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PubMed2002

Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper.

A lattice-based model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a sequence of interaction centers arranged on a cubic lattice, with effective interaction potentials that are both of physical and statistical nature. The Monte Carlo simulation method is then used to sample the partition functions of both the monomer and dimer forms as a function of temperature. A method is described to estimate the entropy loss upon dimerization, a quantity that enters the free energy difference between monomer and dimer, and the corresponding dimerization reaction constant. As expected, but contrary to previous numerical studies, we find that the entropy loss of dimerization is a strong function of energy (or temperature), except in the limit of large energies in which the motion of the two dimer chains becomes largely uncorrelated. At the monomer-dimer transition temperature we find that the entropy loss of dimerization is approximately five times smaller than the value that would result from ideal gas statistics, a result that is qualitatively consistent with a recent experimental determination of the entropy loss of dimerization of a synthetic peptide that also forms a two-stranded alpha-helical coiled coil.

Biophysical Phenomena↗

PubMed2000

Information domain analysis of cardiovascular variability signals: evaluation of regularity, synchronisation and co-ordination.

A unifying general approach to measure regularity, synchronisation and co-ordination is proposed. This approach is based on conditional entropy and is specifically designed to deal with a small amount of data (a few hundred samples). Quantitative and reliable indexes of regularity, synchronisation and co-ordination (ranging from 0 to 1) are derived in a domain (i.e. the information domain) different from time and frequency domains. The method is applied to evaluate regularity, synchronisation and co-ordination among cardiovascular beat-to-beat variability signals during sympathetic activation induced by head-up tilt (T), during the perturbing action produced by controlled respiration at 10, 15 and 20 breaths/min (CR10, CR15 and CR20), and after peripheral muscarinic blockade provoked by the administration of low and high doses of atropine (LD and HD). It is found that: (1) regularity of the RR interval series is around 0.209; (2) this increases during T, CR10 and HD; (3) the systolic arterial pressure (SAP) series is more regular (0.406) and its regularity is not affected by the specified experimental conditions; (4) the muscle sympathetic (MS) series is a complex signal (0.093) and its regularity is not influenced by HD and LD; (5) the RR interval and SAP series are significantly, though weakly, synchronised (0.093) and their coupling increases during T, CR10 and CR15; (6) the RR interval and respiration are coupled (0.152) and their coupling increases during CR10; (7) SAP and respiration are significantly synchronised (0.108) and synchronisation increases during CR10; (8) MS and respiration are uncoupled and become coupled (0.119) after HD; (9) the RR interval, SAP and respiration are significantly co-ordinated (0.118) and co-ordination increases during CR10 and CR15; (10) during HD the co-ordination among SAP, MS and the respiratory signal is larger than that among the RR interval, SAP, MS and the respiratory signal, thus indicating that the RR interval contributes towards reducing co-ordination.

Atropine↗

PubMed2005

Calculation of rotational partition functions by an efficient Monte Carlo importance sampling technique.

The evaluation of the classical rotational partition function represented by a configuration integral over all external and internal rotational degrees of freedom of nonrigid chain polyatomic molecules is described. The method of Pitzer and Gwinn is used to correct the classical partition function for quantum mechanical effects at low temperatures. The internal rotor hindrance and all coupling arising from the external and internal rotational degrees of freedom are explicitly taken into account. Importance sampling Monte Carlo based on the adaptive VEGAS algorithm to perform multidimensional integration is implemented within the TINKER program package. A multidimensional potential energy hypersurface is calculated with the MM3(2000) molecular mechanics force field. Numerical tests are performed on a number of small n-alkanes (from ethane to octane), for which the absolute entropies calculated at three different temperatures are compared both with the experimental values and with the previous theoretical results. The application of a more efficient importance sampling technique developed here results in a substantial reduction of statistical errors in the evaluation of the configuration integral for a given number of Monte Carlo steps. Error estimates for the calculated entropies are given, and possible sources of systematic errors, and their importance for a reliable prediction of the absolute entropy, are discussed.

