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At least 973 records · Page 54Linked to original sources
PubMed1985

Isoleucyl-tRNA synthetase from bakers' yeast: multistep proofreading in discrimination between isoleucine and valine with modulated accuracy, a scheme for molecular recognition by energy dissipation.

For discrimination between isoleucine and valine by isoleucyl-tRNA synthetase from yeast, a multistep sequence is established. The initial discrimination of the substrates is followed by a pretransfer and a posttransfer hydrolytic proofreading process. The overall discrimination factor D was determined from kcat and Km values observed in aminoacylation of tRNAIle-C-C-A with isoleucine and valine. From aminoacylation of the modified tRNA species tRNAIle-C-C-3'dA and tRNAIle-C-C-A (3'NH2), the initial discrimination factor I (valid for the reversible substrate binding) and the proofreading factor P1 (valid for the aminoacyl adenylate formation) could be determined. Factor I was computed from ATP consumption and D1, the overall discrimination factor for this partial reaction which can be obtained from kinetic constants, and P1 was calculated from AMP formation rates. Proofreading factor P2 (valid for aminoacyl transfer reaction) was determined from AMP formation rates observed in aminoacylation of tRNAIle-C-C-A and tRNAIle-C-C-3'dA. From the initial discrimination factor I and the AMP formation rates, discrimination factor DAMP in aminoacylation of tRNAIle-C-C-A can be calculated. These values deviate by a factor II from factor D obtained by kinetics which may be due to the fact that for acylation of tRNAIle-C-C-A an initial discrimination factor I' = III is valid. The observed overall discrimination varies up to a factor of 16 according to conditions. Under optimal conditions, 38 000 correct aminoacyl-tRNAs are produced per 1 error while the energy of 5.5 ATPs is dissipated. With the determined energetic and molecular flows for the various steps of the enzymatic reaction, a coherent picture of this new type of "far away from equilibrium enzyme" emerges.

Amino Acyl-tRNA Synthetases↗
PubMed1998

Estimation of mass transfer through a hemodialyzer: theoretical approach and clinical applications.

The estimation of the solute mass transfer through a dialyzer is generally based on the solute dialysance, but the concept of dialysance has been precisely defined only in the case of a merely diffusive transfer. In actuality the mass transfer of a solute is also influenced by the ultrafiltration responsible for a convective transfer and, if the solute is an ionic substance, by the transmembrane gradient of electrical potential due to the Gibbs-Donnan effect. The aim of this paper is to generalize the concept of dialysance when the diffusive, convective, and electric components of the transfer are simultaneously active. There are at least 3 modes to generalize the concept of dialysance for it to be identical, when the amount of ultrafiltration and the Gibbs-Donnan effect are negligible, to the usual dialysance defined in the case of a merely diffusive transfer. The dialysance can be defined so that it can be equal to the clearance for a solute absent from the dialysate again, so that it still represents the rate at which the plasma concentration of a given solute is reaching its equilibrium value, or so that it represents the merely diffusive component (independent of the ultrafiltration rate) of the mass transfer. This generalized concept of dialysance can be useful to provide a real-time estimation of the effective dialysis dose actually delivered to the patient; to automatically optimize, by a biofeedback process, the sodium balance during a hemodialysis session; and to adapt dialysate concentrations for new hemodialysis techniques with convective transfer (acetate-free biofiltration).

Acetates↗
PubMedDate not supplied

[Principals of surgical treatment of paresis due to damage to the central nervous system (author's transl)].

In pareses due to cerebral affections there is a sensomotoric disturbance of coordination and function which usually leads to typical contractions. The aim of treatment consists primarily in the creation or restitution of the greatest possible degree of dynamic equilibrium in unequally affected musculature. In addition to detonization of the spastically hypertonic muscles this also includes the elimination of deformities which disturb function. Only by detailed analysis of neuro-orthopedic findings can adequate conditions be created for the comprehensive therapeutic measures to be taken. For optimal surgical results not only accurate and detailed indication are required, but also specifically oriented preoperative and postoperative physiotherapy and ergotherapy.

Cerebral Palsy↗
PubMed2006

Forward flux sampling-type schemes for simulating rare events: efficiency analysis.

