Multiple Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase

Severe acute respiratory syndrome coronavirus (SARS-CoV), a newly identified group 2 coronavirus, is the causative agent of severe acute respiratory syndrome, a life-threatening form of pneumonia in humans. Coronavirus replication and transcription are highly specialized processes of cytoplasmic RNA synthesis that localize to virus-induced membrane structures and were recently proposed to involve a complex enzymatic machinery that, besides RNA-dependent RNA polymerase, helicase, and protease activities, also involves a series of RNA-processing enzymes that are not found in most other RNA virus families. Here, we characterized the enzymatic activities of a recombinant form of the SARS-CoV helicase (nonstructural protein [nsp] 13), a superfamily 1 helicase with an N-terminal zinc-binding domain. We report that nsp13 has both RNA and DNA duplex-unwinding activities. SARS-CoV nsp13 unwinds its substrates in a 5'-to-3' direction and features a remarkable processivity, allowing efficient strand separation of extended regions of double-stranded RNA and DNA. Characterization of the nsp13-associated (deoxy)nucleoside triphosphatase ([dNTPase) activities revealed that all natural nucleotides and deoxynucleotides are substrates of nsp13, with ATP, dATP, and GTP being hydrolyzed slightly more efficiently than other nucleotides. Furthermore, we established an RNA 5'-triphosphatase activity for the SARS-CoV nsp13 helicase which may be involved in the formation of the 5' cap structure of viral RNAs. The data suggest that the (d)NTPase and RNA 5'-triphosphatase activities of nsp13 have a common active site. Finally, we established that, in SARS-CoV-infected Vero E6 cells, nsp13 localizes to membranes that appear to be derived from the endoplasmic reticulum and are the likely site of SARS-CoV RNA synthesis.

Neighboring Group-Controlled Hydrolysis: Towards “Designer” Drug Release Biomaterials

To give the first demonstration of neighboring group-controlled drug delivery rates, a series of novel, polymerizable ester drug conjugates was synthesized and fully characterized. The monomers are suitable for copolymerization in biomaterials where control of drug release rate is critical to prophylaxis or obviation of infection. The incorporation of neighboring group moieties differing in nucleophilicity, geometry, and steric bulk in the conjugates allowed the rate of ester hydrolysis, and hence drug liberation, to be rationally and widely controlled. Solutions (2.5 x 10-5 mol dm-3) of ester conjugates of nalidixic acid incorporating pyridyl, amino, and phenyl neighboring groups hydrolyzed according to first-order kinetics, with rate constants between 3.00 ( 0.12 10-5 s -1 (fastest) and 4.50 ( 0.31 10- 6 s-1 (slowest). The hydrolysis was characterized using UV-visible spectroscopy. When copolymerized with poly(methyl methacrylate), free drug was shown to elute from the resulting materials, with the rate of release being controlled by the nature of the conjugate, as in solution. The controlled molecular architecture demonstrated by this system offers an attractive class of drug conjugate for the delivery of drugs from polymeric biomaterials such as bone cements in terms of both sustained, prolonged drug release and minimization of mechanical compromise as a result of release. We consider these results to be the rationale for the development of 'designer' drug release biomaterials, where the rate of required release can be controlled by predetermined molecular architecture.

Human coronavirus 229E nonstructural protein 13: characterization of duplex-unwinding, nucleoside triphosphatase, and RNA 5'-triphosphatase activities.

The human coronavirus 229E (HCoV-229E) replicase gene-encoded nonstructural protein 13 (nsp13) contains an N-terminal zinc-binding domain and a C-terminal superfamily 1 helicase domain. A histidine-tagged form of nsp13, which was expressed in insect cells and purified, is reported to unwind efficiently both partial-duplex RNA and DNA of up to several hundred base pairs. Characterization of the nsp13-associated nucleoside triphosphatase (NTPase) activities revealed that all natural ribonucleotides and nucleotides are substrates of nsp13, with ATP, dATP, and GTP being hydrolyzed most efficiently. Using the NTPase active site, HCoV-229E nsp13 also mediates RNA 5'-triphosphatase activity, which may be involved in the capping of viral RNAs.

Mechanistic studies of amide bond scission during acidolytic deprotection of Pip containing peptide.

Unusual TFA catalyzed cleavage reaction is reported for peptide containing pipecolic acid residues. Although the use of TFA under standard cleavage conditions is sufficiently mild to prevent degradation of the desired products. the amide bond between consecutive pipecolic acid residues is unexpectedly hydrolyzed by standard TFA treatment. The hydrolysis is proposed to proceed via an oxazolinium ion intermediate, This mechanism is supported by H/D exchange as observed by ESI-MS and NMR experiments.