Algorithms↗

PubMed2001

Steady-state and picosecond time-resolved fluorescence studies on native and apo seed coat soybean peroxidase.

Seed coat soybean peroxidase (SBP) belongs to class III of the plant peroxidase super family. The protein has a very similar 3-dimensional structure with that of horseradish peroxidase (HRP-C). The fluorescence characteristics of the single tryptophan (Trp117) present in SBP and apo-SBP have been studied by steady-state and pico-second time-resolved fluorescence spectroscopy. Fluorescence decay curve of SBP was best described by a four exponential model that gave the lifetimes, 0.035 ns (97.0%), 0.30 ns (2.0%), 2.0 ns (0.8%), and 6.3 ns (0.2%). These lifetime values agreed very well with the values obtained by the model independent maximum entropy method (MEM). The three longer lifetimes that constituted 3% of the fluorophore population in the SBP sample are attributed to the presence of trace quantities of apo-SBP. The pico-second lifetime value of SBP is indicative of efficient energy transfer from Trp117 to heme. From fluorescence resonance energy transfer (FRET) calculations, the energy-transfer efficiency in SBP is found to be relatively higher as compared to HRP-C and is attributed mainly to the higher value of orientation factor, kappa(2) for SBP. Decay-associated spectra of SBP indicated that the tryptophan of SBP is relatively more solvent exposed as compared to HRP-C and is attributed to the various structural features of SBP. Linear Stern-Volmer plots obtained from the quenching measurements using acrylamide gave k(q) = 5.4 x 10(8) M(-1) s(-1) for SBP and 7.2 x 10(8) M(-1) s(-1) for apo-SBP and indicated that on removal of heme in SBP, Trp117 is more solvent exposed.

Entropy↗

PubMed2005

Detecting differentially expressed genes by relative entropy.

DNA microarray experiments have generated large amount of gene expression measurements across different conditions. One crucial step in the analysis of these data is to detect differentially expressed genes. Some parametric methods, including the two-sample t-test (T-test) and variations of it, have been used. Alternatively, a class of non-parametric algorithms, such as the Wilcoxon rank sum test (WRST), significance analysis of microarrays (SAM) of Tusher et al. (2001), the empirical Bayesian (EB) method of Efron et al. (2001), etc., have been proposed. Most available popular methods are based on t-statistic. Due to the quality of the statistic that they used to describe the difference between groups of data, there are situations when these methods are inefficient, especially when the data follows multi-modal distributions. For example, some genes may display different expression patterns in the same cell type, say, tumor or normal, to form some subtypes. Most available methods are likely to miss these genes. We developed a new non-parametric method for selecting differentially expressed genes by relative entropy, called SDEGRE, to detect differentially expressed genes by combining relative entropy and kernel density estimation, which can detect all types of differences between two groups of samples. The significance of whether a gene is differentially expressed or not can be estimated by resampling-based permutations. We illustrate our method on two data sets from Golub et al. (1999) and Alon et al. (1999). Comparing the results with those of the T-test, the WRST and the SAM, we identified novel differentially expressed genes which are of biological significance through previous biological studies while they were not detected by the other three methods. The results also show that the genes selected by SDEGRE have a better capability to distinguish the two cell types.

Acute Disease↗

PubMed1978

Application of immersional calorimetry to investigation of solid-liquid interactions: microcrystalline cellulose-water system.

A comprehensive characterization of the specific solid-liquid interaction for microcrystalline cellulose and water is presented. The procedure consisted of a conjoint vapor adsorption and immersional wetting experiment. The following information was obtained with respect to the solid. Estimates of the total surface are (138 m2/g) and the external surface (9.2 m2/g) were calculated from the adsorption and immersion data, respectively. Existence of an energetically homogeneous surface was verified by a linear decrease in the heat of immersion of samples containing adsorbed moisture approximately up to monolayer capacity. Integral and differential free energy, enthalpy, and entropy changes accompanying the adsorption process were calculated, and a lack of swelling was substantiated by comparison with a similar study of cellulose fibers. Immersional hysteresis was observed, and its magnitude suggested that sorption hysteresis was of enthalpic as well as entropic origin. The experimental method is potentially valuable for routine characterization of hydrophilic powders.

