Protein-Binding Polynomials

Using a new method recently published for analyzing the binding isotherms of biopolymers (Poland, 2000a), we calculate the complete binding polynomials for lysozyme, insulin, and serum albumin from published titration data. These three proteins have, respectively, 22, 32, and 184 dissociable protons and hence are represented by series in powers of the hydrogen ion concentration with the highest powers in the series being the numbers just indicated. Given the complete binding polynomial, the distribution function giving the concentration of all states of proton binding can then be calculated at any pH.     

Application of polyelectrolyte limiting laws to virial and asymptotic expansions for the Donnan equilibrium

We have applied a general polyelectrolyte theory to an analysis of the Donnan equilibrium. The polyelectrolyte concentration is measured by a dimensionless parameter x, equal to the ratio of the equivalent polyelectrolyte concentration to the concentration of salt in the external compartment. For small x, virial series - expansions in powers of x - are developed for the Donnan salt-exclusion, osmotic pressure, and electromotive force. For large x, asymptotic expansions for these effects are presented. Polyion-polyion interactions are explicitly neglected, so that the physical significance of the virial series differs from its meaning in neutral polymer chemistry. Numerical results illustrate large deviations from ideal Donnan behavior as well as satisfactory agreement with published data on the salt-exclusion and emf effects. However, results for the Donnan osmotic pressure disagree with the data, except in the case of zero salt concentration in the external compartment, for which agreement is almost exact.     

An appraisal of multiple NADPH binding-site models proposed for cytochrome P450 reductase, NO synthase, and related diflavin reductase systems

The diflavin reductases exemplified by mammalian cytochrome P450 reductase catalyze NADPH dehydrogenation and electron transfer to an associated monooxygenase. It has recently been proposed that double occupancy of the NADPH dehydrogenation site inhibits the NADPH to FAD hydride transfer step in this series of enzymes. This has important implications for the mechanism of enzyme turnover. However, the conclusions are drawn from a series of pre-steady-state stopped-flow experiments in which the data analysis and interpretation are flawed. Recent data published for P450-BM3 reductase show a decrease in the rate constant for pre-steady-state flavin oxidation with increasing NADP(+) concentration. This is interpreted as evidence of inhibition by multiple substrate binding. A detailed reanalysis shows that the data are in fact consistent with a simple single-binding-site model in which reversible hydride transfer causes the observed effect. Data for the related systems are also discussed.     

Ligand binding distributions in nucleic acids

We illustrate a new method for the determination of the complete binding polynomial for nucleic acids based on experimental titration data with respect to ligand concentration. From the binding polynomial, one can then calculate the distribution function for the number of ligands bound at any ligand concentration. The method is based on the use of a finite set of moments of the binding distribution function, which are obtained from the titration curve. Using the maximum-entropy method, the moments are then used to construct good approximations to the binding distribution function. Given the distribution functions at different ligand concentrations, one can calculate all of the coefficients in the binding polynomial no matter how many binding sites a molecule has. Knowledge of the complete binding polynomial in turn yields the thermodynamics of binding. This method gives all of the information that can be obtained from binding isotherms without the assumption of any specific molecular model for the nature of the binding. Examples are given for the binding of Mn(2+) and Mg(2+) to t-RNA and for the binding of Mg(2+) and I(6) to poly-C using literature data.     

Voltage and Current Clamp Transients with Membrane Dielectric Loss

Transient responses of a space-clamped squid axon membrane to step changes of voltage or current are often approximated by exponential functions of time, corresponding to a series resistance and a membrane capacity of 1.0 μF/cm². Curtis and Cole (1938, J. Gen. Physiol. 21:757) found, however, that the membrane had a constant phase angle impedance z = z₁(jωτ)^-α, with a mean α = 0.85. (α = 1.0 for an ideal capacitor; α < 1.0 may represent dielectric loss.) This result is supported by more recently published experimental data. For comparison with experiments, we have computed functions expressing voltage and current transients with constant phase angle capacitance, a parallel leakage conductance, and a series resistance, at nine values of α from 0.5 to 1.0. A series in powers of t^α provided a good approximation for short times; one in powers of t^-α, for long times; for intermediate times, a rational approximation matching both series for a finite number of terms was used. These computations may help in determining experimental series resistances and parallel leakage conductances from membrane voltage or current clamp data.     