We analyze the efficiency of several simulation methods which we have recently proposed for calculating rate constants for rare events in stochastic dynamical systems in or out of equilibrium. We derive analytical expressions for the computational cost of using these methods and for the statistical error in the final estimate of the rate constant for a given computational cost. These expressions can be used to determine which method to use for a given problem, to optimize the choice of parameters, and to evaluate the significance of the results obtained. We apply the expressions to the two-dimensional nonequilibrium rare event problem proposed by Maier and Stein [Phys. Rev. E 48, 931 (1993)]. For this problem, our analysis gives accurate quantitative predictions for the computational efficiency of the three methods.

Journal Article↗
PubMed2006

Statistical mechanics of histories: a cluster Monte Carlo algorithm.

We present an efficient computational approach to sample the histories of nonlinear stochastic processes. This framework builds upon recent work on casting a d-dimensional stochastic dynamical system into a (d+1)-dimensional equilibrium system using the path-integral approach. We introduce a cluster algorithm that efficiently samples histories and discuss how to include measurements that are available into the estimate of the histories. This allows our approach to be applicable to the simulation of rare events and to optimal state and parameter estimation. We demonstrate the utility of this approach for Phi4 Langevin dynamics in two spatial dimensions where our algorithm improves sampling efficiency up to an order of magnitude.

Journal Article↗
PubMed1991

Kinetic characterization of the normal and procaine-perturbed reaction cycles of the sarcoplasmic reticulum calcium pump.

We investigated the effect of the local anesthetic procaine on the activity of the calcium pump protein of sarcoplasmic reticulum (SR) vesicles. Procaine slowed down the rate of calcium uptake by SR vesicles without enhancing the vesicles' passive permeability. This slowing of the unidirectional pumping rate was reflected by the inhibition of the maximal rate of the transport-coupled Ca(2+)-ATPase activity. The inhibition was dependent on Mg2+ concentration; at optimal (i.e. low) concentrations of magnesium, half-maximal inhibition occurred with procaine concentrations close to 15-20 mM. Inhibition of ATPase was not mediated by a change in the properties of the bulk lipid phase. Procaine moderately reduced the true affinity of ATPase for ATP, whereas equilibrium binding of calcium to ATPase in the absence of ATP was virtually not modified by procaine. In fast-kinetics studies, we explored the various intermediate steps in the ATPase catalytic cycle, in order to determine which of them were targets for inhibition by procaine. We found that procaine slowed down ATPase dephosphorylation, an effect which is at least partly responsible for the observed inhibition of overall ATPase activity. In contrast, procaine accelerated the calcium-induced transconformation of unphosphorylated ATPase in the absence of ATP, and altered neither the rate of the Ca(2+)-dependent phosphorylation of ATPase, nor the rate of the dissociation of Ca2+ from phosphorylated ATPase towards the SR lumen, a critical step, the rate of which was measured by a novel fast-filtration method. These results are discussed with respect to the possible site(s) of binding of this amphiphile on the ATPase, and in relation to the contribution of individual steps in the catalytic cycle to the rate limitation of unperturbed SR ATPase activity.

Animals↗
PubMed1974

Binding of [14C]erythromycin to Escherichia coli ribosomes.

Erythromycin binding to Escherichia coli ribosomes required K(+) and Mg(2+). Under optimal conditions, the dissociation constant for erythromycin binding to E. coli ribosomes was found to be 1.0 x 10(-8) M and 1.4 x 10(-8) M at 24 C and 5 C, respectively. One molecule of [(14)C]erythromycin was bound to each 70S ribosome at equilibrium. Binding of erythromycin to ribosomes was rapid and reversible. The specific rate constants for the forward and reverse reactions were 1.7 x 10(7) liters per mol per min and 0.15 per min, respectively.

Carbon Radioisotopes↗
PubMed2004

Properties of a novel thermostable glucoamylase from the hyperthermophilic archaeon Sulfolobus solfataricus in relation to starch processing.

A gene (ssg) encoding a putative glucoamylase in a hyperthermophilic archaeon, Sulfolobus solfataricus, was cloned and expressed in Escherichia coli, and the properties of the recombinant protein were examined in relation to the glucose production process. The recombinant glucoamylase was extremely thermostable, with an optimal temperature at 90 degrees C. The enzyme was most active in the pH range from 5.5 to 6.0. The enzyme liberated beta-d-glucose from the substrate maltotriose, and the substrate preference for maltotriose distinguished this enzyme from fungal glucoamylases. Gel permeation chromatography and sedimentation equilibrium analytical ultracentrifugation analysis revealed that the enzyme exists as a tetramer. The reverse reaction of the glucoamylase from S. solfataricus produced significantly less isomaltose than did that of industrial fungal glucoamylase. The glucoamylase from S. solfataricus has excellent potential for improving industrial starch processing by eliminating the need to adjust both pH and temperature.