Adsorption↗

PubMed1988

Stoichiometry of electron uptake and oxidation-reduction midpoint potentials of NADH:nitrate reductase.

Microcoulometric titrations of NADH:nitrate reductase at 25 degrees C in Mops buffer, pH 7.0, showed that the native enzyme, containing functional FAD, haem and Mo, required addition of five electrons for complete reduction. Reduction of the native enzyme occurred in three waves corresponding to addition of reducing equivalents to the centres in the order: Mo, haem, FAD. Oxidation-reduction midpoint potentials (E'0) for the various redox couples were calculated to be as follows: MoVI/MoV, +16 mV; MoV/MoIV, -27 mV; haemoxidized/haemreduced, -172 mV; FAD/FADH2, -283 mV. The values for the haem and flavin are in excellent agreement with those obtained by visible titrations, namely -164 mV and -288 mV respectively. In contrast, the results for the Mo centre are 28-50 mV more positive than the values previously determined by e.p.r. analysis of frozen enzyme samples poised at defined potentials at 25 degrees C and suggest different pH-dependencies or entropies of reduction for the Mo couples.

Chlorella↗

PubMed2006

Thigh intermuscular fat is inversely associated with spontaneous GH release in post-menopausal women with abdominal obesity.

CONTEXT: The metabolic syndrome is characterized by an increased accumulation of visceral adipose tissue (VAT) and blunted GH secretion. There are, however, no data on the association between GH secretion and other fat depots (in liver and muscle). OBJECTIVE/DESIGN: The aim of this cross-sectional study, which included 20 post-menopausal women with abdominal obesity, was to determine the association between GH secretion and regional adipose tissue (AT) distribution. Twelve-hour GH profiles (2000-0800 h) were performed by blood sampling every 20 min. GH was analyzed using an ultra-sensitive assay followed by approximate entropy (ApEn) and deconvolution analysis. RESULTS: In simple regression analyses, both basal and pulsatile GH secretions correlated negatively with VAT and thigh intermuscular adipose tissue (IMAT), but not with hepatic fat content. There was no correlation between ApEn and the AT depots studied. In multiple regression analysis, pulsatile GH secretion correlated inversely with thigh IMAT (B-coefficient=-0.67; P<0.01), whereas the correlation with VAT became non-significant. Furthermore, in multiple regression analysis, basal GH secretion correlated negatively with VAT (B-coefficient=-0.77; P=0.001), but not significantly with thigh IMAT. CONCLUSION: In post-menopausal women with abdominal obesity, pulsatile GH secretion demonstrated an independent, negative association with thigh IMAT, whereas basal GH secretion showed an independent, negative association with VAT. These findings suggest that the neuroendocrine association between fat mass and somatotropic axis is depot-dependent. We have identified thigh IMAT to be important in this interplay.

Abdominal Fat↗

PubMed2000

Biased Brownian dynamics for rate constant calculation.

An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampling of trajectories is then biased, but the sampling is unbiased when the trajectory outcomes are multiplied by their weights. With a suitable choice of the biasing force, more reacted trajectories are sampled. As a consequence, the variance of the estimate is reduced. In our test case, biased Brownian dynamics gives a sevenfold improvement in central processing unit (CPU) time with the choice of a simple centripetal biasing force.

Biochemistry↗

PubMed2006

Structural relaxation of acetaminophen glass.