Estimation of foot joint kinetics in three and four segment foot models using an existing proportionality scheme: Application in paediatric barefoot walking

Recent studies which estimated foot segment kinetic patterns were found to have inconclusive data on one hand, and did not dissociate the kinetics of the chopart and lisfranc joint. The current study aimed therefore at reproducing independent, recently published three-segment foot kinetic data (Study 1) and in a second stage expand the estimation towards a four-segment model (Study 2).Concerning the reproducibility study, two recently published three segment foot models (Bruening et al., 2014; Saraswat et al., 2014) were reproduced and kinetic parameters were incorporated in order to calculate joint moments and powers of paediatric cohorts during gait. Ground reaction forces were measured with an integrated force/pressure plate measurement set-up and a recently published proportionality scheme was applied to determine subarea total ground reaction forces. Regarding Study 2, moments and powers were estimated with respect to the Instituto Ortopedico Rizzoli four-segment model. The proportionality scheme was expanded in this study and the impact of joint centre location on kinetic data was evaluated.Findings related to Study 1 showed in general good agreement with the kinetic data published by Bruening et al. (2014). Contrarily, the peak ankle, midfoot and hallux powers published by Saraswat et al. (2014) are disputed. Findings of Study 2 revealed that the chopart joint encompasses both power absorption and generation, whereas the Lisfranc joint mainly contributes to power generation.The results highlights the necessity for further studies in the field of foot kinetic models and provides a first estimation of the kinetic behaviour of the Lisfranc joint.     

Relaxation kinetics of DNA-ligand binding including direct transfer

The relaxation kinetics of binding of ethidium to calf-thymus DNA as studied previously by the temperature-jump method with absorption detection [Bresloff, J. & Crothers, D. M. (1975) J. Mol. Biol. 95 , 103] is reanalyzed in terms of a series of models for DNA-ligand interactions that include cases with and without internal and bimolecular direct transfer of ligands between different binding modes or different binding sites. The experimental results are shown to be consistent with two alternative binding mechanisms. Both models include bimolecular “direct transfer” steps and a site size of two base pairs per site. In the first model, there exist two distinct modes of binding to the DNA double helix at each binding site. In the second model, sites containing at least one GC base pair constitute a different and stronger class of binding sites than those containing only AT base pairs. The existence of a direct transfer pathway between two classes of bound ligands is supported by the linear increase of reciprocal relaxation times far beyond the concentration regions, where off-rates should have become rate limiting. The second model, incorporating the notion of base selectivity, is in quantitative agreement with published work on ethidium binding to DNAs of different base compositions and with nmr measurements of bound ligand lifetimes.     

Endogenous opiates: 1983

This paper is the sixth in an annual series of reviews of research involving the endogenous opiates, each installment being restricted to work published during the previous year. Although the early articles in the series attempted to be comprehensive and cover the complete range of research with the opiate peptides, in the last two years we have limited our coverage to non-analgesic and behavioral work due to the enormous number of articles published in the field. The specific areas discussed here include stress, tolerance and dependence, consummatory responses, other gastrointestinal functions, interactions with alcohol, mental illness, learning and memory, cardiovascular responses, respiratory effects, thermoregulation, neurological disorders, activity, and miscellaneous other topics. As in previous years, we have attempted to present a relatively complete review of the subjects covered only for the previous year and generally have not tried to evaluate their contributions relative to those of past years.     

Proline inhibition of pyrroline-5-carboxylate reductase: differences in enzymes obtained from animal and tissue culture sources

The complete amino acid sequence for the 148 amino acid flavodoxin from $\text{Desulfovibrio}\text{vulgaris}$ is presented. This is the first flavoenzyme for which both the complete amino acid sequence and a 2.5 Å resolution x-ray diffraction structure are now known. The position of some important residues in the binding of FMN are given. The D. vulgaris sequence is compared with other published flavodoxin sequences.     

Effect of a contaminating competitive ligand on ligand-binding curves. Inverse protein concentration dependence

A theoretical binding model is considered which provides an explanation for the inverse protein concentration dependence observed for a variety of ligands. The model describes the inhibition of binding caused by a highly bound contaminant. The complete binding equation is derived and examined in terms of form, limits, and protein dependence. Furthermore, several approximate relations are derived which are useful for obtaining initial estimates of the model parameters and for a qualitative test of the applicability of the model. It is found that the binding curve may show a characteristic plateau at a saturation equal to the uncontaminated fraction of the protein and that the free ligand concentration at half saturation depends linearly on protein concentration. The practical implications of the present findings are discussed based on an analysis of simulated as well as experimental data.     

