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Repeated transfer of small RNA virus populations leading to balanced fitness with infrequent stochastic drift.

The population dynamics of RNA viruses have an important influence on fitness variation and, in consequence, on the adaptative potential and virulence of this ubiquitous group of pathogens. Earlier work with vesicular stomatitis virus showed that large population transfers were reproducibly associated with fitness increases, whereas repeated transfers from plaque to plaque (genetic bottlenecks) lead to losses in fitness. We demonstrate here that repeated five-plaque to five-plaque passage series yield long-term fitness stability, except for occasional stochastic fitness jumps. Repeated five-plaque passages regularly alternating with two consecutive large population transmissions did not cause fitness losses, but did limit the size of fitness gains that would otherwise have occurred. These results underscore the profound effects of bottleneck transmissions in virus evolution.

Animals↗

Evaluation of a high temperature immobilised enzyme reactor for production of non-reducing oligosaccharides.

There is interest in the production of non-reducing carbohydrates due to their potential application in various industrial fields, particularly the food industry. In this paper, we describe the development of an immobilised cell bioprocess for the synthesis of non-reducing maltodextrins at high temperatures. The trehalosyl-dextrins-forming enzyme (TDFE) isolated from the thermoacidophilic archaeon Sulfolobus solfataricus (strain MT4), was recently expressed at high yields in Escherichia coli (strain Rb-791). Here, we evaluate different matrices, such as polyacrylamide gel, crude egg white, chitosan and calcium alginate for their effectiveness in immobilising whole recombinant E. coli cells subjected to prior thermal permeabilisation. Calcium-alginate based gels formed a solid biocatalyst with a good activity yield and the best enzymatic stability at the operating temperature (75 degrees C). Therefore, these beads were used to pack a glass column reactor to perform the bioconversion of interest. Optimal operating parameters were defined in relation to the substrate stream flow-rate and the substrate-to-biocatalyst ratio. The production of trehalosylmaltotetraose from maltohexaose reached equilibrium with a constant of about 2.6 at 75 degrees C. The bioreactor was exploited for production of trehalosylmaltodextrins from a commercial mixture of maltodextrins, achieving a productivity of 106.5 mg ml(-1) h(-1) (g biocatalyst)(-1) with ~40% conversion when using a 30% (w/v) solution.

Bioreactors↗

Oxidized forms of ovine erythrocyte glutathione peroxidase. Cyanide inhibition of a 4-glutathione:4-selenoenzyme.

[75Se]Glutathione peroxidase (glutathione:hydrogen-peroxide oxidoreductase, EC 1.11.1.9) containing 4 mol selenium per mol was isolated in 33% yield using 10% ethanol to stabilize the purified enzyme. When reduced with GSH and rapidly separated from GSH by gel filtration chromatography, GSH peroxidase was eluted in a labile oxidized (iodoacetate-insensitive) form which was stable at 4 degrees C but unstable at 25 degrees C (form A). When GSH-reduced enzyme was allowed to oxidize in the course of dialysis a more stable oxidized form was obtained (form C) which was rapidly inactivated by cyanide. Using [35S]GSH, form C was shown to contain tightly bound glutathione in approx. equimolar ratio with selenium. The cyanide sensitivity of GSH peroxidase is therefore correlated with the presence of a glutathione moiety in the enzyme. The isolation of GSH peroxidase containing bound glutathione suggests that intermediates containing glutathione bound to selenium may be formed during the catalytic cycle.

Animals↗

Selection and performance of monoclonal anti-C-reactive protein in ELISA quantitative assay.

Nine monoclonal anti C-reactive protein (CRP) antibodies were tested as peroxidase-conjugates in a CRP binding to a solid-phase phosphorylethanolamine (PE) assay. One monoclonal antibody was selected due to its high yield of conjugate, titre and stability. The use of monoclonal antibodies increased assay sensitivity, precision and allowed assay simplification by the simultaneous rather than sequential incubation of CRP and conjugate. Comparison with nephelometry and CRP binding to PE assay using polyclonals gave correlations greater than or equal to 0.9. By using monoclonal conjugates to assay human sera, healthy adult CRP levels were found to be lower than by using polyclonal conjugates. Samples with very low CRP contents might now be assayed with higher precision.