Amino Acid Sequence↗
PubMed1991

Evaluation of parameters for adequate dialysis therapy: (1). Monitoring of parameters by urea kinetic modeling.

In an attempt to evaluate the adequacy of regular dialysis therapy, calculations of Kt/V-urea and protein catabolic rate (pcr) from the data of routine laboratory examinations by means of urea kinetic modeling were performed in 59 regular dialysis patients (28 males and 31 females; mean age, 59 +/- 2 years old; mean dialysis duration, 83 +/- 10 months). The mean values of Kt/V-urea and pcr were 1.10 +/- 0.04 and 0.98 +/- 0.03 g/kgBW.day, respectively. The number of patients who were within the optimal range (0.9-1.4 for Kt/V urea and 0.9-1.5 for pcr) was 37 (62.7%) for Kt/V-urea and 38 (64.4%) for pcr. Furthermore, we inferred that, based on an appropriate dietary protein intake, removal of urea by intermittent dialysis should be adjusted to maintain the patient in equilibrium for a defined pre-dialysis plasma urea concentration. From the data obtained, we concluded that: (1) it is possible to apply urea kinetic modeling on the basis of routine laboratory examinations, (2) it is important to maintain the pre-dialysis plasma urea concentration at more than a certain level, and (3) it is also important to control the post-dialysis plasma urea concentration at a low level.

Creatinine↗
PubMed2000

Feeding, growth, and fecundity of Abarenicola pacifica in relation to sediment organic concentration.

For marine deposit-feeding invertebrates, the distribution of species with different life history strategies has long been known to be correlated with sediment organic concentration. Large populations of opportunistic species are found in sediments with enriched organic concentration, while equilibrium species populate low organic concentration sediments. Differences in both behavioral (e.g. feeding rate) and physiological (e.g. growth rate, reproductive output) adaptations determine the ability of species to establish populations in different environments. By systematically documenting differences in the way these factors vary as sediment organic concentration varies for both opportunistic and equilibrium species, we can better understand the mechanisms underlying this correlation between sediment organic concentration and species distributions. Here, we present the results of experiments examining the interactions among food concentration, feeding rate, growth rate, and reproductive output (measured as egg number and size) for the equilibrium species Abarenicola pacifica. A. pacifica is a large, long-lived, iteroparous, sub-surface deposit-feeding polychaete. Individual worms were reared throughout most of one generation in sediments differing only in the concentration of organic matter. Juveniles (<20 mg AFDW) had higher feeding rates and growth rates in sediments of higher organic concentration throughout the range tested. These results are consistent with the predictions from optimal foraging theory. As worms grew, however, these patterns changed. Once worms reached a mean body size of approximately 50 mg AFDW, feeding rate was greater on sediments of lower organic concentration (although it took worms in the sediments with lower organic concentration longer to reach this size). Differences in growth rates among treatments decreased as worms grew. For worms >100 mg AFDW, growth rates were uniformly low ( approximately 1%/day) on all sediments, but the early advantage obtained by worms in the high organic treatments resulted in much greater body sizes after 200 days. Worms had higher tissue triacylglyceride concentrations and produced more eggs (independent of worm size) as sediment organic concentration increased. We conclude that A. pacifica alters its feeding rate in response to variations in food resources in such a way as to maximize its energy intake and thereby maximize fitness. Future studies should investigate whether opportunistic species (as well as other equilibrium species) also have this ability.

Journal Article↗
PubMed2001

Structure and surface energy of the surfactant layer on the alveolar surface.

The surface energy of the alveolar surfactant layer is determined in the scope of a modification of the structural model of Larsson et al. [(1999) J Disp Sci Technol 20:1-12], according to which this layer is built up of a lipid monolayer adsorbed at the hypophase/air interface and supported by a network of lipid bilayers immersed into the hypophase, i.e., the alveolar liquid. Formulae are derived for the dependence of the specific surface energy of the surfactant layer on the distance between the bilayers constituting the layer. It is shown that at equilibrium this energy can have values comparable with or less than 1 mJ/m2 needed for normal functioning of the alveolus during the respiration cycle. The specific surface energy of the surfactant layer with monolayer-bilayer structure can have such low values only if the layer is of optimal thickness and if the specific line energy of the monolayer-bilayer contact lines is negative and that of the bilayer-bilayer contact lines is positive. It is found that in dynamic regime the change in the specific surface energy of the alveolar surfactant layer with bilayer-monolayer structure is in qualitative agreement with that determined experimentally during lung inflation and deflation.

