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PubMedDate not supplied

Representation of phase equilibrium behavior of antibiotics.

The phase equilibrium behavior of biomolecules is important both in understanding the partition mechanisms and in the design and optimization of downstream recovery processes. Chen et al. (1989) proposed a molecular thermodynamic framework that successfully represents the liquid-solid equilibrium behavior of amino acids and small peptides as functions of temperature, ionic strength, solvent compositions, and pH. Based on this theoretical framework, this paper presents recent results in representing the liquid-solid equilibrium behavior (solubilities) and the liquid-liquid equilibrium behavior (phase partitioning) of beta-lactam antibiotics, which are amino acid derivatives and important chemotherapeutic agents.

Ammonium Chloride↗
PubMed1982

Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method.

Chemical shifts of base and sugar protons of the modified ribodinucleoside monophosphate N6-dimethyladenylyl(3'-5')uridine (m2(6)A-U) were measured at 100, 360 and 400 MHz in aqueous solution. Seven different samples were used with concentrations ranging from 0.28 mM to 32.7 mM. The temperature was varied from -5 degrees C to 105 degrees C. An internal temperature calibration was used. The effects of intermolecular self-association and of intramolecular stacking on the chemical shifts were quantitatively separated by means of a new approach: differential concentration/temperature profiles (DCTP). Several computational models were tested and the analysis allowed deeper insight into the behaviour of m2(6)A-U at the molecular level. The simple two-state approach for both self-association and stacking already afforded a significant improvement over models in which the association is entirely neglected. A computer least-squares analysis of the chemical shift behaviour of each individual proton yielded thermodynamic parameters for self-association and stacking. However, the two-state model did not suffice to reproduce accurately all of the observations. A satisfactory fit required two additional assumptions: (a) the aromatic protons experience different association shifts in stacked and in unstacked molecules: (b) a temperature-dependent conformational equilibrium exists between sets of unstacked microstates. The stacked state is taken to represent a single conformational species. The implementation of this extended model in the least-squares optimization allowed the reproduction of over one thousand chemical shift observations within experimental error. Thermodynamic equilibrium parameters deduced for intramolecular stacking are: delta H degrees x = -28.8 kJ mol-1, delta S degrees x = -93 J mol-1 K-1. These numbers agree well with those obtained earlier by us from circular dichroism spectra. The equilibrium enthalpy and entropy values deduced for the association process are: delta H degrees A = -35 kJ mol-1 and delta S degrees A = -95 J mol-1 K-1.

Adenosine Monophosphate↗
PubMed1981

L-Aspartate binding sites in rat cerebellum: a comparison of the binding of L-[3H]aspartate and L-[3H]glutamate to synaptic membranes.

The binding of L-[3H]aspartate to sonicated, extensively washed and preincubated cerebellar synaptic membranes was investigated. Binding was optimal under physiological conditions of pH and temperature, and attained equilibrium within 10 min. Binding was saturable, and Eadie-Hofstee analysis revealed interaction with a single population of binding sites (Kd = 874 nM and Bmax = 44 pmol/mg protein), which displayed no cooperativity (Hill coefficient approx. = 1). Specific [3H]aspartate was readily and reversibly displayed by unlabelled L-aspartate (the D-isomer being less than half as active) with a half-life of dissociation of 32 sec. Quisqualate, 4-fluoroglutamate and 2-amino-4-phosphonobutyrate, which are good displacers of [3H]glutamate binding, were only weakly active against the aspartate system. The excitatory amino acid antagonists, DL-alpha-aminoadipate, DL-alpha-aminosuberate and HA-966 were effective displacers, but the proposed aspartate receptor-preferring agonist, N-methyl-D-aspartate was inactive. Kainic acid exhibited negligible affinity for the aspartate binding site, in common with that for glutamate. While freezing or cold storage of membranes resulted in diminished [3H]-aspartate binding, lyophilization was not only able to confer substantial stability, but induced a marked increase in affinity of the binding site. Differential effects of various cations on [3H]aspartate binding were observed--monovalent cations reduced, while divalent cations enhanced L-[3H]aspartate binding.

Animals↗
PubMed1995

Optical detection of macromolecular heparin via selective coextraction into thin polymeric films.