Adult↗

Conformational analysis of segments of oxidized cellulose. Part I: Molecular modelling of glucuronic acid dimers considering the effect of counter-ions and a polar environment.

Conformational analysis of various forms of glucuronic acid dimers as the model structures of oxidized cellulose has been performed using molecular mechanics with a CVFF force field. The effects of ionization of carboxyl groups, ion pairing with explicit consideration of counter-ions (Na+, Mg2+) and the implicit inclusion of a solvent effect via the dielectric constant, epsilon, have been simulated. The non-ionized glucuronic acid dimer shows conformational behaviour similar to that of unoxidized cellobiose. The ionization of COOH groups leads to strong destabilization of C and D conformers (with both COO- groups on the same side of the molecule), while complexation with counter-ions leads to strong stabilization of these forms which yield highly wound low-pitch helices. An increase in the solvent polarity has an attenuating effect on the behaviour described above.

Anions↗

Investigation of the properties of bovine heart creatine kinase cross-linked with dimethyl suberimidate.

Dimeric bovine heart creatine kinase (EC 2.7.3.2, ATP: creatine N-phosphotransferase) has been cross-linked with the bifunctional reagent dimethyl suberimidate at several concentrations to yield modified enzyme with enhanced stability towards heat denaturation. The degree of thermal stability is dependent on the degree of cross-linking with optimal stabilization occurring when approx. half of all the available amino groups are covalently attached to dimethyl suberimidate. Accelerated storage studies were performed and the results used to predict the storage time of the native and modified enzyme at lower temperatures. The cross-linked derivative was predicted to have a longer shelf-life at 4 degrees C than the native enzyme. Modification caused a reduction in the specific activity of the enzyme. The pH profile was altered following cross-linking, but the Michaelis constants were not changed. The modified enzyme exhibited a marked resistance to the action of some denaturing agents.

Animals↗

Labeling of hematoporphyrin with 105Rh and binding studies with human gamma globulin.

Labeling of hematoporphyrin with 105Rh at stoichiometric concentrations is described. Labeling efficiencies of up to 93% could be obtained at pH 9.0 in bicarbonate buffer. Solvent extraction of 105Rh-hematoporphyrin into methyl isobutyl ketone was used to estimate the complex yield. The complex showed high stability and no loss of 105Rh was seen throughout the 6 days of study. 105Rh-hematoporphyrin when incubated with human gamma globulin was seen to be quantitatively bound to the protein. This procedure may be used for labeling monoclonal antibodies with 105Rh for therapeutic applications.

Hematoporphyrins↗

Synthesis of R and S tritiated reduced beta-nicotinamide adenine dinucleotide 2' phosphate.

Nicotinamides are ubiquitous cofactors used by many biological systems as redox agents. Stereospecifically labeled cofactors are useful in many studies of nicotinamide-dependent enzymes. Enzyme-directed synthesis of these cofactors is rather common but their stability imposes significant challenges on yield, purity, and preservation. This paper presents the stereospecific synthesis of reduced R- and S-[4-3H] beta-nicotinamide adenine dinucleotide 2' phosphate (NADPH). The method of Valera et al. [Biochem. Biophys. Res. Commun. 148 (1987) 515] was modified to a synthetic procedure that produces both isotopic diastereomers within 2h with an improved yield of 75-90% after purification and lyophilization. In the synthesis, [4-3H]NADP+ was generated as an intermediate (which can be isolated if desired). The specific radioactivities reported here are 2.7 and 1.1 Ci/mmol for the S and R diastereomers, respectively. Specific radioactivities ranging from carrier-free to trace labeling can be achieved with a minor change to the procedure.

