Main Cleavage Research Articles

Structure characterization and spectroscopic investigation of ciprofloxacin drug

Ciprofloxacin (CPF, C17H18FN3O3) drug is used in the treatment of some bacterial infectious diseases. The drug was investigated using thermal analysis (TA) measurements (TG/DTG) and electron impact mass spectral (EI-MS) fragmentation at 70 eV techniques. Furthermore, the drug was characterized and investigated by other spectroscopic tools as IR, UV–Vis, 1H-, and 13C-NMR. Semi-empirical MO calculation using PM3 procedure has been carried out on neutral molecule and positively charged species. The calculations included, bond length, bond order, bond strain, partial charge distribution, ionization energy, and heat of formation (ΔH f). The PM3 procedure provides a basis for fine distinction among sites of initial bond cleavage, which is crucial to the rationalization of subsequent fragmentation of the molecule. The mass spectra and thermal analysis fragmentation pathways were proposed and compared to each other to select the most suitable scheme representing the correct fragmentation of this drug. From EI-MS, the main primary cleavage site of the charged molecule is that due to C–COOH bond cleavage with H-rearrangement to skeleton and CO2 loss which can further decompose by piperazine loss. Thermal analysis of the neutral form of the drug reveals the high response of the drug to the temperature variation with very fast rate. Thermal decomposition has carried out in several sequential steps in the temperature range 40–650 °C. The initial thermal decomposition is similar to that obtained by mass spectrometric fragmentation (C–COOH fragment) but differ in that a rearrangement occurs by OH and CO loss. Therefore, comparison between MS and TA helps in selection the proper pathway representing the fragmentation of this drug. This comparison successfully confirmed by MO calculation. Finally, the effect of fluorine atom on the stability of the drug was discussed.

A new way APP mismetabolism can lead to Alzheimer's disease

Amyloid precursor protein (APP) is a transmembrane protein, which is sequentially cleaved at several sites by different enzymes. Cleavage leads to the production of different Aβ (β amyloid) species, which—when overproduced and aggregated—are a major cause of Alzheimer's disease. The main cleavage sites in APP are the β‐ and γ/e‐sites mediated by the respective secretases (Fig 1). Importantly, mutations in APP and the presenilins have been shown to cause Alzheimer's disease by a remarkable number of mechanisms. Now, it seems there is one at a previously underestimated site. Figure 1. Pathogenic mutations in APP. Amino acids highlighted in red are known to be pathogenic. The newly discovered mutation affecting cleavage at the β′‐site is highlighted in grey. Cleavage sites for different secretases are indicated. Note that the γ‐secretase cleaves APP at multiple sites starting between amino acid 718 and 719 and then proceeding …

Identification and quantification of oleanolic acid and ursolic acid in Chinese herbs by liquid chromatography-ion trap mass spectrometry

A rapid and sensitive method for the identification and quantification of ursolic acid (UA) and oleanolic acid (OA) in Chinese herbs is described. The method combines liquid chromatography (LC) with ion trap-mass spectrometry (IT-MS) detection. The UA and OA standard solution were directly infused into IT-MS for collecting MS(n) spectra. The major fragment ions of UA and OA were confirmed by MS(n) at m/z 455, 407, 391, 377 and 363 in negative ion mode, and m/z 457, 439, 411 and 393 in positive mode, respectively. The possible main cleavage pathway of fragment ions was studied. UA and OA provided good signals corresponding to the deprotonated molecular ion [M - H](-). The method is reliable and reproducible, and the detection limit is 5 ng/mL. The method was validated in the concentration range of 0.04-40 μg/mL; intra- and inter-day precisions ranged from 0.78 to 2.15%, and the accuracy was 96.5-108.2% for UA and OA. The mean recovery of UA and OA was 97.1-106.2% with RSD less than 1.86%. An LC-IT-MS method was successfully applied to determine the UA and OA in nine Chinese herbs.

Characterization of Unusual Proanthocyanidins in Leaves of Bayberry (Myrica rubra Sieb. et Zucc.)