Thin plasticized polymer films, poly(vinyl chloride) doped with a specific ion pairing quaternary ammonium compound, tridodecylmethylammonium chloride, and a lipophilic pH indicator, 3-hydroxy-4-(4-nitrophenylazo)phenyl octadeconate, are shown to exhibit significant and analytically useful optical response toward macromolecular heparin. The response mechanism is based on favorable extraction of heparin into the bulk organic film, owing to the specific ion-pairing complexation reaction between the quaternary ammonium species and the polyanion. A simultaneous coextraction of hydrogen ions results in protonation of the pH chromophore and hence a change in the optical absorbance of the polymeric film. When used in a limited volume/fixed exposure (10 min) detection mode, film absorbances change as a function of the initial heparin concentration in the range of 0.2-3.0 units/mL (1.2-18 micrograms/mL). The practical measurement response time is controlled by heparin diffusion through the stagnant diffusion layer adjacent to the surface of the film as well as within the bulk of the polymer film and is shown to increase with the molecular weight of the heparin species tested. No optical response to heparin is observed when a strong heparin complexing agent (e.g., protamine) is present in the test solution, suggesting that the polymer film can be used to conveniently monitor heparin-protamine (or other antagonist) titrations. The theory relating to the operation of the sensing film in either the equilibrium or the kinetic mode and the selectivity of the optimized film to heparin relative to small anions are presented.

Anions↗
PubMed1976

Axoplasmic free magnesium levels and magnesium extrusion from squid giant axons.

The free magnesium concentration in the axoplasm of the giant axon of the squid, Loligo pealei, was estimated by exploting the known sensitivity of the sodium pump to intracellular Mg2+ levels. The Mg-citrate buffer which, when injected into the axon, resulted in no change in sodium efflux was in equilibrium with a Mg2+ level of about 3--4 mM. Optimal [Mg2+] for the sodium pump is somewhat higher. Total magnesium content of axoplasm was 6.7 mmol/kg, and that of hemolymph was 44 mM. The rate coefficient for 28Mg efflux was about 2 X 10(-3) min-u for a 500-mum axon at 22-25degreesC, with a very high temperature coefficient (Q10=4-5). This efflux is inhibited 95% by injection of apyrase and 75% by removal of external sodium, and seems unaffected by membrane potential or potassium ions. Increased intracellular ADP levels do not affect Mg efflux nor its requirement for Na+/o, but extracellularl magnesium ions do. Activation of 28Mg efflux by Na+/o follows hyperbolic kinetics, with Mg2+/o reducing the affinity of the system for Na+/o. Lanthanum and D600 reversibly inhibit Mg efflux. In the absence of both Na+ and Mg2+, but not in their presence, removal of Ca2+ from the seawater vastly increased 28Mg efflux; this efflux was also strongly inhibited by lanthanum. A small (10(-14) mol cm-2) extra Mg efflux accompanies the conduction of an action potential.

Action Potentials↗
PubMed1987

[The stability of hydrochlorothiazide and cyclopenthiazide in various dosage forms. 4. Stability of hydrochlorothiazide injection solutions II].

The hydrolytic decomposition of hydrochlorothiazide (1) in an optimized dispensing with polyethyleneglycol 400/ethanol as solvent led to an equilibrium in the isothermic short-term test as well as in the long-term stability test. Corresponding equilibrium concentrations were obtained for forward and back reaction. When comparing the precalculated equilibrium values with the long-term results the evaluation after Van't Hoff proved superior compared with an evaluation after the Arrhenius plot which is only applicable when the equilibrium concentrations are taken into consideration. By adding the decomposition product aminodisulfamide (2) the hydrolysis of 1 can be inhibited completely.

Cyclopenthiazide↗
PubMed1981

Protease mitogenic response of chick embryo fibroblasts and receptor binding/processing of human alpha-thrombin.