Alcohol Dehydrogenase↗

Experiment-guided thermodynamic simulations on reversible two-state proteins: implications for protein thermostability.

Here, we perform protein thermodynamic simulations within a set of boundary conditions, effectively blanketing the experimental data. The thermodynamic parameters, melting temperature (TG), enthalpy change at the melting temperature (DeltaHG) and heat capacity change (DeltaCp) were systematically varied over the experimentally observed ranges for small single domain reversible two-state proteins. Parameter sets that satisfy the Gibbs-Helmholtz equation and yield a temperature of maximal stability (TS) around room temperature were selected. The results were divided into three categories by arbitrarily chosen TG ranges. The TG ranges in these categories correspond to typical values of the melting temperatures observed for the majority of the proteins from mesophilic, thermophilic and hyperthermophilic organisms. As expected, DeltaCp values tend to be high in mesophiles and low in hyperthermophiles. An increase in TG is accompanied by an up-shift and broadening of the protein stability curves, however, with a large scatter. Furthermore, the simulations reveal that the average DeltaHG increases with TG up to approximately 360 K and becomes constant thereafter. DeltaCp decreases with TG with different rates before and after approximately 360 K. This provides further justification for the separate grouping of proteins into thermophiles and hyperthermophiles to assess their thermodynamic differences. This analysis of the Gibbs-Helmholtz equation has allowed us to study the interdependence of the thermodynamic parameters TG, DeltaHG and DeltaCp and their derivatives in a more rigorous way than possible by the limited experimental protein thermodynamics data available in the literature. The results provide new insights into protein thermostability and suggest potential strategies for its manipulation.

Computer Simulation↗

Biotransformation of (R)-(+)- and (S)-(-)-citronellol by Aspergillus sp. and Penicillium sp., and the use of solid-phase microextraction for screening.

The biotransformation of (R)-(+)- and (S)-(-)-citronellol by fungi was studied. For screening experiments, solid-phase microextraction (SPME) was used as analytical sampling technique. It was found that sporulated surface cultures of Aspergillus niger were able to convert the substrate into cis- and trans-rose oxides and nerol oxide. The relative contents in the headspace SPME extract of the three bioconversion products cis- and trans-rose oxide and nerol oxide were up to 54, 21 and 12%, respectively. Rose oxide is found in minor amounts in some essential oils, such as Bulgarian rose oil and geranium oil and contributes to its unique odor. It is one of the most important fragrance materials in perfumery in creating rosy notes. Other bioconversion products were 6-methyl-5-hepten-2-one, 6-methyl-5-hepten-2-ol, limonene, terpinolene, linalool and alpha-terpineol. These bioconversion reactions were confirmed by sporulated surface cultures on larger scale and sampling by dynamic headspace sweep and steam distillation solvent extraction. The same conversions were noticed with A. tubingensis and Penicillium roqueforti. This bioconversion was enantioselective since more of the chiral cis- than trans-rose oxide was obtained (cisitrans ratio up to 95/5). Submerged liquid cultures of P. roqueforti yielded two unidentified metabolites after conversion of citronellol (yield up to 5%). The stability and acid-catalyzed conversion of citronellol was also investigated. No chemical oxidation or auto-oxidation products were detected in acidified liquid control broths up to pH 3.5. However, when control tests were run with solid media, acid-catalyzed conversion of the substrate to small amounts of cis- and trans-rose oxides, nerol oxide, linalool and alpha-terpineol was observed at pH 3.5 and when heat treatment (steam distillation solvent extraction) was applied.

Acyclic Monoterpenes↗

Modification of low-density lipoprotein by different radioiodination methods.