Extractable and unextractable proanthocyanidins (EPAs and UEPAs) from leaves of bayberry were characterized. Both EPAs and UEPAs were analyzed by acid catalysis in the presence of excess phloroglucinol. The main cleavage product, epigallocatechin-3-O-gallate-(4β→2)-phloroglucinol, was successfully identified. The EPAs were of the prodelphinidin type. In fact, epigallocatechin-3-O-gallate (EGCG) and traces of epigallocatechin (EGC) were detected as the extension units, but only EGCG was present in the terminal units. All of the compounds exhibited a 2,3-cis configuration, and >98% of them were galloylated. The mean degree of polymerization (mDP) of bayberry leaf EPAs was 6.5, and the most abundant EPAs were the polymers, with mDP values of 9.5-26.7. The UEPAs were highly polymerized prodelphinidins consisting of EGCG and traces of EGC. In addition, EGCG, three EPA dimers, and two trimers were identified. The EPAs and UEPAs consisted mostly of EGCG, which is unusual in the plant kingdom.

Bactericidal oncocin derivatives with superior serum stabilities

The proline-rich antimicrobial peptide oncocin is remarkably active in vitro against a number of important Gram-negative bacteria of concern to humans owing to their increasing resistance to antibiotics, i.e. Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae) and non-fermenting species (Acinetobacter baumannii and Pseudomonas aeruginosa). Degradation of oncocin in mouse serum was investigated in this study. Several approaches to stabilise the main cleavage sites (C-terminal to Arg-15 and N-terminal to Arg-19) by substituting either or both arginine (Arg) residues with non-proteinogenic amino acids, i.e. α-amino-3-guanidino-propionic acid, homoarginine, nitro-arginine, N-methyl-arginine, β-homoarginine, d-arginine (d-Arg) or ornithine (Orn), were tested. These modifications were found to increase the half-life of oncocin in full mouse serum. For oncocin with two Orn residues in positions 15 and 19, the half-life in full serum increased from 25min to 3h. An increase of >8h was observed for oncocin with two d-Arg residues at these same positions. The antibacterial activities of these modified sequences were slightly better than the original oncocin sequence. Moreover, the three most stable analogues were found to be bactericidal against E. coli and were not toxic to HeLa cells or haemolytic to human erythrocytes.

Core-shell silica nanoparticles synthesized for quantitative study of DNA cleavage by laser-induced fluorescence microscopy

Dye-doped silica nanoparticles (C dots) were synthesized in reverse microemulsions and used to quantitatively examine DNA cleavage in the presence of transition metal ions. The cores were synthesized as fluorescein isothiocyanate (FITC)-doped silica nanoparticles and the shells' surfaces were modified with single-stranded DNA oligomers tagged with Cy5 fluorophores. DNA cleavage induced by heavy metal ions was estimated by comparing the fluorescence of Cy5 before and after reaction with metal ions. For this, a lab-built laser-induced fluorescence microscope equipped with a charge coupled device (CCD) camera, for imaging, and photomultiplier tube, for photon counting, was used. FITC fluorescence from the core was measured as an internal standard to compensate for possible loss of the beads during the treatment. The cleavage of DNA in air in the presence of Pb(2+), Cd(2+), and Hg(2+) at 1 ng/mL was found to be 14%, 6%, and 20%, respectively, and was significantly reduced to below 9% under N(2) gas, indicating that the main cleavage source was oxygen in air. The most significant DNA cleavage was observed with the addition of hydrogen peroxide. This analytical method using dye-doped C dots provided convenient handling and quantification of the estimation of metal-DNA interaction with a detection limit of 34.9 pmol/mL.

Influence of biological assay conditions on stability assessment of radiometal-labelled peptides exemplified using a 177Lu-DOTA-minigastrin derivative