Quiescent cultures of chick embryo fibroblasts incubated with human alpha-thrombin (14-219 pM) incorporated [methyl-3H]thymidine proportional to concentration. Inactivated forms of this protease (e.g. active-site-conjugated alpha-thrombin or its hirudin complex) had no mitogenic activity and did not compete with 124I-alpha-thrombin for binding to specific plasma membrane receptors. The noncoagulant but esterolytic active forms, gamma- and nitro-alpha-thrombins, were weakly mitogenic and correspondingly competed weakly for binding. Trypsin competed equally as well as native thrombin for binding, whereas chymotrypsin, elastase, and human urokinase competed with 80-fold less affinity. Plasma, arginine-specific proteases associated with nerve or epidermal growth factors, insulin, and insulin-like growth factors did not compete for binding. These data demonstrate that (a) functional catalytic residues of the thrombin active site are necessary for mitogenic activity and for specific binding; (b) regions adjacent to the active site, i.e. the high affinity protein recognition site, appear to enhance binding; and (c) the receptor can discriminate between other proteases and binds those which are also mitogens for the avian cells. The characteristics of 125I-alpha-thrombin binding were determined, and it was found to be (i) proportional to cell number; (ii) optimal at pH 6.8; (iii) 70-90% specific; (iv) at equilibrium after 60 min of incubation at 22-24 degrees C or 180 min at 0-4 degrees C (the rate constants for association, i.e. ka, at 22 and 4 degrees C were 18 and 1.1 x 10(7) M-1 min-1, respectively); and (v) essentially nondissociable. Nondissociable thrombin that bound during incubation at 0-4 degrees C was distributed equally between trypsin-sensitive and insensitive compartments. Thrombin associated with the former was released into the media when the cells were incubated at 0-4 degrees C with hirudin or hydroxylamine, or transferred to the insensitive compartment when incubated at 22 degrees C. Finally, confluent cultures of fibroblasts bind 2-3 x 10(4) 125I-alpha-thrombin molecules/cell with an apparent binding constant, i.e. Kd, of 0.7 nM (a true Kd could not be determined because of the irreversible nature of thrombin binding). The binding capacity per cell and the apparent Kd value increased proportionally to an increase in culture density.

Animals↗
PubMed1993

Choice of optimality criteria for the design of crossbreeding experiments.

Crossbreeding experiments carried out over several generations and analyzed using genetic models including additive, dominance, and epistatic effects deserve careful planning. Designs should be optimized with respect to the specific aim of the experiment. Using an experiment with guinea pigs as an example, designs were optimized for three different criteria: D-optimality, where the determinant of the variance-covariance matrix of all parameters in the genetic model is minimized, DS-optimality, where a specific subset of parameters is of special interest and the respective determinant is minimized, and DA-optimality, where a linear function or a set of linear functions of the parameters in the model is of interest. The linear function used in this particular case relates to the comparison of a composite line of two breeds and a rotational crossbreeding system at equilibrium. The designs produced by a sequential design algorithm depend very much on the optimality criterion. Designs that are optimal for the comparison of composites and rotations are very inefficient for the estimation of the whole set of parameters in the model or the specific subset of special interest in this case. Assuming that the underlying genetic model is correct, composites and rotations at equilibrium may be compared extremely efficiently using only crosses arising in the first three generations of crossbreeding.

Algorithms↗
PubMed1986

Theoretical models for predicting the effect of bridging group recognition and conjugate substitution on hapten enzyme immunoassay dose-response curves.

Models for predicting the effect of immunological recognition of the bridge group on the dose-response curves obtained with heterogeneous hapten enzyme immunoassays are presented. Appropriate theoretical treatment shows that the greater affinity of antibodies toward the enzyme-labeled species than for the unlabeled hapten analyte results in assays with limited detection capabilities. This problem is compounded when enzyme conjugates possessing multiple haptens are used. In equilibrium type competitive arrangements, the concentrations of binder and labeled hapten may be optimized to some extent to improve assay performance. However, the results presented show that only when assays are performed in a sequential binding mode using carefully controlled timing of reagent incubations can the detection capabilities of the assays be fully maximized for analyte measurements. Unfortunately, it is also shown that such sequential binding approaches render the assays essentially nonselective. The effect of decreasing the affinity of the binder to the enzyme-labeled hapten relative to the unlabeled analyte by using heterologous conjugates in equilibrium arrangements is shown to improve detection capabilities but also at the expense of reduced selectivity. Suggestions for reagent concentrations and conjugate substitution (degree of conjugation), which provide optimized dose-response curves at a given ED50 value, are also presented as are proposals for using different binders which do not exhibit bridging group recognition.

