common use, therefore efficient tools for the characterization of drug candidates and the extent of interaction between a drug and its target protein is a central question of analytical interest. While biological activity is tested today by enzyme assays, MS techniques attract more and more attention as an alternative for a rapid comparison of drug,target interactions. CE enables the separation of proteins and drug,enzyme complexes preserving their physiological activity in aqueous media. By hyphenating CE with ESI-MS/MS, the binding strength of enzyme inhibitors can be deduced from MS/MS experiments, which selectively release the inhibitor from the drug,target complex after CID. In this study, ,-chymotrypsin (CT), a serine protease, was chosen as a model compound. Chymostatin is a naturally occurring peptide aldehyde binding to CT through a hemiacetal bond and electrostatic interaction. First, a CE separation was developed, which allows the analysis of ,-CT and a chymotrypsin,chymostatin complex under MS-compatible conditions. The use of neutral-coated CE capillaries was mandatory to reduce analyte,wall interactions. ESI-quadrupole ion trap-MS was worked out to demonstrate the selective drug release after CID. Fragmentation of the drug,enzyme complex was monitored in dependence from the excitation energy in the ion trap, leading to the V50 voltage that enables 50% complex fragmentation as a reference value for chymotrypsin,chymostatin complex. A stable CE-ESI-MS/MS setup was established, which preserves the drug,enzyme complexes during ionization,desolvation processes. With this optimized setup, different CT inhibitors could be investigated and compared. [source] Glycine cleavage system in neurogenic regionsEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 9 2004Akiko Ichinohe Abstract The glycine cleavage system (GCS) is the essential enzyme complex for degrading glycine and supplying 5,10-methylenetetrahydrofolate for DNA synthesis. Inherited deficiency of this system causes nonketotic hyperglycinemia, characterized by severe neurological symptoms and frequent association of brain malformations. Although high levels of glycine have been considered to cause the above-mentioned problems, the detailed pathogenesis of this disease is still unknown. Here we show that GCS is abundantly expressed in rat embryonic neural stem/progenitor cells in the neuroepithelium, and this expression is transmitted to the radial glia,astrocyte lineage, with prominence in postnatal neurogenic regions. These data indicate that GCS plays important roles in neurogenesis, and suggest that disturbance of neurogenesis induced by deficiency of GCS may be the main pathogenesis of nonketotic hyperglycinemia. [source] Cytochrome c oxidase as the target of the heat shock protective effect in septic liverINTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY, Issue 5 2004Hsiang-Wen Chen Summary Liver function failure is one of the characteristics of critically ill, septic patients and is associated with worse outcome. Our previous studies have demonstrated that heat-shock response protects cells and tissue from subsequent insults and improves survival during sepsis. In this study, we have shown that mitochondrial cytochrome c oxidase (CCO) is one of the major sources of that protective effect. Experimental sepsis was induced by the cecal ligation and puncture (CLP) method. Heat-shock treatment was induced in rats by hyperthermia 24 h before CLP operation. The results showed that ATP content of the liver declined significantly, and the enzymatic activity of mitochondrial CCO was apparently suppressed during the late stages of sepsis. The mitochondrial ultrastructure of septic liver showed the deformity, mild swelling and inner membrane budding. Heat-shock treatment led to heat-shock protein 72 overexpression and prevented the downregulation of Grp75 during sepsis. On the contrary, the expression of the enzyme complex and its activity were preserved, associated with the minimization of ultrastructural deformities. In conclusion, the maintenance of mitochondrial function, especially the CCO, may be an important strategy in therapeutic interventions of a septic liver. [source] Production, characterization and determination of the real catalytic properties of the putative ,succinate dehydrogenase' from Wolinella succinogenesMOLECULAR MICROBIOLOGY, Issue 5 2009Hanno D. Juhnke Summary Both the genomes of the epsilonproteobacteria Wolinella succinogenes and Campylobacter jejuni contain operons (sdhABE) that encode for so far uncharacterized enzyme complexes annotated as ,non-classical' succinate:quinone reductases (SQRs). However, the role of such an enzyme ostensibly involved in aerobic respiration in an anaerobic organism such as W. succinogenes has hitherto been unknown. We have established the first genetic system for the manipulation and production of a member of the non-classical succinate:quinone oxidoreductase family. Biochemical characterization of the W. succinogenes enzyme reveals that the putative SQR is in