Lack of correlation between in vitro and in vivo stability is a general problem for the development of radiopeptides especially in the case of minigastrin derivatives for therapeutic applications. In this study, we compared the influence of experimental conditions on radiopeptide stability results in vitro using a model Minigastrin (MG) analogue labelled with Lu-177. Additionally, we attempted to characterize the main serum enzymatic cleavage sites by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) analysis. In vitro stability of a DOTA-minigastrin derivative ((177)Lu-DOTA-His-His-Glu-Ala-Tyr-Gly-Trp-NIe-Asp-Phe-NH(2)) was tested in serum, rat tissue homogenates and two different standardised enzymatic mixtures. Quantification of the metabolised radiopeptides at different time intervals was performed using reversed-phase high-performance liquid chromatography (RP-HPLC). Metabolites were characterised by MALDI-TOF-MS. Urine was collected after 15 min p.i. into the mice and compared with in vitro metabolites by RP-HPLC. Faster degradation of the radiopeptide was found in blood in comparison with plasma and serum incubation and in components from rats faster than from human origin. Fast degradation was observed in kidney and liver homogenates as well as in standardised enzymatic mixtures, also revealing variations in the metabolic profile. In urine, no intact peptide was detected already 5 min post injection. MALDI-TOF-MS revealed major cleavage sites at the carboxy terminus of the peptide. Very variable results may be found when different kind of incubation media for testing radiopeptide stabilities is used. Serum incubation studies may overestimate stability; therefore, results should be interpreted with care and combined with alternative in vitro and in vivo investigations.

Mass Spectrometric Identification of Key Proteolytic Cleavage Sites in Statherin Affecting Mineral Homeostasis and Bacterial Binding Domains

Human salivary statherin inhibits both primary and secondary calcium phosphate precipitation and, upon binding to hydroxyapatite, associates with a variety of oral bacteria. These functions, crucial in the maintenance of tooth enamel integrity, are located in defined regions within the statherin molecule. Proteases associated with saliva, however, cleave statherin effectively, and it is of importance to determine how statherin functional domains are affected by these events. Statherin was isolated from human parotid secretion by zinc precipitation and purified by reversed-phase high performance liquid chromatography (RP-HPLC). To characterize the proteolytic process provoked by oral proteases, statherin was incubated with whole saliva and fragmentation was monitored by RP-HPLC. The early formed peptides were structurally characterized by reversed phase liquid chromatography electrospray-ionization tandem mass spectrometry. Statherin was degraded 3.6× faster in whole saliva than in whole saliva supernatant. The main and primary cleavage sites were located in the N-terminal half of statherin, specifically after Arg(9), Arg(10), and Arg(13); after Phe(14) and Tyr(18); and after Gly(12), Gly(15), Gly(17) and Gly(19) while the C-terminal half of statherin remained intact. Whole saliva protease activities separated the charged N-terminus from the hydrophobic C-terminus, negatively impacting on full length statherin functions comprising enamel lubrication and inhibition of primary calcium phosphate precipitation. Cryptic epitopes for bacterial binding residing in the C-terminal domain were likewise affected. The full characterization of the statherin peptides generated facilitates the elucidation of their novel functional roles in the oral and gastro-intestinal environment.

Temperature‐dependent pyrolytic product evolution profile for polypropylene

AbstractThe composition of the pyrolysis products of plastics depends on disintegration of the macromolecule into variety of hydrocarbon fractions. In this work, a detailed gas chromatographic study of pyrolysis products of polypropylene (PP) between 200 and 600°C was carried out. The pyrograms have been analyzed in terms of amount of different products evolved at various pyrolysis temperatures. At low pyrolysis temperatures (200–300°C), the yield of lighter hydrocarbons (C5‐C10) is low; it gradually increases until maximum decomposition temperature (446°C) and decreases thereafter. The following reaction types were considered to explain the decomposition mechanism of PP: (a) main chain cleavage to form chain‐ terminus radicals; (b) intramolecular hydrogen transfer to generate internal radicals; (c) intermolecular hydrogen transfer to form both volatile products and radicals; and (d) β‐scission to form both volatiles and terminally unsaturated polymer chains. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011

Rapid decay of unstable Leishmania mRNAs bearing a conserved retroposon signature 3′-UTR motif is initiated by a site-specific endonucleolytic cleavage without prior deadenylation