Degradation of 1,3-dichloropropene by Pseudomonas cichorii 170

The gram-negative bacterium Pseudomonas cichorii 170, isolated from soil that was repeatedly treated with the nematocide 1,3-dichloropropene, could utilize low concentrations of 1,3-dichloropropene as a sole carbon and energy source, Strain 170 was also able to grow on 3-chloroallyl alcohol, 3-chloroacrylic acid, and several 1-halo-n-alkanes. This organism produced at least three different dehalogenases: a hydrolytic haloalkane dehalogenase specific for haloalkanes and two 3-chloroacrylic acid dehalogenases, one specific for cis-3-chloroacrylic acid and the other specific for trans-3-chloroacrylic acid. The haloalkane dehalogenase and the trans-3-chloroacrylic acid dehalogenase were expressed constitutively, whereas the cis-3-chloroacrylic acid dehalogenase was inducible, The presence of these enzymes indicates that 1,3-dichloropropene is hydrolyzed to 3-chloroallyl alcohol, which is oxidized in two steps to 3-chloroacrylic acid. The latter compound is then dehalogenated, probably forming malonic acid semialdehyde. The haloalkane dehalogenase gene, which is involved in the conversion of 1,3-dichloropropene to 3-chloroallyl alcohol, was cloned and sequenced, and this gene turned out to be identical to the previously studied dhaA gene of the gram-positive bacterium Rhodococcus rhodochrous NCIMB13063, Mutants resistant to the suicide substrate 1,2-dibromoethane lacked haloalkane dehalogenase activity and therefore could not utilize haloalkanes for growth. PCR analysis showed that these mutants had lost at least part of the dhaA gene.

Isotope dilution gas chromatography/mass spectrometry method for the determination of methionine sulfoxide in protein

We have developed a new technique for quantifying methionine sulfoxide (MetSO) in protein to assess levels of oxidative stress in physiological systems. In this procedure, samples are hydrolyzed with methanesulfonic acid (MSA) in order to avoid the conversion of MetSO to methionine (Met) that occurs during hydrolysis of protein in HCl. The hydrolysate is fractionated on a cation exchange column to remove the nonvolatile MSA from amino acids, and the amino acids are then derivatized as their trimethylsilyl esters for analysis by selected ion monitoring-gas chromatography/mass spectrometry. The limit of detection of the assay is 200 pmol of MetSO per analysis, and the interassay coefficient of variation is 5.8%. Compared to current methods, the SIM-GC/MS assay avoids the potential for conversion of Met to MetSO during sample preparation, requires less sample preparation time, has lower variability, and uses mass spectrometry for sensitive and specific analyte detection.

Trimethoxymethane as an alternative fuel for a direct oxidation PBI polymer electrolyte fuel cell

The oxidation of trimethoxymethane (TMM) (trimethyl orthoformate) in a direct oxidation PBI fuel cell was examined by on-line mass spectroscopy and on-line FTIR spectroscopy. The results show that TMM was almost completely hydrolyzed in a direct oxidation fuel cell which employs an acid doped polymer electrolyte to form a mixture of methylformate, methanol and formic acid. It also found that TMM was hydrolyzed in the presence of water at 120°C even without acidic catalyst. The anode performance improves in the sequence of methanol, TMM, formic acid/methanol, and methylformate solutions. Since formic acid is electrochemically more active than methanol, these results suggest that formic acid is probably a key factor for the improvement of the anode performance by using TMM instead of methanol under these conditions. © 1998 Elsevier Science Ltd. All rights reserved.

Thermolyzable polymer networks and star polymers containing a novel, compact, degradable acylal-based dimethacrylate cross-linker: Synthesis, characterization, and thermolysis

A compact, cleavable acylal dimethacrylate cross-linker, 1,1-ethylenediol dimethacrylate (EDDMA), was synthesized from the anhydrous iron(III) chloride-catalyzed reaction between methacrylic anhydride and acetaldehyde. The ability of EDDMA to act as cross-linker was demonstrated by using it for the preparation of one neat cross-linker network, four star polymers of methyl methacrylate (MMA), and four randomly cross-linked MMA polymer networks using group transfer polymerization (GTP). For comparison, the corresponding polymer structures based on the commercially available ethylene glycol dimethacrylate (EGDMA) cross-linker (isomer of EDDMA) were also prepared via GTR The number of arms of the EDDMA-based star polymers was lower than that of the corresponding EGDMA polymers, whereas the degrees of swelling in tetrahydrofuran of the EDDMA-based MMA networks were higher than those of their EGDMA-based counterparts. Although none of the EDDMA-containing polymers could be cleanly hydrolyzed under basic or acidic conditions, they could be thermolyzed at 200 degrees C within 1 day giving lower molecular weight products.

