Cooperativity Index Research Articles

Rearrangements of 55-atom Lennard-Jones and (C60)55 clusters

Roughly 3000 rearrangement pathways have been calculated for each of two clusters bound by simple empirical potentials. The first system is the 55-atom complex described by a pairwise Lennard-Jones potential. The second consists of 55 C60 molecules with an intermolecular potential obtained by spherically averaging atom–atom Lennard-Jones terms, as previously employed in bulk simulations. Various properties of the pathways are calculated, such as a cooperativity index and the integrated path length, and the probability distributions are subjected to statistical analysis. Systematic differences between the atomic Lennard-Jones clusters and the C60 molecular clusters are explained in terms of the effective pair potential; e.g., rearrangements of (C60)55 are generally localized because the potential is relatively short ranged. A pseudo-third-derivative correction is developed to improve the convergence of the eigenvector-following method employed to optimize the geometries and follow the pathways.

3H]Resiniferatoxin binding by the human vanilloid (capsaicin) receptor

We report here that we were able to detect the human vanilloid receptor in all three major central endings of primary afferent neurons - in the dorsal horn of the spinal cord, in the cuneate and gracile nuclei and in the spinal nucleus of the trigeminal nerve - and to characterize the binding properties of the receptor in the dorsal horn. Specific [ 3H]resiniferatoxin (RTX) binding is thought to represent the vanilloid (capsaicin) receptor. [ 3H]RTX binding to membranes obtained from total human spinal cord and dorsal horn followed sigmoidal saturation kinetics indicating apparent positive cooperativity. The cooperativity index determined by fitting the data to the Hill equation was 1.37 ± 0.02 in the total spinal cord and 1.77 ± 0.16 in the dorsal horn. The apparent dissociation constants in whole spinal cord and dorsal horn membranes were 915 ± 12 and 532 ± 27 pM; the receptor densities were 140 ± 6 and 227 ± 15 fmol/mg protein, respectively. Membrane preparations from the spinal nucleus of the trigeminal nerve and the cuneate and gracile nuclei also bound [ 3H]RTX in a similar fashion. In parallel experiments, rat spinal cord membranes bound [ 3H]RTX with 20- to 40-fold higher affinity, somewhat greater positive cooperativity, but at a 3-fold lower receptor density. As predicted by the modified Hill equation, non-radioactive RTX at low receptor occupancy produced biphasic competition curves. Capsaicin and the competitive antagonist capsazepine also fully displaced specifically bound [ 3H]RTX from human dorsal horn membranes with K i values of 1.07 ± 0.04 μM and 353 ± 13 nM, respectively; the corresponding Hill coefficients were 1.69 ± 0.06 and 1.6 ± 0.02. [ 3H]RTX binding was not inhibited by resiniferonol 9,13,14-orthophenylacetate, the biologically inactive parent diterpene of RTX. Capsaicin and capsazepine inhibited specific binding of [ 3H]RTX to rat spinal cord membranes with K i values of 5.3 ± 0.37 μM and 3.55 ± 0.35 μM and Hill coefficients of 2.03 ± 0.08 and 1.9 ± 0.1, respectively. Our results show that there are species differences in the receptor characteristics between man and rat.

22] Hemoglobin-oxygen equilibrium binding: Rapid-scanning spectrophotometry and singular value decomposition

The knowledge of the interaction between oxygen (O2) and hemoglobin (Hb) is essential both for understanding oxygen transport phenomena and for testing theories of protein structure and function. The equilibrium reaction is measured routinely simply to estimate the position and shape of the O2-binding curve from, respectively, the O2 pressure at half saturation (P50) and the index of cooperativity (i.e., the Hill number, n), but thermodynamic analysis of individual binding steps is more difficult because of inherent complexities in the reaction. The Hb conformational transition is another area under study. Strong allosteric effectors, such as inositol hexaphosphate and bezafibrate, are being used to test this by possibly enhancing the signal. In the future, mathematical models will include calculations of tetramer dissociation and subunit differences in ligand binding. As instruments and theory improve, the critical components of the reaction will be resolved better and, once limiting assumptions are no longer required for experimental analyses, the evaluation of Hb-O2 equilibrium binding will become a simpler and more reliable process.