fact a novel methylmenaquinol:fumarate reductase (MFR) with no detectable succinate oxidation activity, clearly indicative of its involvement in anaerobic metabolism. We demonstrate that the hydrophilic subunits of the MFR complex are, in contrast to all other previously characterized members of the superfamily, exported into the periplasm via the twin-arginine translocation (tat)-pathway. Furthermore we show that a single amino acid exchange (Ala86,His) in the flavoprotein of that enzyme complex is the only additional requirement for the covalent binding of the otherwise non-covalently bound FAD. Our results provide an explanation for the previously published puzzling observation that the C. jejuni sdhABE operon is upregulated in an oxygen-limited environment as compared with microaerophilic laboratory conditions. [source] Mechanisms influencing the evolution of resistance to Qo inhibitor fungicides,,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 9 2002Ulrich Gisi Abstract Fungicides inhibiting the mitochondrial respiration of plant pathogens by binding to the cytochrome bc1 enzyme complex (complex III) at the Qo site (Qo inhibitors, QoIs) were first introduced to the market in 1996. After a short time period, isolates resistant to QoIs were detected in field populations of a range of important plant pathogens including Blumeria graminis Speer f sp tritici, Sphaerotheca fuliginea (Schlecht ex Fr) Poll, Plasmopara viticola (Berk & MA Curtis ex de Bary) Berl & de Toni, Pseudoperonospora cubensis (Berk & MA Curtis) Rost, Mycosphaerella fijiensis Morelet and Venturia inaequalis (Cooke) Wint. In most cases, resistance was conferred by a point mutation in the mitochondrial cytochrome b (cyt b) gene leading to an amino-acid change from glycine to alanine at position 143 (G143A), although additional mutations and mechanisms have been claimed in a number of organisms. Transformation of sensitive protoplasts of M fijiensis with a DNA fragment of a resistant M fijiensis isolate containing the mutation yielded fully resistant transformants, demonstrating that the G143A substitution may be the most powerful transversion in the cyt b gene conferring resistance. The G143A substitution is claimed not to affect the activity of the enzyme, suggesting that resistant individuals may not suffer from a significant fitness penalty, as was demonstrated in B graminis f sp tritici. It is not known whether this observation applies also for other pathogen species expressing the G143A substitution. Since fungal cells contain a large number of mitochondria, early mitotic events in the evolution of resistance to QoIs have to be considered, such as mutation frequency (claimed to be higher in mitochondrial than nuclear DNA), intracellular proliferation of mitochondria in the heteroplasmatic cell stage, and cell to cell donation of mutated mitochondria. Since the cyt b gene is located in the mitochondrial genome, inheritance of resistance in filamentous fungi is expected to be non-Mendelian and, therefore, in most species uniparental. In the isogamous fungus B graminis f sp tritici, crosses of sensitive and resistant parents yielded cleistothecia containing either sensitive or resistant ascospores and the segregation pattern for resistance in the F1 progeny population was 1:1. In the anisogamous fungus V inaequalis, donation of resistance was maternal and the segregation ratio 1:0. In random mating populations, the sex ratio (mating type distribution) is generally assumed to be 1:1. Therefore, the overall proportion of sensitive and resistant individuals in unselected populations is expected to be 1:1. Evolution of resistance to QoIs will depend mainly on early mitotic events; the selection process for resistant mutants in populations exposed to QoI treatments may follow mechanisms similar to those described for resistance controlled by single nuclear genes in other fungicide classes. It will remain important to understand how the mitochondrial nature of QoI resistance and factors such as mutation, recombination, selection and migration might influence the evolution of QoI resistance in different plant pathogens. © 2002 Society of Chemical Industry [source] The relationship between changes in the cell wall, lipid peroxidation, proliferation, senescence and cell deathPHYSIOLOGIA PLANTARUM, Issue 1 2003Gerhard Spiteller Plants and mammals contain polyunsaturated fatty acids (PUFAs) in their membranes. PUFAs belong to the most oxygen sensitive molecules encountered in nature. It would seem that nature has selected this property of PUFAs for signalling purposes: PUFAs are stored in the surface of cells and organelles not in free form but conjugated to phospho- and galactolipids. Any change in membrane structure apparently activates membrane-bound phospholipases, which cleave the conjugates. The obtained free PUFAs are substrates for lipoxygenases (LOX). These transform PUFAs to lipidhydroperoxides (LOOHs). LOOHs are converted to a great variety of secondary products. These lipid-peroxidation (LPO) products and the