Antibody Affinity↗
PubMed1992

Base-pair probability profiles of RNA secondary structures.

Dynamic programming algorithms are able to predict optimal and suboptimal secondary structures of RNA. These suboptimal or alternative secondary structures are important for the biological function of RNA. The distribution of secondary structures present in solution is governed by the thermodynamic equilibrium between the different structures. An algorithm is presented which approximates the total partition function by a Boltzmann-weighted summation of optimal and suboptimal secondary structures at several temperatures. A clear representation of the equilibrium distribution of secondary structures is derived from a two-dimensional bonding matrix with base-pairing probability as the third dimension. The temperature dependence of the equilibrium distribution gives the denaturation behavior of the nucleic acid, which may be compared to experimental optical denaturation curves after correction for the hypochromicities of the different base-pairs. Similarly, temperature-induced mobility changes detected in temperature-gradient gel electrophoresis of nucleic acids may be interpreted on the basis of the temperature dependence of the equilibrium distribution. Results are illustrated for natural circular and synthetic linear potato spindle tuber viroid RNA respectively, and are compared to experimental data.

Algorithms↗
PubMed1974

Further analysis of a simple prototypal muscle model near to and far from equilibrium.

The same prototypal model used in a previous paper to illustrate proper construction of a muscle model is modified here with the much more realistic choice e(Deltap) = 10(8) rather than e(Deltap) = 100, where e(Deltap) is the ratio of physiological ATP activity to equilibrium ATP activity. For steady isotonic contractions, the range 1 </= e(Delta) </= 10(4) can be approximated quite well by use of linear terms only in expansions of F (force) and J (ATP flux) in powers of e(Delta) - 1 and v (velocity). This will presumably also be true in most cases of much more complicated models. However, this region is of theoretical interest only (irreversible thermodynamics, etc.) because F and J are very small. In addition, numerical calculations of F and J were made in the region 10(4) </= e(Delta) </= 10(8). The optimal efficiency eta(*) is larger under physiological conditions (about 1%) than at equilibrium by a factor of 2.1 x 10(4). The rate of entropy production is discussed in this connection.

Adenosine Triphosphate↗
PubMed1982

Only the chemotactic subpopulation of human blood monocytes expresses receptors for the chemotactic peptide N-formylmethionyl-leucyl-phenylalanine.

Human peripheral blood monocytes comprise a subpopulation of 20 to 40% that is capable of responding to chemoattractants and a remaining subpopulation that cannot respond. We were able to obtain 99%-pure attractant-responsive monocytes by using a newly constructed separation chamber. The binding of the radioactive chemotactic peptide N-formylmethionyl-leucyl-[3H]phenylalanine to migrating and nonmigrating populations was then studied. The binding was saturable at room temperature in the presence of azide. Saturation occurred at 5 x 10(-8) M, and 50% of the maximal binding was obtained at 10(-8) M, the concentration that induced optimal chemotaxis. The nonmigrating monocytes did not bind the peptide under the same conditions, which shows that at least one reason for a nonresponsiveness to chemotaxin is apparently a lack of receptors. By Scatchard analysis we calculated an equilibrium dissociation constant ranging from 23 to 37 nM; the number of binding sites per cell ranged from 64,000 to 77,000. The binding was very rapid. Fifty percent of the optimal binding occurred at 3.5 min, and equilibrium was reached after 20 to 30 min. Chemotactic deactivation of the monocytes reduced the number of available binding sites by 60%.

Azides↗
PubMedDate not supplied

Codon equilibrium I: Testing for homogeneous equilibrium.