Kinetics↗
PubMed2006

Reducing intrinsic biochemical noise in cells and its thermodynamic limit.

In living cells, the specificity of biomolecular recognition can be amplified and the noise from non-specific interactions can be reduced at the expense of cellular free energy. This is the seminal idea in the Hopfield-Ninio theory of kinetic proofreading: The specificity is increased via cyclic network kinetics without altering molecular structures and equilibrium affinites. We show a thermodynamic limit of the specificity amplification with a given amount of available free energy. For a normal cell under physiological condition with sustained phosphorylation potential, this gives a factor of 10(10) as the upper bound in specificity amplification. We also study an optimal kinetic network design that is capable of approaching the thermodynamic limit.

Cells↗
PubMed2000

Determination of butyltin species in water and sediment by solid-phase microextraction-gas chromatography-flame ionization detection.

A procedure for determination of tetraethyltin (TeET) and tetrabutyltin (TeBT) in water by solid-phase microextraction (SPME) using the headspace approach has been developed. The method has been adapted for the simultaneous determination of mono-, di- and tributyltin species (MBT, DBT and TBT) after derivatization with sodium tetraethylborate in water and sediment samples. The analytical procedures were optimized with respect to stirring conditions, extraction time and extraction temperature. The pH and the amount of derivatizing reagent were also considered in derivatization reaction procedures. The analysis was carried out using gas chromatography equipped with flame ionization detection. The detection limits obtained for TeET and TeBT, in equilibrium conditions (room temperature for TeET and 40 degrees C for TeBT) were 28 and 20 ng/l (as Sn), respectively. The detection limit for butyltin species in water, which was limited by signals which are non-specific for the tin compounds and the sensitivity of the FID system, was found ca. 1 microg/l (as Sn). The SPME method was validated for analysis of sediments by analyzing the certified reference material PACS-2 finding a good agreement with the certified values.

Calibration↗
PubMed2001

A kinetic analysis using fractals of cellular analyte-receptor binding and dissociation.

A fractal analysis is presented for cellular analyte-receptor binding and dissociation kinetics using a biosensor. Data taken from the literature may be modelled, in the case of binding, using a single-fractal analysis or a dual-fractal analysis. The dual-fractal analysis represents a change in the binding mechanism as the reaction progresses on the surface. The predictive relationship developed for the equilibrium constant, K (affinity which is equal to k(d)/k(1or2)), as a function of the analyte concentration is of particular value since it provides a means by which the affinity may be manipulated. This should be of assistance in cell-surface reactions, drug-candidate optimization and for the design of immunodiagnostic devices. Relationships are also presented for the binding and dissociation rate coefficients as a function of their corresponding fractal dimension, D(f) or the degree of heterogeneity that exists on the surface, and the analyte concentration in solution. When analyte-receptor binding or dissociation is involved, an increase in the heterogeneity on the surface (increase in D(f) or D(fd) as the case may be) leads to an increase in the binding and the dissociation rate coefficients. It is suggested that an increase in the degree of heterogeneity on the surface leads to an increase in the turbulence on the surface owing to the irregularities on the surface. This turbulence promotes mixing, minimizes diffusional limitations and leads subsequently to an increase in the binding and the dissociation rate coefficients. The binding and dissociation rate coefficients are rather sensitive to the degree of heterogeneity, D(f) and D(fd), respectively, that exists on the biosensor surface. The heterogeneity on the surface in general affects the binding and dissociation rate coefficients differently. In general, the analyte concentration in solution has a mild affect on the fractal dimension for binding or the fractal dimension for dissociation. This is indicated by the low values of the exponent in the predictive relationships developed.

Fractals↗
PubMed2006

Counterpoise corrected geometries of hydrated complexes.

We have calculated the equilibrium geometries of the hydrated complexes, H2O.CO2, H2O.CS2,H2O.OCS, H2O.SO2, and H2O.SO3, in the electronic ground state. We have used the coupled cluster with singles, doubles, and perturbative triples ab initio method with a correlation consistent augmented triple-zeta basis set. We find that a counterpoise corrected optimization scheme is important for an accurate description of the geometries. These high level ab initio calculated geometries are of comparable quality to those obtained experimentally.