resulting generated products thereof represent biological signals, which do not require a preceding activation of genes. They are produced as a non-specific response to a large variety of external or internal impacts, which therefore do not need interaction with specific receptors. When, due to an external impact, e.g. attack of a microorganism, or to a change in temperature, the amount of liberated free PUFAs exceeds a certain threshold, LOX commit suicide. Thus iron ions, located in the active centre of LOX, are liberated. Iron ions react with LOOHs in the close surroundings by generating alkoxy radicals (LO.). These induce a non-enzymatic LPO. A fraction of the LO. radicals generated from linoleic acid (LPO products derived from linoleic acid play a dominant role in signalling which was previously overlooked) is converted to 2,4-dienals which induce the programmed cell death (PCD) and the hypersensitive reaction (HR). While peroxyl radicals (LOO.) generated as intermediates in the course of an enzymatic LPO are transformed within the enzyme complex to corresponding anions (LOO,), and thus lose their reactivity, peroxyl radicals generated in non-enzymatic reactions are not deactivated. They not only react by abstraction of hydrogen atoms from activated X-H bonds of molecules in their close vicinity, but also by epoxidation of double bonds and oxidation of a variety of biological molecules, causing a dramatic change in molecular structure which finally leads to cell death. As long as reducing agents, like glutathione, or compounds with free phenolic groups are available, the amount of LOOHs is kept low. Cell death is induced in a defined way by apoptosis. But when the reducing agents have been consumed, PCD seems to switch to necrotic processes. Thus proliferation is induced by minor changes at the cell membrane, while slow changes at cell membranes are linked with apoptosis (e.g. response to attack of microorganisms or drought) and necrosis (severe wounding), depending only on the amount, but not on the type, of applied stimulus. [source] Structure of the C-terminal domain of nsp4 from feline coronavirusACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2009Ioannis Manolaridis Coronaviruses are a family of positive-stranded RNA viruses that includes important pathogens of humans and other animals. The large coronavirus genome (26,31,kb) encodes 15,16 nonstructural proteins (nsps) that are derived from two replicase polyproteins by autoproteolytic processing. The nsps assemble into the viral replication,transcription complex and nsp3, nsp4 and nsp6 are believed to anchor this enzyme complex to modified intracellular membranes. The largest part of the coronavirus nsp4 subunit is hydrophobic and is predicted to be embedded in the membranes. In this report, a conserved C-terminal domain (,100 amino-acid residues) has been delineated that is predicted to face the cytoplasm and has been isolated as a soluble domain using library-based construct screening. A prototypical crystal structure at 2.8,Å resolution was obtained using nsp4 from feline coronavirus. Unmodified and SeMet-substituted proteins were crystallized under similar conditions, resulting in tetragonal crystals that belonged to space group P43. The phase problem was initially solved by single isomorphous replacement with anomalous scattering (SIRAS), followed by molecular replacement using a SIRAS-derived composite model. The structure consists of a single domain with a predominantly ,-helical content displaying a unique fold that could be engaged in protein,protein interactions. [source] Multiple crystal forms of the cell-wall invertase inhibitor from tobacco support high conformational rigidity over a broad pH rangeACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2006Michael Hothorn Plant acid invertases catalyse the breakdown of sucrose. Their activity is tightly regulated through interaction with specific protein inhibitors. The complex between the cell-wall invertase inhibitor Nt-CIF and its target enzyme is stable only at acidic pH, as found in the plant cell wall. Since the pH in this compartment can be modulated between pH 4 and 6 in planta, the rapid dissociation of the inhibitor,enzyme complex at neutral pH may represent a regulatory event. Here, it is analyzed whether the inhibitory component undergoes structural rearrangements upon changes in the pH environment. Six crystal forms grown at pH 4.6,9.5 and diffracting up to 1.63,Å indicate only small structural changes in CIF. This suggests that complex dissociation at neutral pH is mediated either by rearrangements in the enzyme or by a complex pattern of surface charges in the inhibitor,enzyme binding interface. [source] Structure of serine acetyltransferase from Haemophilus influenzae RdACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004Jason Gorman The crystal structure of serine acetyltransferase (SAT) from Haemophilus influenzae Rd determined at 2.7,Å resolution is presented. SAT is a member of a family of hexapeptide-containing transferases that contain