We have previously shown that the Leishmania genome possess two widespread families of extinct retroposons termed Short Interspersed DEgenerated Retroposons (SIDER1/2) that play a role in post-transcriptional regulation. Moreover, we have demonstrated that SIDER2 retroposons promote mRNA degradation. Here we provide new insights into the mechanism by which unstable Leishmania mRNAs harboring a SIDER2 retroposon in their 3′-untranslated region are degraded. We show that, unlike most eukaryotic transcripts, SIDER2-bearing mRNAs do not undergo poly(A) tail shortening prior to rapid turnover, but instead, they are targeted for degradation by a site-specific endonucleolytic cleavage. The main cleavage site was mapped in two randomly selected SIDER2-containing mRNAs in vivo between an AU dinucleotide at the 5′-end of the second 79-nt signature (signature II), which represents the most conserved sequence amongst SIDER2 retroposons. Deletion of signature II abolished endonucleolytic cleavage and deadenylation-independent decay and increased mRNA stability. Interestingly, we show that overexpression of SIDER2 anti-sense RNA can increase sense transcript abundance and stability, and that complementarity to the cleavage region is required for protecting SIDER2-containing transcripts from degradation. These results establish a new paradigm for how unstable mRNAs are degraded in Leishmania and could serve as the basis for a better understanding of mRNA decay pathways in general.

Endogenous Proteolytic Cleavage of Disease-associated Prion Protein to Produce C2 Fragments Is Strongly Cell- and Tissue-dependent

The abnormally folded form of the prion protein (PrP(Sc)) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrP(Sc) N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrP(Sc) accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrP(Sc) proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrP(Sc) fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrP(Sc) and cell pathogenesis of prion infection.

Osteopontin Is Cleaved at Multiple Sites Close to Its Integrin-binding Motifs in Milk and Is a Novel Substrate for Plasmin and Cathepsin D

Osteopontin (OPN) is a highly modified integrin-binding protein present in most tissues and body fluids where it has been implicated in numerous biological processes. A significant regulation of OPN function is mediated through phosphorylation and proteolytic processing. Proteolytic cleavage by thrombin and matrix metalloproteinases close to the integrin-binding Arg-Gly-Asp sequence modulates the function of OPN and its integrin binding properties. In this study, seven N-terminal OPN fragments originating from proteolytic cleavage have been characterized from human milk. Identification of the cleavage sites revealed that all fragments contained the Arg-Gly-Asp(145) sequence and were generated by cleavage of the Leu(151)-Arg(152), Arg(152)-Ser(153), Ser(153)-Lys(154), Lys(154)-Ser(155), Ser(155)-Lys(156), Lys(156)-Lys(157), or Phe(158)-Arg(159) peptide bonds. Six cleavages cannot be ascribed to thrombin or matrix metalloproteinase activity, whereas the cleavage at Arg(152)-Ser(153) matches thrombin specificity for OPN. The principal protease in milk, plasmin, hydrolyzed the same peptide bond as thrombin, but its main cleavage site was identified to be Lys(154)-Ser(155). Another endogenous milk protease, cathepsin D, cleaved the Leu(151)-Arg(152) bond. OPN fragments corresponding to plasmin activity were also identified in urine showing that plasmin cleavage of OPN is not restricted to milk. Plasmin, but not cathepsin D, cleavage of OPN increased cell adhesion mediated by the alpha(V)beta(3)- or alpha(5)beta(1)-integrins. Similar cellular adhesion was mediated by plasmin and thrombin-cleaved OPN showing that plasmin can be a potent regulator of OPN activity. These data show that OPN is highly susceptible to cleavage near its integrin-binding motifs, and the protein is a novel substrate for plasmin and cathepsin D.

Temperature-dependent pyrolytic product evolution profile for low-density polyethylene from gas chromatographic study

In this work, a product distribution study from thermal degradation of low-density polyethylene (LDPE) is presented. Thermal degradation of the polymer was investigated under dynamic condition in an inert environment using a thermo-gravimetric analyzer (TGA) coupled with evolved products’ analysis using a gas chromatograph (GC). Fractions evolved at nine different temperatures from 200 to 600 °C were injected into GC for a detailed product analysis. The main objective of the present investigation is to highlight the species-specific evolution profiles of LDPE pyrolyzates (C5–C44) at different stages of its degradation under an inert environment. Pyrograms have been analyzed in terms of amount of different products evolved at various pyrolysis temperatures. Volatile pyrolyzates essentially remain low at low decomposition temperature (200–300 °C) of the polymer, which gradually increase to attain a maximum at maximum decomposition temperature (470 °C) and finally level off at 600 °C. In the mechanistic approach adopted to understand the decomposition mechanism of LDPE, the following reaction types were considered: (a) main chain cleavage to form chain-terminus radicals; (b) intramolecular hydrogen transfer to generate internal radicals; (c) intermolecular hydrogen transfer to form both volatile products and radicals; and (d) β-scission to form both volatiles and terminally unsaturated polymer.