Journal Article↗
PubMed1996

Bradyrhizobium japonicum porphobilinogen synthase uses two Mg(II) and monovalent cations.

Bradyrhizobium japonicum porphobilinogen synthase (B. japonicum PBGS) has been purified and characterized from an overexpression system in an Escherichia coli host (Chauhan, S., and O'Brian, M. R. (1995) J. Biol. Chem. 270, 19823-19827). B. japonicum PBGS defines a new class of PBGS protein, type IV (classified by metal ion content), which utilizes a catalytic MgA present at a stoichiometry of 4/octamer, an allosteric MgC present at a stoichiometry of 8/octamer, and a monovalent metal ion, K+. However, the divalent MgB or ZnB present in some other PBGS is not present in B. japonicum PBGS. Under optimal conditions, the Kd for MgA is <0.2 microM, and the Kd for MgC is about 40 microM. The response of B. japonicum PBGS activity to monovalent and divalent cations is mutually dependent and varies dramatically with pH. B. japonicum PBGS is also found to undergo a dynamic equilibrium between active multimeric species and inactive monomers under assay conditions, a kinetic characteristic not reported for other PBGSs. B. japonicum PBGS is the first PBGS that has been rigorously demonstrated to lack a catalytic ZnA. However, consistent with prior predictions, B. japonicum PBGS can bind Zn(II) (presumably as ZnA) at a stoichiometry of 4/octamer with a Kd of 200 microM; but this high concentration is outside a physiologically significant range.

Amino Acid Sequence↗
PubMed1964

FRUCTOSE-6-PHOSPHATE REDUCTASE FROM SALMONELLA GALLINARUM.

Zancan, Glaci T. (Universidade do Paraná, Curitiba, Paraná, Brazil), and Metry Bacila. Fructose-6-phosphate reductase from Salmonella gallinarum. J. Bacteriol. 87:614-618. 1964.-A fructose-6-phosphate reductase present in cell-free extracts of Salmonella gallinarum was purified approximately 42 times. The optimal pH for this enzyme is 8.0. The enzyme is specific for fructose-6-phosphate and reduced nicotinamide adenine dinucleotide (NADH). The dissociation constants are 1.78 x 10(-4)m for fructose-6-phosphate and 8.3 x 10(-5)m for NADH. The Q(10), reaction order, and equilibrium constant were determined. The enzyme is sensitive to p-chloromercuribenzoic acid, but not to o-iodosobenzoic acid nor to N-ethylmaleimide.

Benzoates↗
PubMed1991

Characterization of plasminogen binding to human capillary and arterial endothelial cells.

Phenotypic diversity of endothelial cells that line the various vascular spaces has been well established. However, it is not known if biochemical differences also exist, particularly in the numbers of receptors for plasma proteins. Equilibrium binding techniques were used to assess potential differences in the binding of 125I-labelled plasminogen to cultured human umbilical arterial endothelial cells and capillary endothelium, as compared with umbilical venous cells. The kinetic behaviour of plasminogen binding to all three types of cells was similar, with optimal binding occurring between 20 and 30 min of incubation. Binding of plasminogen to arterial, capillary, and venous cells was concentration dependent and reversible upon addition to excess unlabelled plasminogen. Scatchard analyses showed that artery, capillary, and venous endothelial cells all possess low affinity sites for plasminogen with Kd values of 0.30 +/- 0.07, 0.40 +/- 0.06, and 0.40 +/- 0.08 microM, respectively. Vein cells also possess an additional higher affinity binding site with a Kd of 0.07 +/- 0.01 microM, exhibiting a 6-fold greater affinity for plasminogen than the lower affinity sites on capillary and arterial endothelial cells. Assuming a stoichiometry of 1:1 for binding, the data indicate that arterial and capillary endothelial cells contain approximately 4.2 (+/- 0.9) x 10(6) and 4.1 (+/- 0.6) x 10(6) plasminogen receptors per cell. Venous cells contain both low and high density binding sites with 6.2 (+/- 0.8) x 10(6) and 12.4 (+/- 2.4) x 10(6) sites per endothelial cell. The presence of a higher affinity site on vein cells, but not on artery or capillary cells, may signal functional differences relating to fibrinolytic activity on the surface of these cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