six-residue tandem repeats (LIV)-G- X4 that have been shown to form left-handed parallel ,-helices. In the current structure, each protomer is comprised of two domains: an N-terminal ,-helical domain and a C-terminal left-handed parallel ,-helix domain. Although other members of this protein family are known to form trimeric structures, SAT forms a dimer of trimers in which the trimer interface is mediated through interactions between both the ,-helix domains and N-terminal domains; these trimers dimerize through contacts in the N-terminal domain. All dimer-of-trimer interactions are mediated through amino acids within an N-terminal extension common only to a subset of SATs, suggesting that members of this subfamily may also adopt hexameric structures. Putative active sites are formed by crevices between adjacent protomers in a trimer. Thus, six independent active sites exist in the hexameric enzyme complex. [source] The Effect of Aromatase Inhibitors on Bone MetabolismBASIC AND CLINICAL PHARMACOLOGY & TOXICOLOGY, Issue 1 2009Lars Folkestad Aromatase is a cytochrome P450 enzyme complex catalysing the conversion of androgens to oestrogens. These properties cause a significant increase in bone loss. In this MiniReview, we present data from the aromatase inhibitor studies and the studies designed to investigate aromatase inhibitor effect on bone metabolism. At the cellular level, oestrogen has profound effects on both osteoblasts and osteoclasts. Oestrogen decreases the osteoblastic production of resorptive cytokines and simultaneously increases the production of antireceptive cytokines, which leads to increased osteoclastic apoptosis and increased osteoblastic activity. Aromatase inhibitors inhibit the endogenous production of oestrogen by 50,90%. Studies designed to look at the effect of aromatase inhibitors on bone mineral density have shown a significant decrease in bone mineral density of the femoral neck in the aromatase inhibitor groups compared to placebo groups. Placebo-controlled studies lack statistical power to detect changes in fracture incidence; however, aromatase inhibitors increase the incidence of fractures in comparison with tamoxifen. We conclude that treatment with aromatase inhibitors leads to an increased bone loss and thus an increase in the risk of fractures in women with breast cancer. [source] Crystallization and preliminary structural analyses of glutamate dehydrogenase from Peptoniphilus asaccharolyticusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2010Tania F. Oliveira Glutamate dehydrogenase (EC 1.4.1.2,4) from Peptoniphilus asaccharolyticus has been expressed as a selenomethionine-derivatized recombinant protein and diffraction-quality crystals have been grown that are suitable for structure determination. Preliminary structural analyses indicate that the protein assembles as a homohexameric enzyme complex in solution, similar to other bacterial and mammalian enzymes to which its sequence identity varies between 25 and 40%. The structure will provide insight into its preference for the cofactor NADH (over NADPH) by comparisons with the known structures of mammalian and bacterial enzymes. [source] A novel noncovalent complex of chorismate mutase and DAHP synthase from Mycobacterium tuberculosis: protein purification, crystallization and X-ray diffraction analysisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2009Mats Ökvist Chorismate mutase catalyzes a key step in the shikimate-biosynthetic pathway and hence is an essential enzyme in bacteria, plants and fungi. Mycobacterium tuberculosis contains two chorismate mutases, a secreted and an intracellular one, the latter of which (MtCM; Rv0948c; 90 amino-acid residues; 10,kDa) is the subject of this work. Here are reported the gene expression, purification and crystallization of MtCM alone and of its complex with another shikimate-pathway enzyme, DAHP synthase (MtDS; Rv2178c; 472 amino-acid residues; 52,kDa), which has been shown to enhance the catalytic efficiency of MtCM. The MtCM,MtDS complex represents the first noncovalent enzyme complex from the common shikimate pathway to be structurally characterized. Soaking experiments with a transition-state analogue are also reported. The crystals of MtCM and the MtCM,MtDS complex diffracted to 1.6 and 2.1,Å resolution, respectively. [source] Novel azapeptide inhibitors of cathepsins B and K. Structural background to increased specificity for cathepsin BCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2005E. Wieczerzak Abstract:, We have designed and synthesized a new series of azapeptides which act as potential inhibitors of cathepsin B and/or cathepsin K. Their structures are based upon the inhibitory sites of natural cysteine protease inhibitors, cystatins. For the synthesized azapeptides, the equilibrium constants for dissociation of inhibitor,enzyme complex, Ki, were determined. Comparison of these values indicated that all of the azainhibitors act much stronger toward cathepsin B. Z-Arg-Leu-His-Agly-Ile-Val-OMe (7) proved to be approximately 