Scintigraphic imaging of radiolabeled low-density lipoproteins (LDL) is an interesting tool for the understanding of its role in pathomechanism of atherosclerosis. Metabolism of native LDL shows quite different pattern and kinetics as compared to that of modified LDL which is not mediated by classical LDL-receptor and accumulates in atherosclerotic lesions to form lipid-laden foam cells. Therefore we were interested whether radiolabelling of LDL induces structural modifications. We performed the iodine labeling of LDL for scintigraphic imaging of atherosclerosis by three different methods: chloramine-T (A), iodine monochloride (B) and iodogen (C). The highest radiolabelling yield of (125)I was obtained by the iodogen method (75.44+/-13.52%) and the lowest (49.01+/-12.74%) by iodine monochloride. Chloramine T showed a labeling yield of 62.82+/-6.17%. The stability of the tracer was very high with all the methods, persisting up to 6 h (98.83+/-1.2% - 91.38+/-4.7%, 15 min vs 6 h after labeling). For the first time we not only investigated the influence of radiolabelling on relative electrophoretic mobility (REM), but also various oxidation parameters such as baseline dienes (BD), thiobarbituric acid reactive substances (TBARS), endogenous peroxides (POX) and oxidation resistance in the copper-mediated oxidation system (expressed as lag-time) were measured. Furthermore, oxidation- derived fragmentation of the lipoproteins was examined with SDS-PAGE electrophoresis. Data are expressed as % change compared to native LDL before radiolabeling. BD were reduced by 32% using the method (A), but increased by 33% and 47% with the monochloride (B) and iodogen method (C), respectively. The effect on lag-time was comparable for all the three methods, ranging from 25 to 36% reduction in lag-time. TBARS were strongly increased 5-7 fold by all the methods. REM was changed by all three methods. While by methods A and C we have found a moderate increase in REM by 1.75 and 2.0 fold, respectively, and no fragmentation of Apo B was observed, in contrast by method B a dramatic 4.5 fold increase in REM was found. SDS-PAGE-electrophoresis showed strong fragmentation of the apoB only for method B. We conclude, that iodine labeling of LDL induces significant modification of the molecule. Once modified, LDL no longer reflects the native molecule, exhibiting altered functional properties. Using radiolabeled LDL this fact should be considered.

Drug Evaluation, Preclinical↗

Real time NMR monitoring of local unfolding of HIV-1 protease tethered dimer driven by autolysis.

Structural studies in proteases have been hampered because of their inherent autolytic function. However, since autolysis is known to be mediated via protein unfolding, careful monitoring of the autolytic reaction has the potential to throw light on the folding-unfolding equilibria. In this paper we describe real time nuclear magnetic resonance investigations on the tethered dimer construct of the human immunodeficiency virus-1 protease, which have yielded insights into the relative stabilities of several residues in the protein. The residues lying along the active site (bottom, side and top of the active site) and those in helix have lower unfolding free energy values than the other parts of the protein. The residue level stability differences suggest that the protein is well suited to adjust itself in almost all the regions of its structure, as and when perturbations occur, either due to ligand binding or due to mutations.

Dimerization↗

Drosophila segmentation: supercomputer simulation of prepattern hierarchy.

Spontaneous prepattern formation in a two level hierarchy of reaction-diffusion systems is simulated in three space co-ordinates and time, mimicking gap gene and primary pair-rule gene expression. The model rests on the idea of Turing systems of the second kind, in which one prepattern generates position dependent rate constants for a subsequent reaction-diffusion system. Maternal genes are assumed responsible for setting up gradients from the anterior and posterior ends, one of which is needed to stabilize a double period prepattern suggested to underly the read out of the gap genes. The resulting double period pattern in turn stabilizes the next prepattern in the hierarchy, which has a short wavelength with many characteristics of the stripes seen in actual primary pair-rule gene expression. Without such hierarchical stabilization, reaction-diffusion mechanisms yield highly patchy short wave length patterns, and thus unreliable stripes. The model yields seven stable stripes located in the middle of the embryo, with the potential for additional expression near the poles, as observed experimentally. The model does not rely on specific chemical reaction kinetics, rather the effect is general to many such kinetic schemes. This makes it robust to parameter changes, and it has good potential for adapting to size and shape changes as well. The study thus suggests that the crucial organizing principle in early Drosophila embryogenesis is based on global field mechanisms, not on particular local interactions.