Bioconversion of cinnamic acid derivatives by Schizophyllum commune

To investigate the production of useful phenols from plant resources, we examined the metabolism of cinnamic acid derivatives by a wood-rotting fungus, Schizophyllum commune. Four cinnamic acid derivatives (cinnamic, p-coumaric, ferulic, and sinapic acids) were tested as substrates. Two main reactions, reduction and cleavage of the side chain, were observed. Reduction of the side chain was confirmed in cinnamic acid and p-coumaric acid metabolism. The side chain cleavage occurred in p-coumaric acid and ferulic acid metabolism but the initial reactions of these acids differed. Sinapic acid was not metabolized by S. commune. p-Hydroxybenzaldehyde accumulation was observed in the culture to which p-coumaric acid was added. This suggests that S. commune is a useful agent for transforming p-coumaric acid into p-hydroxybenzaldehyde.

Enzymatic processing of β‐dystroglycan recombinant ectodomain by MMP‐9: Identification of the main cleavage site

Dystroglycan (DG) is a membrane receptor belonging to the complex of glycoproteins associated to dystrophin. DG is formed by two subunits, alpha-DG, a highly glycosylated extracellular matrix protein, and beta-DG, a transmembrane protein. The two DG subunits interact through the C-terminal domain of alpha-DG and the N-terminal extracellular domain of beta-DG in a noncovalent way. Such interaction is crucial to maintain the integrity of the plasma membrane. In some pathological conditions, the interaction between the two DG subunits may be disrupted by the proteolytic activity of gelatinases (i.e. MMP-9 and/or MMP-2) that removes a portion or the whole beta-DG ectodomain producing a 30 kDa truncated form of beta-DG. However, the molecular mechanism underlying this event is still unknown. In this study, we carried out proteolysis of the recombinant extracellular domain of beta-DG, beta-DG(654-750) with human MMP-9, characterizing the catalytic parameters of its cleavage. Furthermore, using a combined approach based on SDS-PAGE, MALDI-TOF and HPLC-ESI-IT mass spectrometry, we were able to identify one main MMP-9 cleavage site that is localized between the amino acids His-715 and Leu-716 of beta-DG, and we analysed the proteolytic fragments of beta-DG(654-750) produced by MMP-9 enzymatic activity.

Evolving Electoral Cleavages in Korea

This paper explores changes in Korea’s voter alignments. Since Korea has experienced abridged social changes, she appears to have undergone dramatic changes of political cleavages as well which is contrary to the ‘fixation’ theory of Lipset and Rokkan. The main cleavages shown in Korean politics are urbanrural, regional, generation, and ideology cleavages. Urban-rural cleavage dominated the era of authoritarian rule because electoral fraud with threats or bribery was less likely in more modernized urban areas while illegal electioneering was more prevalent in under-modernized rural areas where the level of education was relatively lower. After democratization, regional cleavage became the main cleavage since voters chose candidates based on strong regional ties in the absence of the issue of democratization that had dominated Korean politics for forty years. Though it was still the main one, regional cleavage became weakened by new cleavages of generation and ideology in the 2002 presidential election. In the 2007 presidential election, regional cleavage appears to have been modified significantly. The capital region, used to being a swing region, became a strong electoral basis for Lee Myung-bak. Noticeably voters in the region began to cut their connections to their birthplaces.

Cathepsin D is the main lysosomal enzyme involved in the degradation of alpha-synuclein and generation of its carboxy-terminally truncated species.