PURPOSE: The aim is to determine the structural stability of acetaminophen glass with time and temperature change, and to examine the merits of adapting the structural relaxation models of the glassy state for pharmaceuticals. METHODS: Differential scanning calorimetry technique has been used to study the acetaminophen glass after keeping the samples for various periods at fixed temperatures and after keeping at various temperatures for fixed periods. RESULTS: A general formalism for thermodynamic changes during storage in a temperature fluctuating environment is given and the kinetics of the enthalpy and entropy decrease determined. At a fixed temperature, the decrease occurs according to a non-exponential kinetics. For the same storage time, but at different temperatures, the enthalpy and entropy decrease rises to a maximum value at a certain temperature and then declines. The peak appears at the temperature at which the internally equilibrated state of the sample is reached for a fixed storage time. The change in the normalized heat capacity during the heating of acetaminophen has been analysed in terms of a non-exponential, non-linear enthalpy relaxation model. CONCLUSION: A single set of parameters that fit the data for unannealed acetaminophen glass does not fit the calorimetric data for annealed glass. Since acetaminophen molecules form intermolecular hydrogen-bonds in the crystal state and likely to form such bonds more easily in the disordered state, effect of such bonds on structural relaxation is likely to be significant.

Acetaminophen↗

PubMed2006

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models.

We present an extensive study on hydration thermodynamic properties of analogues of 13 amino acid side chains at 298 K and 1 atm. The hydration free energies DeltaG, entropies DeltaS, enthalpies DeltaH, and heat capacities Deltac(P)() were determined for 10 combinations of force fields and water models. The statistical sampling was extended such that precisions of 0.3, 0.8, 0.8 kJ/mol and 25 J/(mol K) were reached for DeltaG, TDeltaS, DeltaH, and Deltac(P)(), respectively. The three force fields used in this study are AMBER99, GROMOS 53A6, and OPLS-AA; the five water models are SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew. We found that the choice of water model strongly influences the accuracy of the calculated hydration entropies, enthalpies, and heat capacities, while differences in accuracy between the force fields are small. On the basis of an analysis of the hydrophobic analogues of the amino acid side chains, we discuss what properties of the water models are responsible for the observed discrepancies between computed and experimental values. The SPC/E water model performs best with all three biomolecular force fields.

Journal Article↗

PubMed2006

Soil risk assessment of As and Zn contamination in a coal mining region using geostatistics [corrected].

The present paper aims to map As and Zn contamination and assess the risk for agricultural soils in a wider disposal site containing wastes derived from coal beneficiation. Geochemical data related to environmental studies show that the waste characteristics favor solubilisation and mobilization of inorganic contaminants and in some cases the generation of acidic leachates. 135 soil samples were collected from a 34 km(2) area and analysed by using geostatistics under the maximum entropy principle in order to produce risk assessment maps and estimate the probability of soil contamination. In addition, the present paper discusses the main issues related to risk assessment in wider mining and waste disposal sites in order to assist decision makers in selecting feasible rehabilitation schemes.

Arsenic↗

PubMed2003

Retention mechanism of poly(ethylene oxide) in reversed-phase and normal-phase liquid chromatography.

The retention behavior of low- and high-molecular-mass poly(ethylene oxide) (PEO) in reversed-phase (RP) and normal-phase (NP) liquid chromatography was investigated. In RPLC using a C18 bonded silica stationary phase and an acetonitrile-water mixture mobile phase, the sorption process of PEO to the stationary phase showed deltaH(o) > 0 and deltaS(o) > 0. Therefore, PEO retention in RPLC separation is an energetically unfavorable, entropy-driven process, which results in an increase of PEO retention as the temperature increases. In addition, at the enthalpy-entropy compensation point the elution volume of PEO was very different from the column void volume. These observations are quite different from the RPLC retention behavior of many organic polymers. The peculiar retention behavior of PEO in RPLC separation can be understood in terms of the hydrophobic interaction of this class of typical amphiphilic compounds with the non-polar stationary phase, on the one hand, and with the aqueous mobile phase, on the other. The entropy gain due to the release of the solvated water molecules from the PEO chain and the stationary phase is believed to be responsible for the entropy-driven separation process. On the other hand, in NPLC using an amino-bonded silica stationary phase and an acetonitrile-water mixture mobile phase, PEO showed normal enthalpy-driven retention behavior: deltaH(o) < 0 and deltaS(o) < 0, with the retention decreasing with increasing temperature and PEO eluting near the column void volume at the enthalpy-entropy compensation point. Therefore, high-resolution temperature gradient NPLC separation of high-molecular-mass PEO samples can be achieved with relative ease. The molecular mass distribution of high-molecular-mass PEO was found to be much narrower than that measured by size-exclusion chromatography.