Characterization by [ 3H]resiniferatoxin binding of a human vanilloid (capsaicin) receptor in post-mortem spinal cord

Membranes obtained from post-mortem human spinal cord specimens bound [ 3H]resiniferatoxin (RTX) with an affinity of 11 nM in a non-cooperative fashion. This binding behaviour contrasted with the high affinity [ 3H]RTX binding ( K d = 24 pM) to rat spinal cord membranes which displayed apparent positive cooperativity (cooperativity index = 1.8) but was in accord with the low affinity ( K d = 5 nM) non-cooperative RTX binding to guinea pig spinal cord preparations. We conclude that the [ 3H]RTX binding assay utilizing post-mortem human spinal cord membranes affords a novel biochemical approach to explore structure-activity relations at human vanilloid receptors.

3H]Resiniferatoxin binding to pig dorsal horn membranes displays positive cooperativity

In the present report we have reevaluated specific [ 3H]resiniferatoxin (RTX) binding, thought to represent the vanilloid (capsaicin) receptor, to whole spinal cord and dorsal horn membranes of the pig using a modified [ 3H]RTX binding assay. The high nonspecific [ 3H]RTX binding of the original protocol was reduced by the addition of α 1-acid glycoprotein (AGP), a plasma protein that binds RTX, to the assay mixture after the binding reaction had been terminated. Specific [ 3H]RTX binding to pig whole spinal cord and dorsal horn membranes followed sigmoidal saturation kinetics indicating apparent positive cooperativity. The cooperativity index determined by fitting the data to the Hill equation was 2.31±0.24 in the spinal cord and 2.27±0.13 in the dorsal horn. The apparent dissociation constants in spinal cord and dorsal horn membranes were 87.8±2.7 and 103.9±1.9 pM; the receptor densities were 23±3 and 203±5 fmol/mg protein, respectively. In parallel experiments, rat spinal cord membranes bound [ 3H]RTX with 2 - 3 fold higher affinity, equal positive cooperativity, and a 49±6 fmol/mg receptor density. As predicted by the modified Hill equation, at low receptor occupancy nonradioactive RTX produced biphasic competition curves. Capsaicin and the competitive antagonist capsazepine also fully displaced specifically bound [ 3H]RTX from pig dorsal horn membranes with K i values of 9.7±1.7 μM and 6.8±0.7 μM, respectively; the corresponding Hill coefficients were 1.81±0.17 and 2.32±0.11. [ 3H]RTX binding was not inhibited by resiniferonol 9, 13, 14-orthophenylacetate, the biologically inactive parent diterpene of RTX. These findings suggest that the vanilloid receptor present in the dorsal horn of the pig, like those present in human and in the rat, is a receptor cluster in which the subunits cooperate.

The regulation of phospholipase C-gamma 1 by phosphatidic acid. Assessment of kinetic parameters.

A survey of lipids revealed that the anionic phospholipid phosphatidic acid activates both control and tyrosine-phosphorylated PLC-gamma 1. The mechanism by which phosphatidic acid activates both forms of PLC-gamma 1 was investigated using kinetic analysis. In the presence of phosphatidic acid, the substrate concentration response for control PLC-gamma 1 changes from sigmoidal to hyperbolic, while the cooperativity index decreases from 2.5 for control to 1.0 for tyrosine-phosphorylated PLC-gamma 1. The primary influence of phosphatidic acid on the control enzyme is on the cooperativity index and not the association of PLC-gamma 1 with substrate micelles, as phosphatidic acid had little effect on the micellar association constant, Ks. Phosphatidic acid also increases the activity of the tyrosine phosphorylated form of the enzyme. This increase is reflected in a decrease in the Km from 0.3- to 0.03-mol fraction phosphatidylinositol 4,5-bisphosphate. Phosphatidic acid has no effect on the Ks of the tyrosine-phosphorylated enzyme. From this data it is concluded that phosphatidic acid appears to activate PLC-gamma 1 by acting as an allosteric modifier.

Salt and mesophase formation in aqueous suspensions of lauric acid.