Alpha-synuclein is likely to play a key role in the development of Parkinson's disease as well as other synucleinopathies. In animal models, overexpression of full-length or carboxy-terminally truncated alpha-synuclein has been shown to produce pathology. Although the proteosome and lysosome have been proposed to play a role in the degradation of alpha-synuclein, the enzyme(s) involved in alpha-synuclein clearance and generation of its carboxy-terminally truncated species have not been identified. In this study, the role of cathepsin D and calpain I in these processes was analyzed. In vitro experiments, using either recombinant or endogenous alpha-synuclein as substrates and purified cathepsin D or lysosomes, demonstrated that cathepsin D degraded alpha-synuclein very efficiently, and that limited proteolysis resulted in the generation of carboxy-terminally truncated species. Purified calpain I also cleaved alpha-synuclein, but carboxy-terminally truncated species were not the main cleavage products, and calpain I activity present in cellular lysates was not able to degrade the protein. Knockdown of cathepsin D in cells overexpressing wild-type alpha-synuclein increased total alpha-synuclein levels by 28% and lysosomal alpha-synuclein by 2-fold. In in vitro experiments, pepstatin A completely blocked the degradation of alpha-synuclein in purified lysosomes. Furthermore, lysosomes isolated from cathepsin D knockdown cells showed a marked reduction in alpha-synuclein degrading activity, indicating that cathepsin D is the main lysosomal enzyme involved in alpha-synuclein degradation. Our findings suggest that upregulation of cathepsin D could be an additional therapeutic strategy to lessen alpha-synuclein burden in synucleinopathies.

In Vitro Maturation of Oocytes Collected from Unstimulated Ovaries for Oocyte Donation

Objective To assess the role of immature oocyte collection from unstimulated ovaries as a potential source of oocyte donation. Design Prospective cohort study. Setting A tertiary, university-based, in vitro fertilization center. Patient(s) Twelve oocyte donors with ultrasound-only polycystic ovaries or polycystic ovary syndrome matched with 12 oocyte recipients. Intervention(s) Immature oocyte collection without any ovarian stimulation. In vitro maturation of the oocytes. Embryo transfer of the embryos. Main Outcome Measure(s) Immature oocyte collection, maturation, fertilization, and cleavage rates. Implantation, pregnancy, and live birth rates. Result(s) A mean of 12.8 ± 5.1 Germinal-vesicle oocytes were aspirated per collection. The in vitro maturation rate was 68.3% ± 18.4% with a mean of 8.7 ± 3.6 mature oocytes per collection. The mean fertilization rate was 73.3% ± 19.4%. Two to five embryos (median four) were transferred. Six recipients conceived, giving a 50% clinical pregnancy rate per cycle. The mean implantation rate per embryo was 18.2%. The live birth rate per cycle started was 30%. Conclusion(s) Collecting immature oocytes from unstimulated ovaries for the purpose of oocyte donation is a simple procedure that totally avoids ovarian stimulation. With appropriate selection of women with ultrasound-only polycystic ovaries or women with the polycystic ovary syndrome, the pregnancy rates of the recipients are comparable with those achieved through conventional IVF oocyte donor cycles.

Photodegradation of malachite green under natural sunlight irradiation: Kinetic and toxicity of the transformation products

This article describes the photolytic degradation of malachite green (MG), a cationic triphenylmethane dye used worldwide as a fungicide and antiseptic in the aquaculture industry. Photolysis experiments were performed by direct exposure of a solution of MG in water to natural sunlight. The main transformation products (TPs) generated during the process were identified by liquid chromatography time-of-flight mass spectrometry (LC–TOF-MS) and gas chromatography mass spectrometry (GC–MS). The 28 TPs identified with this strategy indicate that MG undergoes three main reactions, N-demethylation, hydroxylation and cleavage of the conjugated structure forming benzophenone derivatives. These processes involve hydroxyl radical attack on the phenyl ring, the N, N-dimethylamine group and the central carbon atom. The Vibrio fischeri acute toxicity test showed that the solution remains toxic after MG has completely disappeared. This toxicity could be assigned, at least in part, to the formation of 4-(dimethylamine)benzophenone, which has an EC 50,30 min of 0.061 mg l −1, and is considered “very toxic to aquatic organisms” by current EU legislation.

Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the Acyl-Enzyme Complex for an Intermolecular Self-cleavage Reaction

Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-A resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser(633)Ogamma forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala(716), of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-A resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ( approximately 19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.