Specific association of the CRP-cyclic AMP complex with the control region of the lactose operon of Escherichia coli K 12: a direct fluorimetric study using DNA fragments of different lengths

Specific-site binding of the cAMP . CRP complex to the control region of the lactose operon of E. coli was measured directly. All of the protein molecules did bind specifically, and the binding constant for the major CRP site was not dependent on the length (62, 219 or 301 base pairs) of the DNA fragments used. Comparing the values of the binding constant measured for the major site and for the weaker "operator" CRP site, and referring to the published "consensus sequence" derived from the known CRP sites in a series of operons, we suggest that two sub-sites support additive contribution to the total binding free energy.     

The role of hydrophobic interactions in ankyrin-spectrin complex formation

Spectrin and ankyrin are the key components of the erythrocyte cytoskeleton. The recently published crystal structure of the spectrin-ankyrin complex has indicated that their binding involves complementary charge interactions as well as hydrophobic interactions. However, only the former is supported by biochemical evidence. We now show that nonpolar interactions are important for high affinity complex formation, excluding the possibility that the binding is exclusively mediated by association of distinctly charged surfaces. Along these lines we report that substitution of a single hydrophobic residue, F917S in ankyrin, disrupts the structure of the binding site and leads to complete loss of spectrin affinity. Finally, we present data showing that minimal ankyrin binding site in spectrin is formed by helix 14C together with the loop between helices 15 B/C.     

Equilibrium competition binding assay: inhibition mechanism from a single dose response

Inhibition of a receptor by a small-molecule compound in many cases is achieved via a competitive, uncompetitive or non-competitive mechanism. The receptor-inhibitor interaction is often probed through the displacement of a ligand in an equilibrium competition binding experiment. The previous solutions to receptor inhibition mechanisms were borrowed from steady-state enzyme inhibition mechanisms. The inhibition mechanism is determined by a visual inspection or a global fit of ligand dose response curves at a series of inhibitor concentrations. However these solutions only apply to situations when both the ligand and the inhibitor are not significantly depleted by the receptor. In most published equilibrium receptor binding studies, only the relative potency of the inhibitor is calculated. Ranking inhibitors tested under differing experimental conditions is often not possible. In the current paper, we offer exact mathematical solutions to uncompetitive and non-competitive inhibition, and demonstrate that in most cases both the inhibition mechanism and absolute potency of an inhibitor can be simultaneously determined from a single dose response of the inhibitor at a fixed concentration of the ligand. Therefore, an equilibrium competition assay provides a quick and facile method to determine the inhibition mechanism of a large number of inhibitors. The theory herein described is applicable to equilibrium competition binding experiments such as radioligand assays and fluorescence polarization assays.     

Kinetics of platelet-activating factor 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine-induced fibrinogen binding to human platelets

Platelet-activating factor 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF-acether) triggers exposure of fibrinogen binding sites on platelets via binding to specific receptors. Comparison of [3H]PAF-acether binding with 125I-fibrinogen binding shows that the rate with which PAF-acether binds to a number of receptors and not the degree of receptor occupancy determines how much fibrinogen binds. At low concentrations of PAF-acether (0.1-1.0 nM) binding site exposure is incomplete and parallels the rate of formation of the PAF-acether-receptor complex. Fibrinogen binding then primarily depends on the concentration of PAF-acether. At a high concentration of PAF-acether (500 nM) binding site exposure is complete within 2-5 min. Fibrinogen binding then depends on the concentration of fibrinogen. Exposure of binding sites in the absence of fibrinogen leads to disappearance of accessible binding sites. At 500 nM PAF-acether, this disappearance is exponential in nature and shows the same characteristics after 5-15 min incubation with fibrinogen as after 60 min. Exposure of binding sites is then complete within 5 min and their disappearance is not disturbed by other processes. At 0.5 nM PAF-acether, the same characteristics are found after 60 min incubation with fibrinogen, but shorter incubation times reveal an ongoing binding site exposure that interferes with the disappearance process. These results demonstrate close coupling between the PAF-acether receptors and fibrinogen binding sites and indicate that the rate of formation of the PAF-acether-receptor complex is a major factor in the regulation of binding site exposure.     