500 times more potent for cathepsin B than for cathepsin K. To be able to explain the obtained experimental values we used the molecular dynamics procedures to analyze the interactions between cathepsin B and compound 7. We also determined the structure of the most potent and selective cathepsin B azainhibitor by means of NMR studies and theoretical calculations. In this report, we describe SAR studies of azapeptide inhibitors indicating the influence of the conformational flexibility of the examined compounds on inhibition of cathepsins B and K. [source] Decreased activities of mitochondrial respiratory chain complexes in non-mitochondrial respiratory chain diseasesDEVELOPMENTAL MEDICINE & CHILD NEUROLOGY, Issue 2 2006Joannie Hui MBBS The aim of this study was to illustrate the difficulties in establishing a diagnosis of mitochondrial respiratory chain (MRC) disorders based on clinical grounds in combination with intermediate activities of the MRC enzyme complexes. We reviewed retrospectively all medical and laboratory records of patients initially considered likely to have MRC disorders on clinical grounds, and subsequently diagnosed with other disorders (n=20; 11 males, 9 females). Data were retrieved from hospital records, referral letters, and results of enzymatic analysis at a reference laboratory. Clinical symptoms included developmental delay, epilepsy, hypotonia, movement disorder, spastic quadriplegia, tetany, microcephaly, visual problems, carpopedal spasms, dysmorphism, hearing loss, muscle weakness and rhabdomyolysis, and fulminant hepatitis. Blood and cerebrospinal fluid lactate levels were elevated in 13/20 and 9/20 respectively. One or more MRC complex activities (expressed as ratios relative to citrate synthase and/or complex II activity) were less than 50% of control mean activity in 11/20 patients (including patients with deficiencies of pyruvate dehydrogenase complex, pantothenate kinase, holocarboxylase synthetase, long-chain hydroxy acyl-CoA dehydrogenase, molybdenum co-factor, and neonatal haemochromatosis). One patient had a pattern suggestive of mitochondrial proliferation. We conclude that intermediate results of MRC enzymes should be interpreted with caution and clinicians should be actively looking for other underlying diagnoses. [source] CE-ESI-MS/MS as a rapid screening tool for the comparison of protein,ligand interactionsELECTROPHORESIS, Issue 7 2010Thomas Hoffmann Abstract In drug development, the combinatorial synthesis of drug libraries is common use, therefore efficient tools for the characterization of drug candidates and the extent of interaction between a drug and its target protein is a central question of analytical interest. While biological activity is tested today by enzyme assays, MS techniques attract more and more attention as an alternative for a rapid comparison of drug,target interactions. CE enables the separation of proteins and drug,enzyme complexes preserving their physiological activity in aqueous media. By hyphenating CE with ESI-MS/MS, the binding strength of enzyme inhibitors can be deduced from MS/MS experiments, which selectively release the inhibitor from the drug,target complex after CID. In this study, ,-chymotrypsin (CT), a serine protease, was chosen as a model compound. Chymostatin is a naturally occurring peptide aldehyde binding to CT through a hemiacetal bond and electrostatic interaction. First, a CE separation was developed, which allows the analysis of ,-CT and a chymotrypsin,chymostatin complex under MS-compatible conditions. The use of neutral-coated CE capillaries was mandatory to reduce analyte,wall interactions. ESI-quadrupole ion trap-MS was worked out to demonstrate the selective drug release after CID. Fragmentation of the drug,enzyme complex was monitored in dependence from the excitation energy in the ion trap, leading to the V50 voltage that enables 50% complex fragmentation as a reference value for chymotrypsin,chymostatin complex. A stable CE-ESI-MS/MS setup was established, which preserves the drug,enzyme complexes during ionization,desolvation processes. With this optimized setup, different CT inhibitors could be investigated and compared. [source] Toxicity assessment of reference and natural freshwater sediments with the LuminoTox assayENVIRONMENTAL TOXICOLOGY, Issue 4 2006P. M. Dellamatrice Abstract We examined the possibility of adapting the LuminoTox, a recently-commercialized bioanalytical testing procedure initially developed for aqueous samples, to assess the toxic potential of sediments. This portable fluorescent biosensor uses photosynthetic enzyme complexes (PECs) to rapidly measure photosynthetic efficiency. LuminoTox testing of 14 CRM (Certified Reference Material) sediments was first undertaken with (1) a "solid phase assay" (Lum-SPA) in which PECs are in intimate contact with sediment slurries for a 15 min exposure period and (2) an elutriate assay (Lum-ELU) in which PECs are exposed for 15 min to sediment water elutriates. CRM sediment toxicity data were then compared with those generated