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  • 1
    ISSN: 0948-5023
    Keywords: Keywords: Amides ; Hydrolysis ; Reaction mechanism ; Peptides ; Theoretical calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The hydrolysis of amides is a model reaction to study peptide hydrolysis. This process has been previously considered in the literature at the ab initio level. In this work, we revisit different reaction mechanisms (water-assisted, non-assisted, neutral and acid-catalyzed) with various theoretical methods : semiempirical, ab initio and Density Functional. The ab initio calculations are carried out at a computational level which is substantially higher than in previous studies. We describe the structure of the transition states and discuss the influence of the catalyst. We also compute the activation free energies for these processes at the Density Functional Theory level. Comparison of the methods allows to outline the main trends of these theoretical approaches which may be useful to design new computational strategies for investigating biological reaction mechanisms through the use of combined Quantum Mechanics/Molecular Mechanics methods.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0948-5023
    Keywords: Keywords Computer Simulations, QM/MM Potentials, Density Functional Theory, Molecular Dynamics, Liquid Water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A hybrid NVE Molecular Dynamics simulation of liquid water is presented using a coupled Density Functional/Molecular Mechanics hamiltonian. The quantum subsystem is a single water molecule described by means of a triple-zeta quality basis set with polarization orbitals on oxygen and hydrogen atoms. Non-local exchange-correlation corrections are included self-consistently. The classical system is constituted by 128 classical TIP3P water molecules. Results are in reasonable agreement with experimental data and in particular a good description of the solute polarization is obtained. Large fluctuations of the instantaneous value of the dipole moment of the quantum molecule are predicted.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 3798-3805 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 158 (1998), S. 0 
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The Nod factors of Azorhizobium caulinodans ORS571 are lipo-chitooligosaccharides that at the reducing end can be unsubstituted, substituted with a l-fucosyl group, with a d-arabinose, or with both groups at the same time. These lipo-chitooligosaccharides are the compounds produced by the bacteria during the signal exchange with their host plant at the onset of the nodulation process. By the use of wild-type and mutant strains, the role of the different Nod factor glycosylations on the nodulation behavior was checked. The mere presence of the d-arabinosyl group at the reducing end of the lipo-chitooligosaccharides resulted in a higher number of nodules on roots of Sesbania rostrata, whereas the presence or absence of l-fucose had no effect. The situation is the opposite in other tropical legumes that respond to A. caulinodans ORS571: the l-fucose is the major determinant of nodulation, whereas the presence of d-arabinose is less significant. By the use of a β-glucuronidase reporter fusion, A. caulinodans ORS571 was shown to colonize nodules or nodule-like tissues induced on cowpea and bean, respectively.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of food safety 16 (1996), S. 0 
    ISSN: 1745-4565
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A total of 116 commercial samples of mixed vegetable salads, packaged in plastic bags, were examined for the presence of Listeria monocytogenes during storage at 4C. Commercial products, belonging to 4 different batches, were sampled over a period of one year and stored for 300 h at 4C in the laboratory. Different sets of enrichment and plating media were used to recover organisms, with subsequent identification by Pasco System and serotyping techniques. Out of a total of 70 control (noninoculated) samples, 21 (30%) were observed to contain Listeria monocytogenes, belonging to serotypes 3a and 3b. A study of salad inoculated with 103 cfu/g Listeria monocytogenes showed that the initial inoculum increased less than tenfold over the experimental period (300 h). During storage of the product, CO2 reached nearly 30% and O2 was no longer detected at 60 h, due to the respiration of the vegetables. The pH inside the packages remained around 6. The specific growth rate in the salad was calculated using the Dmodel Program, which gave a rate of 0.003h-1, a lower figure than that reported by other authors. This study found growth patterns different to those previously reported for salads with separate ingredients. Our results agree with previous reports that modified atmosphere does not greatly inhibit Listeria monocytogenes. This reflects a lower specific growth rate in this food compared to media, and illustrates the difficulty of validating, in complex food systems, mathematic models based on culture media.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1600-0668
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Architecture, Civil Engineering, Surveying , Medicine
    Notes: Abstract To determine the acute effects of environmental tobacco smoke on respiratory tract lung function, 130 asthmatics and 28 non-asthmatics were exposed up to 4 hours to side stream environmental tobacco smoke (SS-ETS) in a dynamic challenge chamber. The vast majority of the subjects exposed to SS-ETS reported upper respiratory and ocular irritant symptoms; the prevalence of these symptoms was not significantly associated with any particular study groups analyzed, or with the self-perception of tobacco smoke allergy by the study subject. All 28 SS-ETS-exposed non-asthmatics had no significant change in lung function, while 26/130 asthmatics demonstrated a significant drop in pulmonary function (FEV1≥20% decline), generally within 90 to 240 minutes after start of exposure. Classical late phase bronchoconstriction was not observed up to 24 hours following the challenge. Six/26 reactors had a significant drop in lung function following a sham control challenge, indicating that 20/130 asthmatics had a specific bronchoconstrictive response to SS-ETS. Responses to diminishing levels of SS-ETS demonstrated that some asthmatics can react to levels as low as 0.0128 cigarette – min/m3 (comparable to ETS levels in the homes of many smokers).
