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PubMed2001

Discriminating the relation between relations: the role of entropy in abstract conceptualization by baboons (Papio papio) and humans (Homo sapiens).

Two baboons (Papio papio) successfully learned relational matching-to-sample: They picked the choice display that involved the same relation among 16 pictures (same or different) as the sample display, although the sample display shared no pictures with the choice displays. The baboons generalized relational matching behavior to sample displays created from novel pictures. Further experiments varying the number of sample pictures and the mixture of same and different sample pictures suggested that entropy plays a key role in the baboons' conceptual behavior. Two humans (Homo sapiens) were similarly trained and tested; their behavior was both similar to and different from the baboons' behavior. The results suggest that animals other than humans and chimpanzees can discriminate the relation between relations. They further suggest that entropy detection may underlie same-different conceptualization, but that additional processes may participate in human conceptualization.

Animals↗

PubMedDate not supplied

[Evolution as resistance to entropy. I. Mechanisms of species homeostasis].

The idea is discussed that the common output of any evolution is creation of the entities that are increasingly resistant to further evolution. The moving force of evolution is entropy, the tendency to disorder. This general aspiration for chaos is a cause of the mortality of organisms and species, however, being prerequisite for any movement, it creates (by chance) novelties, which may occur (by chance) more resistant to further decay and thus survive. The surviving of those who survive is the most general principle of evolution discovered by Darwin for particular case of biological evolution. The second law of thermodynamics states that our Universe is perishing but its ontology is such that it creates resistance to destruction. The evolution is a history of this resistance. Not only those who die do not survive but also those who evolve. The entities that change (evolve) rapidly disappear rapidly and by this reason they are not observed among both the fossils and now-living organisms. We know only about long-living species. All the existing organisms are endowed with an ability to resist other changing. The following main achievements of the species homeostasis are discussed: high fidelity of DNA replication and effective mechanisms of DNA repair; diploidy; normalizing selection; truncated selection; heterozygote superiority; ability to change phenotype adaptively without changing genotype; parental care and the K-strategy of reproduction; behavior that provides independence of the environment. The global resistance of the living systems to entropy is provided the state that all the essential in biology is determined not by physical-chemical interactions but could semantic rules. A conception of "potential zygotic information" that determines the rules of ontogenesis is proposed. A zygote does not contain this information in explicit form. It is created de novo step by step during ontogenesis and it could not be decoded beforehand. The experimental data on the adaptive mutagenesis and the relevant hypothesis are discussed. It is concluded that the special mechanisms for speeding-up of evolution as created by evolution are impossible conceptually.

Adaptation, Biological↗

PubMed2005

Effects and wavelet spectral entropy analysis of rhubarb extracts rhein on synaptic transmission in rat hippocampal ca1 area in vitro.

BACKGROUND: 5-dihydroxyanthraquinone-2-carboxylic acid (rhein) inhibits oxidoreduction induced by reducing nicotingamide adenine dinucleotide in the mitochondria and reducing reactive oxygen species, it also suppresses lipid peroxidation in rat brain homogenates. This study was to assess the effects of anthraquinone derivatives, rhein on synaptic transmission in the rat hippocampal CA1 pyramidal cell layer by intracellular recording. METHODS: The excitatory postsynaptic potential (EPSP) evoked by stimulation of the Schaffer collaterals in the presence of bicuculline (15 micromol/L) was depressed by application of rhein (0.3 - 30 micromol/L). The amplitude of the EPSP was restored within 20 minutes after removal of rhein from the supernatant. At a concentration of 30 micromol/L, rhein reduced the amplitude of the EPSP to 42% +/- 3.7% (n = 24) of the control. Subsequently, wavelet spectral entropy was used to analyze the EPSP. RESULTS: A strong positive correlation was observed between the wavelet spectral entropy and other parameters such as amplitude, slope of rising phase and slope of descending phase of the EPSP. The paired-pulse facilitation (PPF) of the EPSP was significantly increased by rhein (30 micromol/L). The inhibitory postsynaptic potential (IPSP) recorded in the presence of CNQX (20 micromol/L) and APV (40 micromol/L) is not altered by rhein (30 micromol/L). CONCLUSIONS: Rhein (30 micromol/L) can decrease the frequency but not the amplitude of the miniature EPSP (mEPSP). It is suggested that rhein inhibits excitatory synaptic transmission by decreasing the release of glutamate in rat hippocampal CA1 pyramidal neurons.

Animals↗

PubMed2005

[Approximate entropy analysis of fetal heart rate variability and its application in the diagnosis of fetal distress].

To introduce approximate entropy (ApEn) in the analysis of fetal heart rate variability (FHRV) and to discuss the relationship between the ApEn values and perinatal outcomes, 67 computerized cardiotocographs were recorded. Approximate entropy and index in time domain were used to analyze FHRV. After childbirth, the neonatal Apgar scores were recorded and umbilical cord arterial blood gas analyses were performed. The results showed the ApEn values of FHRV were correlated with pH, Pco2, Po2, HCO3-, ABE, SO2 and neonatal Apgar scores (r = 0.51, -0.29, 0.49, 0.29, 0.45, 0.56, 0.28, respectively, P < 0.05). The ApEn values for acidotic fetuses (pH less than 7.20) were significantly different from those of normal fetuses (P < 0.01), however the time domain parameters of FHRV were unable to identify the difference. The results suggest that the ApEn values of FHRV are closely related to the fetal hypoxia and acidemia. Thus the ApEn analysis appears to be useful for improving the sensitivity in the diagnosis of fetal distress.