The solubility and solution behavior of lauric acid (LA) and its 1:1 acid soap (potassium hydrogen dilaurate) were investigated at 32 degrees C over a pH range of 2.5-8.5 and at varying KCl concentrations to examine the self-association of this long-chain carboxylic acid under these conditions. LA's solubility in water exhibited the classical pH dependence of a monocarboxylic acid with no evidence of self-association. In 0.1 M KCl between pH 6.3 and pH 7.3, filtered samples were turbid, suggesting the presence of high molecular weight aggregates (mesophase), which could be removed by ultrafiltration. The apparent LA solubility vs pH profile in ultrafiltered samples was consistent with a solid phase consisting of either the free acid (pH < 6.5) or potassium hydrogen dilaurate (pH > 6.5), again with no evidence of self-association to form low molecular weight species (dimers, etc.). Quasi-elastic light scattering (QLS) studies and mannitol trapping experiments indicated that vesicles were present in samples containing mesophase. The mesophase composition was characterized and a mass-action law for mesophase formation was developed to describe the apparent LA solubility versus pH in the mesophase region in terms of three parameters. The index of cooperativity, theta, indicated that the mesophase consists of approximately 25 molecules of LA with an acid:anion ratio, rho, of 1.7. The standard free energy of mesophase formation per mole of monomer was determined to be -6.3 kcal/mol. The aggregate size determined thermodynamically is several orders of magnitude less than that of the mesophase particle size determined by QLS measurements, suggesting that the LA monomer concentration in equilibrium with mesophase may be governed by a small unit domain of the vesicle. These observations may have a bearing on the thermodynamics of self-assembly of lipid bilayer membranes.

Characterization of a peripheral vanilloid (capsaicin) receptor in the urinary bladder of the rat

Specific binding of [ 3H]resiniferatoxin (RTX) is thought to represent the vanilloid (capsaicin) receptor. In the present study, we have used this binding assay to identify for the first time a vanilloid receptor in the periphery and to compare it to central vanilloid receptors presents in dorsal root ganglia (DRG) as well as in spinal cord of the rat. Rat urinary bladder membranes bound [ 3H]RTX with a K d of 30 ± 4 pM and B max of 65 ± 14 fol/mg protein; the corresponding values were 19 ± 3 pM and 104 ± 14 fmol/mg protein in DRG, and 16 ± 3 pM and 50 ± 9 fmol/mg protein in spinal cord. Capsaicin inhibited [ 3H]RTX binding to membranes from urinary bladder, spinal cord, and DRG with similar potency (K i values were 0.5 ± 0.1 μM, 0.3 ± 0.1, and 0.6 ± 0.1 μM, respectively). Interestingly, [ 3H]RTX bound to urinary bladder in a non-cooperative fashion in contrast with the apparent positive cooperativity of [ 3H]RTX binding in both DRG and spinal cord (cooperativity index = 1.8 and 1.7, respectively). This finding suggests heterogeneity in the properties of the vanilloid receptors in the rat.

An Agreement Between the Libraries of European Business Schools for the Exchange of Documents

The EBSLG is a consortium of almost 30 business school libraries located in contintental Europe, the United Kingdom, and Scandinavia. EBSLG library system serves as a document delivery system as well as a forum for the exchange of ideas and activities common to member schools. In its twenty year history, EBSLG has developed the Selective Cooperative Indexing of Management Periodicals (SCIMP), a data base of 80,000 articles, and produced a union catalog of more than 3,000 journal titles.

A New Game Theoretical Model of Social Dilemma

The study of Social Dilemmas originated in common resources management field. Recently it has been developed to study the puzzling social problems in which a short-term or individual need is pitted against its long-term or group need. Some research and discussions are focused on the choice and decision making in socioeconomic system. In this paper, based on the principle of game theory, a mathematical model is proposed to describe and analyze a typical social dilemma---N-Person Prisoner’s Dilemma in which the individual interest conflicts with the group interest. From the model, a structural cooperation index is defined to indicate the extent of the dilemma and the cooperation trend of the players. An important proposition has been proved that the cooperation choice probability of the players is a monotone increasing function of the structural cooperation index. The way of increasing cooperativeness in N-person Prisoner’s Dilemma is discussed. Using the model, we proved the proposition that the territorial division can break out of the dilemma. In other words, decreasing the size of the group can raise the cooperativeness. Some more discussions and significant results are given.