We present theoretical considerations that suggest that synonymous-codon usage might be expected to be close to an equilibrium distribution given a very homogeneous process of silent substitution. By homogeneous we mean that substitution depends only on the two bases involved, so that 12 base-substitution rates completely describe the silent substitution process. We have developed a method of statistically testing for such homogeneous equilibrium and applied it to reported data on the codon usages of different classes of organisms. Weakly expressed bacterial sequences and both mammalian and nonmammalian eukaryotic sequences deviate significantly from a random pattern of codon usage, in the direction of homogeneous equilibrium. On the other hand, highly expressed bacterial sequences do not exhibit homogeneous equilibrium, which may be correlated with recent experimental results showing that they are optimized to accept the most abundant tRNAs. To examine the effect of amino acid replacements on the homogeneous model of silent substitution, we divided the amino acids with degenerate codes into two classes, those with high mutabilities and those with low, and performed the same analysis on bacterial and eukaryotic data sets. The codon sets of the highly mutable class of amino acids are not further from homogeneous equilibrium than are the codon sets of the class with low mutabilities. We also found for the eukaryotic data that these independent classes of codon sets show very similar equilibrium patterns. The various results suggest a high level of uniformity in the process of silent fixation in the different synonymous-codon sets, especially in eukaryotes.

Amino Acid Sequence↗
PubMed1990

Sodium-dependent D-aspartate 'binding' is not a measure of presynaptic neuronal uptake sites in an autoradiographic assay.

The binding of D-[3H]aspartate to sections of rat brain was examined in an autoradiographic assay. Binding was entirely dependent on the presence of sodium ions, but not chloride ions, and was optimal at 2 degrees C. D-Aspartate bound rapidly, reached equilibrium within 20 min and remained stable for 45 min. The rate of dissociation was relatively rapid with a t1/2 of 56 s, but was not as fast as anticipated, perhaps because of some sequestration of ligand. Binding had a Kd of 6.8 +/- 1.2 microM and a Bmax of 49.4 +/- 8.6 pmol/mg protein. The high Bmax value may further indicate some sequestration of D-aspartate. L-Glutamate, unlabeled D-aspartate, and D,L-threo-hydroxyaspartate, a potent inhibitor of synaptosomal uptake, each competed for D-[3H]aspartate binding with IC50s of 7.0 +/- 4.3 microM, 5.4 +/- 1.5 microM, and 2.5 +/- 1.0 microM, respectively. N-methyl-D-aspartate (NMDA), quisqualate, and kainate had no affinity for this site. The regional distribution of D-aspartate binding sites was unique and did not conform to the distribution of neuronal uptake sites described by others. Striatal D-aspartate binding was unaffected by unilateral decortication or striatal quinolinic acid lesions. In contrast, binding to NMDA, quisqualate, and kainate receptors was reduced by 80-90% by quinolinate lesions of the striatum. The results of D-aspartate binding after lesions strongly suggest that this site is not associated with either lesioned glutamatergic afferents or intrinsic neurons of the striatum; it may be associated with glia.

Animals↗
PubMed1983

Specific binding of [3H]+/- 2-amino-7-phosphono heptanoic acid to rat brain membranes in vitro.

The specific binding of [3H]+/- 2-amino-7-phosphono heptanoic acid (3H-APH), a potent N-methyl-D-aspartate (NMDA) antagonist, to extensively washed, previously frozen crude mitochondrial fractions of rat brain is described. Binding was optimal at physiological pH and temperature and, in Triscitrate buffer, attained equilibrium within 60 minutes. Scatchard analysis of the equilibrium data for forebrain revealed a single, non-interacting population of binding sites (BMapp = 15 picomoles/mg protein; KDapp = 3.6 uM; Hill coefficient = 0.92, r = 0.99; N = 5). Specific binding of the ligand was readily reversible by unlabeled APH and was absent in peripheral tissues including heart, lung, kidney, liver, spleen and striate muscle and in heat treated brain sonicates. An 8-fold variation in the amount of ligand bound to brain membranes prepared from different regions was observed with binding being greatest in the hippocampal formation and least in the midbrain. Kainic acid, NMDA and aspartic acid exhibited negligible affinity for the [3H]-APH site; in contrast, quisqualic acid, ibotenic acid, glutamatic acid, homocysteic acid and 2-amino-4-phosphono butyric acid were moderately potent displacers. The results indicate that [3H]-APH labels a quisqualate preferring site in vitro. Unlike the receptor labeled by [3H]-glutamate however, [3H]-APH binding was attenuated in the presence of chloride ions suggesting that this ligand may label a subpopulation of excitatory amino acid receptors.

2-Amino-5-phosphonovalerate↗
PubMed1989

Semisynthetic hemoglobin A: reconstitution of functional tetramer from semisynthetic alpha-globin.