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Lipo-chitooligosaccharide (LCO) Nod factors are produced and secreted by rhizobia and trigger nodule development in leguminous host plants. The products of the bacterial nodlJ genes are related to transporters of capsular polysaccharides and were proposed to be involved in LCO transport. We have studied nodlJ of Azorhizobium caulinodans ORS571 by analysis of cell-associated and secreted radioactively labelled Nod factors in wild-type ORS571, a nodJ mutant and a complemented strain. Secretion was strongly reduced in the nodJ mutant, and restored to wild-type levels after complementation. Constructs were made for expression of combinations of different nod genes in Escherichia coli DH5a. The strain DH5α(pUCNABCSU) synthesized LCOs, but they were only secreted when a plasmid containing both nodl and nodJ was supplied in trans, nodi or nodJ alone was not sufficient. In E. coli as well as in Azorhizobium, the nod/J-encoded transporter showed a specificity for more hydrophilic LCOs.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The DNA region downstream of the nodABCSUIJ operon of Azorhizobium caulinodans was further characterized and two new genes, nodZ and noeC were identified in the same operon. The A. caulinodans wild-type strain produces a population of Nod factors that, at the reducing end, are either unmodified or carry a D-arabinosyl and/or an L-fucosyl branch. Nod factors produced by Tn5-insertion mutants in nodZnoeC, and the separate nolK locus, were analysed by thin-layer chromatography and mass spectrometry. Fucosylation of Nod factors depended on both nodZ and nolK. Arabinosylation depended on noeC and/or downstream genes. Protein extracts of A. caulinodans contained an enzymatic activity for fucose transfer from GDP-fucose to chitooligosaccharides and to Nod factors. By mutant analysis and expression of nodZ in Escherichia coli, the fucosyltransferase activity was ascribed to the protein encoded by nodZ. In addition, a Nod factor fucosyltransferase activity, independent of nodZ or other known nod genes, was detected in A. caulinodans. Finally, on the basis of sequence similarity of the nolK gene product, and mass spectrometric analysis of Nod factors produced by a nolK mutant, we propose that this gene is involved in the synthesis of GDP-fucose.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-2234
    Keywords: Key words:N-Methylazetidinone ; Molecular dynamics ; β-Lactam hydrolysis ; Solvent effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having similar energy barriers at the rate-limiting step of the reaction path. In the first type, the β-lactam-water interaction takes place through the oxygen carbonyl atom and there is agreement between the maxima of the RDFs obtained here and the ab initio structure of the complexes previously reported. In the second type, the interaction takes place through the nitrogen atom and we do not predict a coordination layer around the β-lactam nitrogen atom. The results suggest that in aqueous solution hydrolysis of the carbonyl group is the most probable starting point for the overall hydrolysis reaction. Some discussion on the use of cluster models to represent the solvent effect is included.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1573-3025
    Keywords: Aeroallergen ; Soybean asthma ; Immunochemical Assay ; Air sampling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract There have been reported epidemics of severe asthma in Barcelona, Spain, linked to a 10 kDa low molecular mass (LMM) allergen from soybean hulls that became airborne during unloading of ships. As a preliminary probe of the potential for dispersion of this allergen in USA cities, four automated air samplers were placed around a grain elevator in New Orleans and operated continuously from May to October 1990. The allergen was extracted from the filters and immunochemically assayed for soybean aeroallergen. On 31 separate days, the airborne allergen concentration in at least one of the samples was over 10000 U/m3 similar to those observed in Barcelona on some epidemic days. Areas North and East of the elevator were most affected. Serologie studies showed that of 50 asthmatics from New Orleans who were participants in an unrelated clinical study 4 or 8% demonstrated elevated titers of IgE antibody to LMM soybean allergen. Only 1 of 475 control sera (half of which were also asthmatic) obtained elsewhere in the US was positive for LMM soybean IgE antibody. Based on the findings in this study, there is a great possibility that on some days there is enough soybean allergen in the air and a sufficient frequency of soybean aeroallergen RAST positive asthmatics in New Orleans to warrant further investigation of the contribution of soybean aeroallergen to asthma around the port of New Orleans.
    Type of Medium: Electronic Resource
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