ATP inhibition competes with activating cations in modulating the NAD(P) +-malic enzyme activity in the mitochondrial matrix of Xenopus laevis oocytes

1. 1. ATP inhibits NAD(P) + -dependent malic enzyme activity by competing with the essential activators Mn 2+ and Mg 2+. 2. 2. The kinetics fit an equation of co-operative kind with K i of 26 μM and K A of 11.3 μM for ATP/Mn 2+ competition; with K i , of 1.1 mM and K A of 0.96 mM for ATP/Mg 2+ competition. 3. 3. In the absence of the inhibitor, the co-operativity index increases from 1.77 to > 4 in the presence of ATP, in the case of ATP/Mn 2+ competition, while it increases from 1.88 to > 9 for ATP/Mg 2+ competition.

The effect of NaCl concentration on NO 3−, K + and orthophosphate-P influx to peanut roots

The effect of relatively low concentrations of NaCl on the vegetative growth of peanut ( Arachis hypogaea L.) plants appeared to be due to its disruption to nutrient uptake. The specific effect of NaCl on the uptake rate of NO 3 −, K + and orthophosphate-P was studied in solution culture. The influxes of the nutrients were calculated according to their depletion in the solution, and the parameters for the Hill Kinetics for low concentrations were calculated as: I n = I max C h (K h + C h) , where I n = net influx, I max = maximal influx, C = concentration, K = the apparent Michaelis-Menten coefficient, and h = the Hill cooperativity index. The reduction in ion influx was greatest for K +, followed by NO 3 −, while phosphate influx was not affected by NaCl. All three parameters of the Hill equation for K + influx were affected by NaCl concentration: I max decreased to about one-third, while the value of K tripled and h doubled, when NaCl concentration increased from 0 to 75 mM. I max of NO 3 − influx was reduced by 40% because of the same increase in NaCl concentration. The other two parameters were unaffected. The results confirm previous results that low concentrations of NaCl disturb the nutritional balance of plants, mainly by Na +-K + competition in uptake, and to a smaller degree, by Cl −-NO 3 − interaction. The possible implications about the nature of ion interaction in uptake by the roots, derived from the differential effect of NaCl on the parameters of the Hill equation are discussed.

Photoreceptor channel activation: interaction between cAMP and cGMP

cAMP activates a current in excised patches from rod outer segments. The current at saturating concentrations of cAMP is approximately 25% of the current activated with 200 microM cGMP, the terminal cytoplasmic messenger in phototransduction. The K0.5 for cAMP is greater than 1.5 mM, and the index of cooperativity is approximately 1.4. cAMP activates the same population of channels as activated by cGMP since currents in the presence of both nucleotides are less than the sum of the individual responses. When increasing concentrations of cAMP, less than its K0.5, are added to a fixed, subsaturating concentration of cGMP, cAMP significantly enhances the total current compared with the current produced by cGMP alone. These results are predicted by a three-site, linear, sequential binding scheme where either cAMP or cGMP may bind to the same site on the channel. At approximately 5 microM cGMP, which is estimated to be the steady-state dark level in vertebrate photoreceptors, cAMP between 1 and 100 microM produces a large increase in the photoreceptor current. A possible physiological role for cAMP-cGMP interaction in phototransduction is discussed.