Genome-wide prediction,display and refinement of binding sites with information theory-based models

Background  

We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined) weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices.     

Stimulation of bone resorption by various prostaglandins in organ culture.

The ability of E, F, A and B prostaglandins to stimulate bone resorption was demonstrated in organ culture. All of the compounds tested were able to increase the release of previously incorporated 45Ca from fetal rat bone by 60 to 135 per cent at maximally effective doses, but prostaglandins of the E series were 10- to 100- fold more potent than F, A or B prostaglandins. Compounds with two double bonds in the side chain were usually more potent than those with one double bond. PGE2 stimulation of bone resorption increased linearly with the logarithm of the medium concentration over the range of 10(-9)M to 10(-5)M, then decreased at higher concentrations. PGE2 stimulated bone resorption more slowly than did parathyroid hormone but caused complete resorption after six days in the culture system. Equilibrium dialysis studies showed no significant binding of F, and 16-34% binding of E and A prostaglandins to bovine serum albumin, which was present in the medium at 1 mg/ml. These differences in albumin binding could not account for differences in potency.     

Substrate ground state binding energy concentration is realized as transition state stabilization in physiological enzyme catalysis

Previously published kinetic data on the interactions of seventeen different enzymes with their physiological substrates are re-examined in order to understand the connection between ground state binding energy and transition state stabilization of the enzyme-catalyzed reactions. When the substrate ground state binding energies are normalized by the substrate molar volumes, binding of the substrate to the enzyme active site may be thought of as an energy concentration interaction; that is, binding of the substrate ground state brings in a certain concentration of energy. When kinetic data of the enzyme/substrate interactions are analyzed from this point of view, the following relationships are discovered: 1) smaller substrates possess more binding energy concentrations than do larger substrates with the effect dropping off exponentially, 2) larger enzymes (relative to substrate size) bind both the ground and transition states more tightly than smaller enzymes, and 3) high substrate ground state binding energy concentration is associated with greater reaction transition state stabilization. It is proposed that these observations are inconsistent with the conventional (Haldane) view of enzyme catalysis and are better reconciled with the shifting specificity model for enzyme catalysis.     

Determination of plasma and tissue levels of tyramine by radioimmunoassay.

Antibodies were prepared against tyramine. The antigen was prepared as follows: p-Aminohippuric acid was coupled to mBSA using a carbodiimide reagent. The amino group was diazotized an attached to the aromatif ring of TYR. The immunogen in Freund's complete adjuvant was injected into rabbits. The specificity of the resulting antibody was determined by radioimmunoassay. Using random-labeled TYR-3H, TYR, its metabolites, phenethylamine analogs, catecholamines, and certain amino acids were evaluated by a competitive binding assay method. With this technique 4 ng of TYR inhibited the binding of TYR-3H by 50%. The radioimmunoassay of TYR was used to measure the plasma, urine, and tissue levels of TYR in rabbits. The plasma disappearance curve of TYR revealed a biphasic pattern with t1/2 of 2 min and 54 min. The highest concentration of TYR was found in adrenals and spleen. The factthat the major metabolites of TYR and a series of pharmacologically important sympathomimetics and catecholamines did not interfere, makes the radioimmunoassay of TYR a useful, simple, sensitive, and spedific method for the direct analysis of TYR in biological meterials.     

Quantitative Footprinting Analysis of the Netropsin-DNA Interaction

Abstract

The results of a series of quantitative footprinting experiments of the netropsin-DNA interaction as studied using two different DNA cleaving probes, the enzyme DNase I and a cationic manganese porphyrin complex, are described. Plots of the relative change in oligonucleotide concentration as a function of drug concentration, covering ～ 110 base pairs of a DNA restriction fragment, revealed netropsin induced changes in the cleavage rates of both probes. These appeared as inhibitions for the binding sites, enhancements where no binding took place, and enhancement/inhibitions for the weak binding sites. Determination of the concentration of drug necessary to reduce the amount of a particular oligomer to half of its initial value allowed a ranking of the affinities of the various binding sites on the fragment. In addition to uncovering the location of a number of overlapping netropsin binding sites, the data allowed additional insight on the manner in which both probes alter their DNA cleavage rates in the drug-footprinting experiment.