with the Microtox Solid Phase Assay (Mic-SPA). A significant correlation (P < 0.05) was shown to exist between Lum-SPA and Mic-SPA, indicating that both tests display a similar toxicity response pattern for CRM sediments having differing contaminant profiles. The sediment elutriate Lum-ELU assay displayed toxicity responses (i.e. measurable IC20s) for eight of the 14 CRM sediments, suggesting that it is capable of determining the presence of sediment contaminants that are readily soluble in an aqueous elutriate. Lum-SPA and Mic-SPA bioassays were further conducted on 12 natural freshwater sediments and their toxicity responses were more weakly, yet significantly, correlated. Finally, Lum-SPA testing undertaken with increasing mixtures of kaolin clay confirmed that its toxicity responses, in a manner similar to those reported for the Mic-SPA assay, are also subject to the influence of grain size. While further studies will be required to more fully understand the relationship between Lum-SPA assay responses and the physicochemical makeup of sediments (e.g., grain size, combined presence of natural and anthropogenic contaminants), these preliminary results suggest that LuminoTox testing could be a useful screen to assess the toxic potential of solid media. © 2006 Wiley Periodicals, Inc. Environ Toxicol 21: 395,402, 2006. [source] Synchronized transcriptional gene expression of H+ -ATP synthase subunits in different tissues of Fischer 344 rats of different agesFEBS JOURNAL, Issue 23 2000Toshiki Himeda Little is known about the relationship between the stoichiometry of polypeptides of multisubunit enzyme complexes and the absolute amount of each transcript of the complexes in mammalian tissues. Here we showed that the absolute amounts of the transcripts of most subunits of rat H+ -ATP synthase examined greatly differed in the different tissues, showing the following hierarchy of tissue-specificity: heart > kidney > brain , liver. However, surprisingly, there was no difference in the expression pattern of these in terms of the molar ratio of each transcript, indicating a nearly similar stoichiometric expression pattern irrespective of tissue or age of the rat. Therefore, the present finding clearly indicates that most of the transcripts of the 16 subunits of rat H+ -ATP synthase were concertedly and synchronously expressed, having a constant expression pattern of the transcripts, irrespective of tissue or age of the rats. This is the first report of the absolute amounts of the transcripts of this multisubunit enzyme. [source] The expansion of mechanistic and organismic diversity associated with non-ribosomal peptidesFEMS MICROBIOLOGY LETTERS, Issue 2 2000Michelle C Moffitt Abstract Non-ribosomal peptides are a group of secondary metabolites with a wide range of bioactivities, produced by prokaryotes and lower eukaryotes. Recently, non-ribosomal synthesis has been detected in diverse microorganisms, including the myxobacteria and cyanobacteria. Peptides biosynthesized non-ribosomally may often play a primary or secondary role in the producing organism. Non-ribosomal peptides are often small in size and contain unusual or modified amino acids. Biosynthesis occurs via large modular enzyme complexes, with each module responsible for the activation and thiolation of each amino acid, followed by peptide bond formation between activated amino acids. Modules may also be responsible for the enzymatic modification of the substrate amino acid. Recent analysis of biosynthetic gene clusters has identified novel integrated, mixed and hybrid enzyme systems. These diverse mechanisms of biosynthesis result in the wide variety of non-ribosomal peptide structures and bioactivities seen today. Knowledge of these biosynthetic systems is rapidly increasing and methods of genetically engineering these systems are being developed. In the future, this may lead to rational drug design through combinatorial biosynthesis of these enzyme systems. [source] Production, characterization and determination of the real catalytic properties of the putative ,succinate dehydrogenase' from Wolinella succinogenesMOLECULAR MICROBIOLOGY, Issue 5 2009Hanno D. Juhnke Summary Both the genomes of the epsilonproteobacteria Wolinella succinogenes and Campylobacter jejuni contain operons (sdhABE) that encode for so far uncharacterized enzyme complexes annotated as ,non-classical' succinate:quinone reductases (SQRs). However, the role of such an enzyme ostensibly involved in aerobic respiration in an anaerobic organism such as W. succinogenes has hitherto been unknown. We have established the first genetic system for the manipulation and production of a member of the non-classical succinate:quinone oxidoreductase family. Biochemical characterization of the W. succinogenes enzyme reveals that the putative SQR is in fact a novel methylmenaquinol:fumarate reductase (MFR) with no detectable succinate oxidation activity, clearly indicative of its involvement in anaerobic metabolism. We demonstrate that the hydrophilic subunits of the MFR complex