Photoreceptor channel activation by nucleotide derivatives

Cyclic nucleotide activated sodium currents were recorded from photoreceptor outer segment membrane patches. The concentration of cGMP and structurally similar nucleotide derivatives was varied at the cytoplasmic membrane face; currents were generated at each concentration by the application of a voltage ramp. Nucleotide-activated currents were analyzed as a function of both concentration and membrane potential. For cGMP, the average K0.5 at 0 mV was 24 microM, and the activation was cooperative with an average Hill coefficient of 2.3. Of the nucleotide derivatives examined, only 8-[[(fluorescein-5-yl-carbamoyl)methyl]thio]-cGMP (8-Fl-cGMP) activated the channel at lower concentrations than cGMP with a K0.5 of 0.85 microM. The next most active derivative was 2-amino-6-mercaptopurine riboside 3',5'-monophosphate (6-SH-cGMP) which had a K0.5 of 81 microM. cIMP and cAMP had very high K0.5 values of approximately 1.2 mM and greater than 1.5 mM, respectively. All nucleotides displayed cooperativity in their response and were rapidly reversible. Maximal current for each derivative was compared to the current produced at 200 microM cGMP; only 8-Fl-cGMP produced an identical current. The partial agonists 6-SH-cGMP, cIMP, and cAMP activated currents which were approximately 90%, 80%, and 25% of the cGMP response, respectively. 5'-GMP, 2-aminopurine riboside 3',5'-monophosphate, and 2'-deoxy-cGMP produced no detectable current. The K0.5 values for cGMP activation, examined from -90 to +90 mV, displayed a weak voltage dependence of approximately 400 mV/e-fold; the index of cooperativity was independent of the applied field.(ABSTRACT TRUNCATED AT 250 WORDS)

Dysregulation of glucose transport and transporters in perfused hearts of genetically obese (fa/fa) rats

The regulation of glucose transport in normal and insulin-resistant obese rat hearts have been studied by measuring glucose transport via the efflux of labelled 3-0-methyl-D-glucose. Glucose transporters in obese rat hearts were also investigated using the labelled cytochalasin B-binding assay. Basal, and insulin- or increasing workload-induced stimulation of glucose transport was decreased in obese rat hearts compared to those of normal ones. Total number of glucose transporters (plasma membrane plus microsomal ones) was about half that previously reported for normal rat hearts. Insulin or workload favoured the translocation of glucose transporters from an intercellular pool (microsomes) to the plasma membrane, as they do in normal rats. Due to the measured decrease in total number of transporters of obese rat hearts, those present in the plasma membrane (under basal conditions, or following stimulation by insulin or workload) were less than those previously found in normal rat hearts tested under identical conditions. In obese rat hearts, regulation of plasma membrane transporters was perturbed. The Hill coefficient (an index of positive cooperativity amongst glucose transporters) was paradoxically decreased by insulin while leaving affinity values unaltered. The Hill coefficient was unaltered by workload, although the affinity values were increased compared to respective controls. To sum up, obese rat hearts have decreased total transporter number, and although the two stimuli studied favour the translocation of available transporters, they fail to "activate" them adequately once present in the plasma membrane.

Site-specific substitutions of the Tyr-165 residue in the catalytic chain of aspartate transcarbamoylase promotes a T-state preference in the holoenzyme.

The amino acid residue Tyr-165C of aspartate transcarbamoylase (EC 2.1.3.2) of Escherichia coli has been proposed to be involved in the transition from the T-state to the R-state upon binding of the bisubstrate analogue N-(phosphonacetyl)-L-aspartate. Site-specific mutagenesis has been used to substitute phenylalanine for tyrosine, thus maintaining the aromatic R-group but removing the charged hydroxyl moiety. This mutation dramatically altered the aspartate requirements for the holoenzyme but did not substantially affect the homotropic or heterotropic characteristics of the oligomer. The aspartate requirements for half-maximal saturation increased from 5.5 mM at pH 7.0 for the native holoenzyme to approximately 90 mM in the mutant enzyme. Nonetheless, estimates of the kinetic cooperativity index remained similar (Hill coefficients: Tyr-165C, n = 2.1; Phe-165C, n = 2.5). CTP inhibited both enzymes approximately 70% and ATP activated approximately 40% at the aspartate concentrations required for half-maximal saturation (5 and 90 mM, respectively). The maximal velocity of the mutant holoenzyme is almost identical to that of the wild-type enzyme. The phenylalanine substitution does not affect the stability of the holoenzyme to heat or mercurials, and the Vmax of the catalytic trimer was 444% greater than that of the holoenzyme. Upon dissociation of the wild-type native enzyme into catalytic trimers, the Vmax increased 450%. The Km for aspartate in the separated catalytic trimer is approximately 2-fold higher than for the native catalytic trimer (16.5 versus 8 mM at pH 7.0). It is clear from the data that although Tyr-165C is not directly involved in the active site of the enzyme, it does play a pivotal role in catalytic transitions of the holoenzyme. In addition, the homotropic and heterotropic characteristics of the enzyme do not seem to be altered by the substitution of phenylalanine for Tyr-165C in the E. coli aspartate transcarbamoylase, although other substitutions have been reported (Robey, E. H., and Schachman, H. K. (1984) J. Biol. Chem. 259, 11180-11183) which show more complex effects.