Synthesis and characterization of star polymers and cross-linked star polymer model networks with cores based on an asymmetric, hydrolyzable dimethacrylate cross-linker

A hydrolyzable dimethacrylate cross-linker, 2-methyl-2,4-pentanediol dimethacrylate (MPDMA), was synhesized by the reaction of 2-methyl-2,4-pentanediol and methacryloyl chloride in the presence of triethylamine. This cross-linker was used to prepare a neat cross-linker network and three cross-linked star polymer model networks (CSPMNs) of methyl methacrylate (MMA), as well as star-shaped polymers of MMA, by group transfer polymerization (GTP). Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions (MWDs) of the linear polymer precursors, and demonstrated the increase in molecular weight (MW) on each successive addition of cross-linker or monomer. Characterization of the star polymers by static light scattering (SLS) in THF showed that star polymers with MPDMA cores bear a relatively small number of arms, between 7 and 35. All star polymers and polymer networks containing the MPDMA cross-linker were hydrolyzed at room temperature in neat trifluoroacetic acid to yield lower-MW products.

Synthesis and characterization of polymer networks and star polymers containing a novel, hydrolyzable acetal-based dimethacrylate cross-linker

An acid-labile dimethaerylate acetal cross-linker,di(methacryloyloxy-l-ethoxy)methane(DMOEM), was synthesized by the reaction of 2-hydroxyethyl methacrylate and paraformaldehyde using p-toluenesulfonic acid and toluene as catalyst and solvent, respectively. Group transfer polymerization was employed to use this cross-linker in the preparation of nine hydrolyzable polymer structures: one neat cross-linker network, one randomly cross-linked network of methyl methacrylate (MMA), and seven star-shaped polymers of MMA. Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions of the linear polymer precursors to the stars and demonstrated the increase in molecular weight upon the addition of cross-linker for the formation of star-shaped polymers. Characterization of the star polymers in THF using static light scattering and GPC showed that the molecular weights and the number of arms of each star polymer increased with an increase in the molar ratio of cross-linker to initiator and with a decrease in the molar ratio of monomer to initiator. The star polymers with DMOEM cores bore a smaller number of arms than those cross-linked with the non-hydrolyzable commercial cross-linker ethylene glycol dimethacrylate due to the bulkier structure of DMOEM. All DMOEM-containing polymer networks and star polymers were completely hydrolyzed within 48 h using hydrochloric acid in THF.

Synthesis and characterization of star polymers and cross-linked star polymer model networks containing a novel, silicon-based, hydrolyzable cross-linker

An acid-labile dimethacrylate cross-linker, dimethyldi(methacryloyloxy-l-ethoxy)silane (DMDMAES), was synthesized by the reaction of 2-hydroxyethyl methacrylate (HEMA) and dichlorodimethylsilane in the presence of triethylamine. Group transfer polymerization (GTP) was employed to use this cross-linker in the preparation of six hydrolyzable polymer structures: one neat cross-linker network, one randomly cross-linked network of methyl methacrylate (MMA), two star-shaped polymers of MMA, and two cross-linked star polymer model networks (CSPMNs) of MMA. A nonhydrolyzable CSPMN of MMA, based on a stable cross-linker, was also synthesized. Gel permeation chromatography (GPC) in tetrahydrofuran (THF) confirmed the narrow molecular weight distributions (MWDs) of the linear polymer precursors and demonstrated the increase in molecular weight (MW) upon each successive addition of cross-linker or monomer. Characterization by static light scattering (SLS) and GPC showed that star polymers with DMDMAES cores bear a relatively small number of arms, around 7. All star polymers and polymer networks were hydrolyzed using hydrochloric acid in THF. While the MWs of the products from the hydrolysis of the star polymers, the neat cross-linker network, and the randomly cross-linked network were as expected, those from the CSPMNs were of a much higher than expected MW, indicating extensive star-star coupling.

Hydrogel-Forming Microneedles Increase in Volume During Swelling in Skin, but Skin Barrier Function Recovery is Unaffected

We describe, for the first time, quantification of in-skin swelling and fluid uptake by hydrogel-forming microneedle (MN) arrays and skin barrier recovery in human volunteers. Such MN arrays, prepared from aqueous blends of hydrolyzed poly(methylvinylether/maleic anhydride) (15%, w/w) and the cross-linker poly(ethyleneglycol) 10,000 Da (7.5%, w/w), were inserted into the skin of human volunteers (n = 15) to depths of approximately 300 μm by gentle hand pressure. The MN arrays swelled in skin, taking up skin interstitial fluid, such that their mass had increased by approximately 30% after 6 h in skin. Importantly, however, skin barrier function recovered within 24 h after MN removal, regardless of how long the MN had been in skin or how much their volume had increased with swelling. Further research on closure of MN-induced micropores is required because transepidermal water loss measurements suggested micropore closure, whereas optical coherence tomography indicated that MN-induced micropores had not closed over, even 24 h after MN had been removed. There were no complaints of skin reactions, adverse events, or strong views against MN use by any of the volunteers. Only some minor erythema was noted after patch removal, although this always resolved within 48 h, and no adverse events were present on follow-up.