are, in contrast to all other previously characterized members of the superfamily, exported into the periplasm via the twin-arginine translocation (tat)-pathway. Furthermore we show that a single amino acid exchange (Ala86,His) in the flavoprotein of that enzyme complex is the only additional requirement for the covalent binding of the otherwise non-covalently bound FAD. Our results provide an explanation for the previously published puzzling observation that the C. jejuni sdhABE operon is upregulated in an oxygen-limited environment as compared with microaerophilic laboratory conditions. [source] LplA1-dependent utilization of host lipoyl peptides enables Listeria cytosolic growth and virulenceMOLECULAR MICROBIOLOGY, Issue 3 2007Kristie M. Keeney Summary The bacterial pathogen Listeria monocytogenes replicates within the cytosol of mammalian cells. Mechanisms by which the bacterium exploits the host cytosolic environment for essential nutrients are poorly defined. L. monocytogenes is a lipoate auxotroph and must scavenge this critical cofactor, using lipoate ligases to facilitate attachment of the lipoyl moiety to metabolic enzyme complexes. Although the L. monocytogenes genome encodes two putative lipoate ligases, LplA1 and LplA2, intracellular replication and virulence require only LplA1. Here we show that LplA1 enables utilization of host-derived lipoyl peptides by L. monocytogenes. LplA1 is dispensable for growth in the presence of free lipoate, but necessary for growth on low concentrations of mammalian lipoyl peptides. Furthermore, we demonstrate that the intracellular growth defect of the ,lplA1 mutant is rescued by addition of exogenous lipoic acid to host cells, suggesting that L. monocytogenes dependence on LplA1 is dictated by limiting concentrations of available host lipoyl substrates. Thus, the ability of L. monocytogenes and other intracellular pathogens to efficiently use host lipoyl peptides as a source of lipoate may be a requisite adaptation for life within the mammalian cell. [source] OsNOA1/RIF1 is a functional homolog of AtNOA1/RIF1: implication for a highly conserved plant cGTPase essential for chloroplast functionNEW PHYTOLOGIST, Issue 1 2010Hongjia Liu Summary ,The bacterial protein YqeH is a circularly permuted GTPase with homologs encoded by plant nuclear genomes. The rice homolog OsNOA1/RIF1 is encoded by the single-copy gene Os02g01440. OsNOA1/RIF1 is expressed in different tissues and is light-inducible. The OsNOA1/RIF1-EYFP fusion protein was targeted to chloroplasts in transgenic Arabidopsis plants. In addition, the rice homolog was able to rescue most of the growth phenotypes in an Arabidopsis rif1 mutant. ,Rice (Oryza sativa) OsNOA1/RIF1 RNAi mutant seedlings were chlorotic with reduced pigment contents and lower photosystem II (PSII) efficiency. However, the expressions of the chloroplast-encoded genes rbcL, atpB, psaA and psbA were not affected. By contrast, reduced abundance of the chloroplast 16S rRNA was observed in the mutant. ,Quantitative iTRAQ-LC-MS/MS proteomics investigations revealed proteome changes in the rice mutant consistent with the expected functional role of OsNOA1/RIF1 in chloroplast translation. The RNAi mutant showed significantly decreased expression levels of chloroplast-encoded proteins as well as nuclear-encoded components of chloroplast enzyme complexes. Conversely, upregulation of some classes of nonchloroplastic proteins, such as glycolytic and phenylpropanoid pathway enzymes, was detected. ,Our work provides independent indications that a highly conserved nuclear-encoded cGTPase of likely prokaryotic origin is essential for proper chloroplast ribosome assembly and/or translation in plants. [source] Preferential regeneration of the NADPH: protochlorophyllide oxidoreductase oligomer complexes in pea epicotyls after bleachingPHYSIOLOGIA PLANTARUM, Issue 1 2010Andrea Szenzenstein The regeneration and stability of the NADPH:protochlorophyllide oxidoreductase (POR, EC 1.3.1.33) enzyme complexes were studied in bleached epicotyls of 9-day-old dark-germinated pea (Pisum sativum L. cv. Zsuzsi) seedlings. Middle segments were illuminated with 1300 µmol m,2 s,1photon flux density (PFD) white light and subsequently incubated in total darkness for 4,24 h at 24°C. Almost the full amount of protochlorophyllide (Pchlide) was degraded after 60 min illumination. The preferential regeneration of the 655 nm emitting Pchlide form was observed after 4 h dark incubation; the accumulation of the short-wavelength Pchlide form,dominating in epicotyls of dark-grown seedling,required 18,24 h dark. The Pchlide content of bleached samples was around 2.5% of that of the etiolated samples; after 4 h of dark incubation this value increased to 4,7%. Polyacrylamide gel electrophoresis and western blot showed that the amount of the POR protein decreased to about 50% during bleaching; after 4 h regeneration it reached almost the same level as that of dark-grown samples. We concluded that much more POR protein compared with Pchlide pigment remained stable during