The publisher's corner: The making of A Matter of Fact: An evolving conception : Part 3: Quality control and cooperative indexing

The publisher's corner: The making of A Matter of Fact: An evolving conception : Part 3: Quality control and cooperative indexing

Initiation of chromosome replication in bacteria: analysis of an inhibitor control model.

This article contains an analysis of a version of the well-known inhibitor-dilution model for the control of initiation of chromosome replication in bacteria. According to this model, an unstable inhibitor interacts with an initiation primer in a hit-and-destroy fashion to prevent successful initiation; both constituents are presumed to be RNA species that are synthesized constitutively. The model further postulates that the inhibitor interacts cooperatively with the primer, that the inhibitor gene is removed some distance from the origin of replication, and that an eclipse period exists during which the chromosome origin is not able to reinitiate. This unstable-inhibitor version is characterized by four parameters: the inhibitor half-life, the cooperativity index, the location of the inhibitor gene, and the eclipse period; computer simulations are used to study the effect of each of these on the DNA and interdivision time distributions in exponentially growing steady-state cultures. In neither case was any combination of parameter values found that could provide even moderately satisfactory agreement between the simulation results and experimental data. From the examples furnished and the associated discussion, it appears that there are none--that no combination of parameter values exists that can reasonably be expected to produce a significantly better fit than those tested. We conclude that the model in its present form cannot be a valid description of chromosome replication control in bacteria. It is pointed out that this does not necessarily apply to negative initiation control models in general, or even to all inhibitor-dilution systems, merely to the particular ColE1-like mechanism considered here. Nevertheless, recent experimental results, which can only be understood in terms of a very high degree of initiation synchrony within individual cells, offer strong evidence against stochastic models of this kind for the control of chromosome replication.

Kinetic model for micellar catalysed hydrolysis of esters-biomolecular reactions

The cationic micelles of cetyltrimethylammonium bromide, cetyldibenzylammonium chloride and cetylpyridinium chloride stabilize the tetrahedral intermediate formed in the hydrolysis of carboxylic esters (e.g.p-nitrophenylbenzoate) to a greater extent, preferring a\(B_{Ac^2 } \) mechnism, than the anionic intermediate formed in the hydrolysis ofm-nitrophenyl-N-N-diphenylphosphorodiamidate, which prefers aE 1cB mechanism. The co-operative index,n 1, calculated for these reactions is greater than 1 indicating that the substrate induced micellation is responsible for the observed catalysis. Based on the present kinetic model for a bimolecular reaction the fraction of substrate and nucleophile bound to the micelle have been calculated. The above results suggest that reaction occurs between the substrate solubilised into the micelle and the nucleophile residing at the Stern layer rather than at the micelle-water interface. The equilibrium constant, and critical micelle concentration evaluated using the present model are in agreement with the values obtained by using earlier models, suggesting a method of evaluating these parameters from kinetic data only.

Artificial Allosteric System 5. Allosteric Gain, Total Cooperativity and Local Cooperativity as Appropriate Indices for Allosteric Effect

AbstractMagnitude of cooperativity of a hypothetical m‐subunit allosteric system of hemoglobin type is discussed, based on computation of the amount of O2 to be transferred to the corresponding monomeric nonallosteric system of myoglobin type. For quantitative discussion, “allosteric gain” is defined as the difference between the amount of O2 to be transferred from the allosteric to the nonallosteric system and that from the hypothetical system of average O2 affinity to the nonallosteric system. These two quantities, allosteric gain and amount of O2 transfer, are quite sensitive to equilibrium constant ratio, especially Km/K1, (Ki+1/Ki)max, and i. Hill's coefficient appropriately describes neither the amount of O2 transferred nor allosteric gain. Allosteric gain or the amount of O2 transfer which is best characterized by the total cooperativity index (Km/K1) and the local cooperativity indices (Ki+1/Ki) seem to be appropriate measures of the magnitude of cooperativity.