Animals↗

Enzyme catalysis in ionic liquids.

Ionic liquids offer new possibilities for the application of solvent engineering to biocatalytic reactions. Although in many cases ionic liquids have simply been used to replace organic solvents, they have often led to improved process performance. Unlike conventional organic solvents, ionic liquids possess no vapor pressure, are able to dissolve many compounds, and can be used to form two-phase systems with many solvents. To date, reactions involving lipases have benefited most from the use of ionic liquids, but the use of ionic liquids with other enzymes and in whole-cell processes has also been described. In some cases, remarkable results with respect to yield, (enantio)selectivity or enzyme stability were observed.

Bacteria↗

177Lu-labeled cyclic polyaminophosphonates as potential agents for bone pain palliation.

177Lu (T 1/2 = 6.71 d, Ebeta(max) = 497 keV) has radionuclidic properties suitable for use in palliative therapy of bone pain due to metastasis. 177Lu was produced in high-specific activity (3-4TBq/g) and excellent radionuclidic purity (100%) by thermal neutron bombardment of natural Lu target. Two cyclic tetraaminomethylene phosphonate ligands, namely DOTMP and CTMP were synthesized and radiolabeled with 177Lu. The 177Lu-DOTMP complex was formed with very high yield (> 99%) and showed excellent stability (up to 40 d at room temperature). Biodistribution of 177Lu-DOTMP was carried out in Wistar rats and the complex showed significant bone uptake (4.23%/g in femur and 5.23% in tibia at 3 h p. i.), rapid clearance from blood (no activity at 3 h p. i.) and minimum uptake in soft tissues.

Animals↗

Trifunctional conjugation reagents. Reagents that contain a biotin and a radiometal chelation moiety for application to extracorporeal affinity adsorption of radiolabeled antibodies.

A method of removing radiolabeled monoclonal antibodies (mAbs) from blood using a device external to the body, termed extracorporeal affinity-adsorption (EAA), is being evaluated as a means of decreasing irradiation of noncancerous tissues in therapy protocols. The EAA device uses an avidin column to capture biotinylated-radiolabeled mAbs from circulated blood. In this investigation, three trifunctional reagents have been developed to minimize the potential deleterious effect on antigen binding brought about by the combination of radiolabeling and biotinylation of mAbs required in the EAA approach. The studies focused on radiolabeling with (111)In and (90)Y, so the chelates CHX-A' '-DTPA and DOTA, which form stable attachments to these radionuclides, were incorporated in the trifunctional reagents. The first trifunctional reagent prepared did not incorporate a group to block the biotin cleaving enzyme biotinidase, but the two subsequent reagents coupled aspartic acid to the biotin carboxylate for that purpose. All three reagents used 4,7,10-trioxa-1,13-tridecanediamine as water-soluble spacers between an aminoisophthalate core and the biotin or chelation group. The mAb conjugates were radioiodinated to evaluate cell binding as a function of substitution. Radioiodination was used so that a direct comparison with unmodified mAb could be made. Evaluation of the number of conjugates per antibody versus cell binding immunoreactivities indicated that minimizing the number of conjugates was best. Interestingly, a decrease of radioiodination yield as a function of the number of isothiocyanate containing conjugates per mAb was noted. The decreased yields were presumably due to the presence of thiourea functionality formed in the conjugation reaction. Radiolabeling with (111)In and (90)Y was facile at room temperature for conjugates containing the CHX-A' ', but elevated temperature (e.g., 45 degrees C) was required to obtain good yields with the DOTA chelate. Stability of (90)Y labeled mAb in serum, and when challenged with 10 mM EDTA, was high. However, challenging the (90)Y labeled mAb with 10 mM DTPA demonstrated high stability for the DOTA containing conjugate, but low stability for the CHX-A' ' containing conjugate. Thus, the choice between these two chelating moieties might be made on requirements for facile and gentle labeling versus very high in vivo stability. Application of the trifunctional biotinylation reagents to the blood clearance of labeled antibodies in EAA is under investigation. The new reagents may also be useful for other applications.