bleaching and the non-destroyed POR units were able to form preferentially oligomers during the dark-regeneration which could collect de novo synthesized Pchlide into 655 nm emitting complexes. These data indicate the high stability of the POR protein in pea epicotyls and the importance of the molecular environment in stimulating the aggregation of POR units. [source] Structure of a fibronectin type III-like module from Clostridium thermocellumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Markus Alahuhta The 1.6,Å resolution structure of a fibronectin type III-like module from Clostridium thermocellum (PDB code 3mpc) with two molecules in the asymmetric unit is reported. The crystals used for data collection belonged to space group P212121, with unit-cell parameters a = 35.43, b = 45.73, c = 107.72,Å, and the structure was refined to an R factor of 0.166. Structural comparisons found over 800 similar structures in the Protein Data Bank. The broad range of different proteins or protein domains with high structural similarity makes it especially demanding to classify these proteins. Previous studies of fibronectin type III-like modules have indicated that they might function as ligand-binding modules, as a compact form of peptide linkers or spacers between other domains, as cellulose-disrupting modules or as proteins that help large enzyme complexes remain soluble. [source] Optimization of enzyme complexes for lignocellulose hydrolysisBIOTECHNOLOGY & BIOENGINEERING, Issue 2 2007Alex Berlin Abstract The ability of a commercial Trichoderma reesei cellulase preparation (Celluclast 1.5L), to hydrolyze the cellulose and xylan components of pretreated corn stover (PCS) was significantly improved by supplementation with three types of crude commercial enzyme preparations nominally enriched in xylanase, pectinase, and ,-glucosidase activity. Although the well-documented relief of product inhibition by ,-glucosidase contributed to the observed improvement in cellulase performance, significant benefits could also be attributed to enzymes components that hydrolyze non-cellulosic polysaccharides. It is suggested that so-called "accessory" enzymes such as xylanase and pectinase stimulate cellulose hydrolysis by removing non-cellulosic polysaccharides that coat cellulose fibers. A high-throughput microassay, in combination with response surface methodology, enabled production of an optimally supplemented enzyme mixture. This mixture allowed for a ,twofold reduction in the total protein required to reach glucan to glucose and xylan to xylose hydrolysis targets (99% and 88% conversion, respectively), thereby validating this approach towards enzyme improvement and process cost reduction for lignocellulose hydrolysis. Biotechnol. Bioeng. 2007;97: 287,296. © 2006 Wiley Periodicals, Inc. [source] Analysis of Classical and Quantum Paths for Deprotonation of Methylamine by Methylamine DehydrogenaseCHEMPHYSCHEM, Issue 12 2007Kara E. Ranaghan Abstract The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions,an area of great current interest,for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified,to either of the carboxylate oxygen atoms of the catalytic base (Asp428,),and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5±0.9 kcal,mol,1 for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal,mol,1. In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474,(MADH)/Thr172,(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471,(MADH)/Phe169,(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions. [source] Conjugated Polyelectrolytes for Protein Assays and for the Manipulation of the Catalytic Activity of EnzymesCHEMISTRY - AN ASIAN JOURNAL, Issue 8-9 2008Lingling An Abstract A new method has been developed to discriminate between proteins with different isoelectric points by using fluorescent conjugated polyelectrolytes. Charged water-soluble polyfluorenes that contain 2,1,3-benzothiadiazole (BT) units demonstrate intramolecular energy transfer from the fluorene units to the BT sites when oppositely charged proteins are added to the mixture. This results in a shift in emission color from blue to green and a change in the emission intensity of conjugated polyelectrolytes, which makes it possible to assay proteins. The formation of conjugated polyelectrolyte/enzyme complexes by electrostatic interactions can be utilized to manipulate the activity of enzymes by means of local alteration of enzyme charge density. The oppositely charged substrate binds to conjugated polyelectrolyte and reduces the distance between the enzyme and the substrate, leading to an increase in the cleavage reaction rate. The new method has three important features: 1),it offers a convenient "mix-and-detect" continuous approach for protein assays and rapid detection of enzyme activity; 2),the use of water-soluble conjugated polyelectrolytes imparts the sensor with a high sensitivity; 3),this method does not require fluorescent labels on the targets, which should significantly reduce the cost. [source] | ||||||||||||||||