The optimal conditions for the semisynthesis of alpha-globin through Staphylococcus aureus V8 protease condensation of a synthetic fragment (alpha 1-30) with the complementary apo fragment (alpha 31-141) in the presence of structure-inducing organic cosolvents and the reconstitution of the functional tetramer from semisynthetic alpha-globin have been investigated. The protease-catalyzed ligation of the complementary apo fragments alpha 1-30 and alpha 31-141 proceeds with very high selectivity at pH 6.0 and 4 degrees C in the presence of 1-propanol as the organic cosolvent. A 30% 1-propanol solution was optimal for the semisynthetic reaction, and the synthetic reaction attained an equilibrium (approximately 50%) in 72 h. The synthetic reaction proceeds smoothly over a wide pH range (pH 5-8). Besides, the semisynthetic system is flexible, and it also proceeded well if trifluoroethanol or 2-propanol was used instead of 1-propanol. However, glycerol, a versatile organic cosolvent used in all other proteosynthetic reactions reported in the literature, was not very efficient as an organic cosolvent in the present synthetic reaction. The semisynthetic alpha-globin prepared with 1-propanol as the organic cosolvent has been reconstituted into HbA. The semisynthetic HbA was then purified by CM-cellulose chromatography. The semisynthetic HbA is indistinguishable from native HbA, in terms of its structural and functional properties. The semisynthetic approach provides the flexibility in protein engineering studies for the incorporation of spectroscopic labels (13C- and/or 15N-labeled amino acids), noncoded amino acids, or unnatural bond functionalities, which at present is not possible with genetic approaches.

Circular Dichroism↗
PubMed1987

Regulation of nitrogenase activity by oxygen in Azospirillum brasilense and Azospirillum lipoferum.

The nitrogenase activity of the microaerophilic bacteria Azospirillum brasilense and A. lipoferum was completely inhibited by 2.0 kPa of oxygen (approximately 0.02 atm of O2) in equilibrium with the solution. The activity could be partially recovered at optimal oxygen concentrations of 0.2 kPa. In contrast to the NH4+ switch off, no covalent modification of the nitrogenase reductase (Fe protein) was involved, as demonstrated by Western-blotting and 32P-labeling experiments. However, the inhibition of the nitrogenase activity under anaerobic conditions was correlated with covalent modification of the Fe protein. In contrast to the NH4+ switch off, no increase in the cellular glutamine pool and no modification of the glutamine synthetase occurred under anaerobic switch-off conditions. Therefore, a redox signal, independent of the nitrogen control of the cell, may trigger the covalent modification of the nitrogenase reductase of A. brasilense and A. lipoferum.

Amino Acids↗
PubMed1988

Approach to stationary two-dimensional pattern: influence of focusing time and immobiline/carrier ampholytes concentrations.

Horizontal two-dimensional (2-D) electrophoresis with immobilized pH gradients (IPG) in the first dimension for buffer soluble proteins and for complex proteins solubilized in the presence of Nonidet P-40 (Görg et al., Electrophoresis 1987, 8, 45-51), has been extended to analyze basic proteins of yeast cells focused under non-equilibrium and equilibrium conditions. Transient state isoelectric focusing (IEF) in IPG gels revealed sample smearing and background staining, displaying horizontal streaks in the resultant 2-D patterns. Inclusion of 0.5% carrier ampholytes (CA) to the IPG gel (IPG-CA), resulted in the formation of many sharp protein bands after transient state IEF with resultant distinct spots in the 2-D patterns; however, resolution was poor and the gel contained heavy background staining. With prolonged focusing time, background staining disappeared and there was less difference in the final steady state IEF patterns obtained with IPG and IPG-CA. Reduction of the Immobiline concentration to one third the manufacturer's recommended amount did not improve IEF resolution with respect to streaking and background staining under either transient state or equilibrium conditions. In general, spot intensities were less on 2-D gels using diluted IPG gels than with "standard" IPG gels. Optimization of 2-D electrophoresis with IPGs in the first dimension was strongly related to IEF conditions. The use of IPG gels focused to equilibrium should not only improve inter-gel reproducibility and resolution but also the quality of the final 2-D patterns with respect to background staining and horizontal streaking.

Ampholyte Mixtures↗