Affinity Labels↗

An expanded two-state model accounts for homotropic cooperativity in biosynthetic threonine deaminase from Escherichia coli.

The linkage between substrate and regulatory effector binding to separate sites on allosteric enzymes results in shifts in their sigmoidal kinetics to regulate metabolism. Control of branched chain amino acid biosynthesis in Escherichia coli occurs in part through shifts in the sigmoidal dependence of alpha-ketobutyrate production promoted by isoleucine and valine binding to biosynthetic threonine deaminase. The structural similarity of threonine, valine, and isoleucine have given rise to suggestions that there may be competition among different ligands for the same sites on this tetrameric enzyme, resulting in a complex pattern of regulation. In an effort to provide a coherent interpretation of the cooperative association of ligands to the active sites and to the effector sites of threonine deaminase, binding studies using single amino acid variants were undertaken. A previously-isolated, feedback-resistant mutant identified in Salmonella typhimurium, ilvA219, has been cloned and sequenced. The phenotype is attributable to a single amino acid substitution in the regulatory domain of the enzyme in which leucine at position 447 is substituted with phenylalanine. The mutant exhibits hyperbolic saturation curves in both ligand binding and steady-state kinetics. These results, in addition to calorimetric and spectroscopic measurements of isoleucine and valine binding, indicate that the low affinity (T) state is destabilized in the mutant and that it exists predominantly in the high affinity (R) conformation in the absence of ligands, providing an explanation for its resistance to isoleucine. Chemical and spectroscopic analyses of another mutant, in which alanine has replaced an essential lysine at position 62 that forms a Schiff base with pyridoxal phosphate, indicate that the cofactor is complexed to exogenous threonine and is therefore unable to bind additional amino acids at the active sites. Isoleucine and valine binding to this inactive, active site-saturated enzyme revealed that it too was stabilized in the R state, yielding binding constants in excellent agreement with the leucine to phenylalanine mutant. The lysine to alanine mutant was further utilized to demonstrate that both threonine and 2-aminobutyrate bind with stronger affinity to the regulatory sites than to the active sites. A direct consequence of these results is that substrates and analogs have a synergistic effect on the allosteric transition since, in effect, they act as both homotropic and heterotropic effectors.(ABSTRACT TRUNCATED AT 250 WORDS)

Allosteric Regulation↗

Transient kinetics of electron transfer from a variety of c-type cytochromes to plastocyanin.

Plastocyanin (PC) and its physiological reaction partner cytochrome (cyt) f form a complex which is electrostatically stabilized by interactions between complementary localized charges. We have measured the kinetics of intracomplex electron transfer between several reduced cytochromes and PC using laser flash photolysis. With spinach cyt f and spinach PC, we obtain first-order rate constants, kforward = 2780 s-1 and kreverse = 1050 s-1, for the reversible reaction and a complex dissociation constant of about 23 microM at an ionic strength (I) of 5 mM. The observed rate constant increases by a factor of 2 between I = 5 and 40 mM and then decreases monotonically at higher ionic strengths. This indicates that the complex is not completely dissociated until I = 150 mM and that the proteins within the electrostatically most stable complex are not optimally oriented for electron transfer. Similar results were obtained with turnip cyt f and spinach PC, although in this case intracomplex electron transfer is about 4 times as fast. Horse cyt c also forms an electrostatically stabilized complex with PC, and yields a limiting rate constant for intracomplex electron transfer (1750 s-1) and a dissociation constant (10 microM) comparable to those for spinach cyt f. The ionic strength dependence shows that the complex is more readily dissociated (complete at I = 25 mM) than is that of cyt f and that rearrangement is not required for optimal electron transfer. Addition of polylysine results in 10-fold inhibition of the rate of electron transfer. Pseudomonas cyt c-551 is an acidic cytochrome which does not form a complex with PC.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