Chromatography, Liquid↗

PubMed2005

Inverse magnetocaloric effect in ferromagnetic Ni-Mn-Sn alloys.

The magnetocaloric effect (MCE) in paramagnetic materials has been widely used for attaining very low temperatures by applying a magnetic field isothermally and removing it adiabatically. The effect can also be exploited for room-temperature refrigeration by using giant MCE materials. Here we report on an inverse situation in Ni-Mn-Sn alloys, whereby applying a magnetic field adiabatically, rather than removing it, causes the sample to cool. This has been known to occur in some intermetallic compounds, for which a moderate entropy increase can be induced when a field is applied, thus giving rise to an inverse magnetocaloric effect. However, the entropy change found for some ferromagnetic Ni-Mn-Sn alloys is just as large as that reported for giant MCE materials, but with opposite sign. The giant inverse MCE has its origin in a martensitic phase transformation that modifies the magnetic exchange interactions through the change in the lattice parameters.

Alloys↗

PubMed1989

Neural coding of gustatory information in the thalamus of Macaca mulatta.

1. Extracellular action potentials were recorded from single neurons in the parvicellular division of the ventroposteromedial (VPMpc) nucleus of the thalamus of restrained, but alert, Old World monkeys during gustatory, tactile, and thermal stimulation of the oral cavity. In contrast to previous reports in anesthetized or paralyzed rats, the spontaneous activity of these neurons was brisk and their evoked responses robust. 2. Each of 50 taste-responsive neurons was tested with 1.0 M sucrose, 0.1 M NaCl, 0.003 M HCl, and 0.001 M QHCl before other concentrations of the same stimuli were used. Sucrose, which was effective in 80% of the neurons tested, evoked the largest responses of the 4 standard gustatory stimuli (16.1 spikes/s). The average response to NaCl, an effective stimulus for 44% of the neurons in the sample, was 7.5 spikes/s. HCl and QHCl, which few neurons responded to, typically evoked smaller responses. 3. Most of the neurons tested showed monotonic intensity-response (I-R) functions. The power functions showed about the same degree of compression (range = 0.39-0.53), which has been described previously for brain stem neurons in anesthetized rodents. Only 9.1% of the responses were inhibitory, and there was no tendency for these responses to be associated with either specific neurons or stimuli. These data suggest that quality coding of gustatory information in the thalamus is not radically different from that seen among lower-order neurons in other species. 4. Through the use of hierarchical cluster analysis, it was possible to divide the neuron sample into 2 groups, one of which consisted of sucrose-best neurons that had an average entropy value of 0.56. The neurons in the other group, though more heterogeneous, showed either primary or side-band sensitivity to NaCl. The average breadth of responsiveness of the 50 thalamic neurons as described by the entropy coefficient was 0.73. 5. In addition to gustatory neurons, tactile (n = 15), thermal (n = 1), and nonresponsive (n = 25) neurons also were located within VPMpc. An additional 48 neurons that could not be classified as either sensory or motor in nature, inhibited their bursting spontaneous discharge just prior to the onset of fluid stimulation. Only 2 of these neurons demonstrated differential chemical sensitivity. The presence of these nongustatory neurons within the thalamic taste area suggests that the traditional characterization of VPMpc as a gustatory relay may understate its role in ingestive behavior and ignore other noningestive functions of the area.