Mechanistic studies of the photocatalytic oxidation of microcystin-LR: An investigation of byproducts of the decomposition process

Microcystins (cyclic heptapeptides) are produced by a number of freshwater cyanobacteria and cause concern in potable water supplies due to their acute and chronic toxicity. The present study reports the structural characterization of the degradation products of the photocatalytic oxidation of microcystin-LR, so aiding the mechanistic understanding of this process. TiO₂ photocatalysis is a promising technology for removal of these toxins from drinking water. However, before it can be adopted in any practical application it is necessary to have a sufficient knowledge of degradation byproducts and their potential toxicity. Liquid chromatography-mass spectrometry analysis demonstrated that the major destruction pathway of microcystin appears to be initiated via three mechanisms: UV irradiation, hydroxyl radical attack, and oxidation. UV irradiation caused geometrical isomerization of microcystin converting the (4E), (6E) of the Adda configuration to (4E), 6(Z) or 4(Z), 6(E). Hydroxyl radical attack on the conjugated diene structure of Adda moiety produced dihyroxylated products. Further oxidation cleaved the hydroxylated 4-5 and/or 6-7 bond of Adda to form aldehyde or ketone peptide residues, which then were oxidized into the corresponding carboxylic acids. Photocatalysis also hydrolyzed the peptide bond on the ring structure of microcystin to form linear structures although this appeared to be a minor pathway.

The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases

UNLABELLED: Cyclic-di-GMP is a near-ubiquitous bacterial second messenger that is important in localized signal transmission during the control of various processes, including virulence and switching between planktonic and biofilm-based lifestyles. Cyclic-di-GMP is synthesized by GGDEF diguanylate cyclases and hydrolyzed by EAL or HD-GYP phosphodiesterases, with each functional domain often appended to distinct sensory modules. HD-GYP domain proteins have resisted structural analysis, but here we present the first structural representative of this family (1.28 Å), obtained using the unusual Bd1817 HD-GYP protein from the predatory bacterium Bdellovibrio bacteriovorus. Bd1817 lacks the active-site tyrosine present in most HD-GYP family members yet remains an excellent model of their features, sharing 48% sequence similarity with the archetype RpfG. The protein structure is highly modular and thus provides a basis for delineating domain boundaries in other stimulus-dependent homologues. Conserved residues in the HD-GYP family cluster around a binuclear metal center, which is observed complexed to a molecule of phosphate, providing information on the mode of hydroxide ion attack on substrate. The fold and active site of the HD-GYP domain are different from those of EAL proteins, and restricted access to the active-site cleft is indicative of a different mode of activity regulation. The region encompassing the GYP motif has a novel conformation and is surface exposed and available for complexation with binding partners, including GGDEF proteins.

IMPORTANCE: It is becoming apparent that many bacteria use the signaling molecule cyclic-di-GMP to regulate a variety of processes, most notably, transitions between motility and sessility. Importantly, this regulation is central to several traits implicated in chronic disease (adhesion, biofilm formation, and virulence gene expression). The mechanisms of cyclic-di-GMP synthesis via GGDEF enzymes and hydrolysis via EAL enzymes have been suggested by the analysis of several crystal structures, but no information has been available to date for the unrelated HD-GYP class of hydrolases. Here we present the multidomain structure of an unusual member of the HD-GYP family from the predatory bacterium Bdellovibrio bacteriovorus and detail the features that distinguish it from the wider structural family of general HD fold hydrolases. The structure reveals how a binuclear iron center is formed from several conserved residues and provides a basis for understanding HD-GYP family sequence requirements for c-di-GMP hydrolysis.

Techno-Economic and Life Cycle Assessment for the Production of Green Composites

Botanically, green composites belong to an economically important seed plant family that includes maize, wheat, rice, and sorghum known as Saccharum offi cinarum. There are so many natural fibers available in the environment such as rice husk, hemp fibers, flax fibers, bamboo fibers, coconut fiber, coconut coir, grawia optiva and many others also. Life Cycle Assessment (LCA) is a process to estimate the environmental feature and potential impacts related to a product, by organizing a directory of pertinent inputs and outputs of a product system, assessing the potential environmental impacts related with the said inputs and outputs, explaining the results of the inventory analysis and impact evaluation phases in connection to the objectives of the study. Particularly Bagasse, an agricultural residue not only becomes a problem from the environmental point of view, but also affects the profitability of the sugarcane industries. This chapter discusses the properties, processing methods and various other aspects including economic and environmental aspects related to green composites.