Animals↗

PubMed2000

Effect of weight loss on the pulsatile insulin secretion.

The aim of the study was to assess whether pulsatile insulin secretion is variable in the same individual and is related to changes in insulin sensitivity. Insulin sensitivity and pulsatility were measured before and after weight reduction in nine obese subjects. A pulsatility analysis was done using the PulsDetekt program. Blood was sampled every 2 min over a period of 90 min. The secretion randomness was quantified using approximate entropy (ApEn), and ApEn normalized by SD of the insulin time series (nApEn). Lower values indicate more regular secretion. Insulin sensitivity was measured using the homeostasis model assessment. Data are presented as median, minimum-maximum. After weight loss insulin sensitivity was increased (12.16, 7.60-76.70 vs. 38.96, 19.88-74.96%), the number of insulin pulses was reduced (11, 8-16 vs. 9,6-12), and they were more regular (ApEn, 0.92, 0.53-133 vs. 0.69,0,40-1.27; nApEn, 1.07, 0.74-1.33 vs. 0.97, 0.54-1.42). Before and after the weight loss there was a correlation between ApEn and nApEn and insulin sensitivity. Therefore, insulin secretion regularity is variable in the same individual and is related to insulin sensitivity.

Adult↗

PubMed2003

Genomic data sampling and its effect on classification performance assessment.

BACKGROUND: Supervised classification is fundamental in bioinformatics. Machine learning models, such as neural networks, have been applied to discover genes and expression patterns. This process is achieved by implementing training and test phases. In the training phase, a set of cases and their respective labels are used to build a classifier. During testing, the classifier is used to predict new cases. One approach to assessing its predictive quality is to estimate its accuracy during the test phase. Key limitations appear when dealing with small-data samples. This paper investigates the effect of data sampling techniques on the assessment of neural network classifiers. RESULTS: Three data sampling techniques were studied: Cross-validation, leave-one-out, and bootstrap. These methods are designed to reduce the bias and variance of small-sample estimations. Two prediction problems based on small-sample sets were considered: Classification of microarray data originating from a leukemia study and from small, round blue-cell tumours. A third problem, the prediction of splice-junctions, was analysed to perform comparisons. Different accuracy estimations were produced for each problem. The variations are accentuated in the small-data samples. The quality of the estimates depends on the number of train-test experiments and the amount of data used for training the networks. CONCLUSION: The predictive quality assessment of biomolecular data classifiers depends on the data size, sampling techniques and the number of train-test experiments. Conservative and optimistic accuracy estimations can be obtained by applying different methods. Guidelines are suggested to select a sampling technique according to the complexity of the prediction problem under consideration.

Computational Biology↗

PubMed2004

Smoking and respiratory irregularity in panic disorder.

BACKGROUND: The biological mechanisms underlying the link between smoking and panic attacks are unknown. Smoking might increase the risk of panic by impairing respiratory system function. METHODS: We evaluated the effect of smoking on respiratory irregularity in patients with panic disorder (PD) and healthy comparison subjects and the role of the respiratory disorders in this effect. We applied the Approximate Entropy index (ApEn), a nonlinear measure of irregularity, to study breath-by-breath baseline respiratory patterns in our sample. RESULTS: Both smoker and nonsmoker patients had more irregular respiratory patterns than healthy subjects. Smoker patients showed higher ApEn indices of baseline respiratory rate and tidal volume than nonsmoker patients (R = 5.4, df = 2,55, p < .01), whereas smoking in healthy subjects did not influence the regularity of respiratory patterns. Respiratory disorders did not account for the influence of smoking on respiratory irregularity. Smokers had more severe panic attacks than nonsmokers. CONCLUSIONS: Smoking may impair vulnerable respiratory function and act as disruptive factor on intrinsic baseline respiratory instability in patients with PD, possibly influencing the onset or maintenance of the disorder.

Adult↗