Apgar Score↗

PubMed1997

Loss of translational entropy in binding, folding, and catalysis.

There is a loss of translational entropy associated with the formation of a complex between two molecules in solution. Estimation of this contribution is essential for understanding binding, protein-protein association, and catalysis. Based on the cell model of liquids, it is possible to estimate the loss of translational entropy in all these cases. The resulting formulas are straightforward, and the calculations are easy to perform. Comparison of the results with experimental data suggests that the proposed method provides estimates that are much more accurate than those obtained with existing methods.

Catalysis↗

PubMed1993

Volume changes correlate with entropies and enthalpies in the formation of nucleic acid homoduplexes: differential hydration of A and B conformations.

We have used a combination of densimetric, calorimetric, and uv absorption techniques to obtain a complete thermodynamic characterization for the formation of nucleic acid homoduplexes of known sequence and conformation. The volume change delta V accompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 mM sodium phosphate buffer at pH 7, the magnitude of the measured delta V's ranged from -2.0 to +7.2 ml/mol base pair and followed the order of poly(rA).poly(dT) approximately poly(dA).poly(dT) < poly(rA).poly(dU) approximately poly(rA).poly(rU). Inclusion of 100 mM NaCl in the same buffer gave the range of -17.4 to -2.3 mL/mol base pair and the following order: poly(dA).poly(dT) < poly(rA).poly(dT) < poly(rA).poly(rU) approximately poly(rA).polyr(dU). Standard thermodynamic profiles of forming these duplexes from their corresponding complementary single strands indicated similar free energies that resulted from the compensation of favorable enthalpies with unfavorable entropies along with a similar counterion uptake at both ionic strengths. The differences in these compensating effects of entropy and enthalpy correlated very well with the volume change measurements in a manner suggesting that the homoduplexes in the B conformation are more hydrated than are those in the A conformation. Moreover, the increased thermal stability of these homoduplexes resulted from an increase in the salt concentration corresponding to larger hydration levels as reflected by the delta V results.

Calorimetry↗

PubMed2002

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

The prediction of a ligand binding constant requires generating three-dimensional structures of the complex concerned and reliably scoring these structures. Here, the scoring problem is investigated by examining benzamidine-like inhibitors of trypsin, a system for which errors in the structures are small. Precise and consistent binding free energies for the inhibitors are determined experimentally for this test system. To examine possible improvement of scoring methods, we test the suitability of continuum electrostatics to account for solvation effects and use an ideal-gas entropy correction to account for the changes in the degrees of freedom of the ligand. The small observed root-mean-square deviation of 0.55 kcal/mol of the calculated relative to the experimental values indicates that the essentials of the binding process have been captured. Even though all six ligands make the same salt bridge and H-bonds to the protein, the electrostatic contribution varies among the ligands by as much as 2 kcal/mol. Moreover, although the ligands are rigid and similar in size, the entropic terms also significantly affect the relative binding affinities (by up to 2.7 kcal/mol). The present approach to solvation and entropy may allow the ranking of the ligands to be considerably improved at a cost that makes the method applicable to the optimization of lead compounds or to the screening of small collections of ligands.

Journal Article↗

PubMed1993

Application of electrospray ionization mass spectrometry with maximum-entropy analysis to allelic 'fingerprinting' of major urinary proteins.

Mixtures of a specific group of proteins, the major urinary proteins (MUPs), believed to have a role in odorant binding, have been analysed by electrospray ionization mass spectrometry. The data obtained from conventional transformed electrospray data confirm that the molecular weights of the protein mixtures, deduced from published sequences, lie in the molecular weight range 18,600 to 19,000 Da. Application of maximum-entropy analysis to the raw electrospray data has confirmed a heterogeneity in MUP composition, consistent with allelic similarities (and differences) between the different mouse strains. This work demonstrates the use of maximum entropy in the assessment of protein content and in the subsequent resolution enhancement of naturally occurring protein mixtures containing components of closely similar molecular mass.

Alleles↗

PubMed1994

Maximum entropy deconvolution of heterogeneity in protein modification: protein adducts of 4-hydroxy-2-nonenal.

To explore the chemistry of the reactions of the cytotoxic aldehyde trans-4-hydroxy-2-nonenal (HNE) with proteins, we incubated this aldehyde in vitro with beta-lactoglobulin B, a model protein of molecular weight 18,277 Da. Direct characterization of reaction products using electrospray ionization mass spectrometry yielded spectra whose complexity suggested extensive product heterogeneity. Spectra were transformed to a true mass scale using both a conventional transform algorithm and a maximum entropy algorithm. Both transformations demonstrated the formation of aldehyde-protein adducts containing from three to nine aldehyde molecules per molecule of protein. Maximum entropy deconvolution resolved Schiff base adducts and/or dehydration products, differing from the Michael addition adducts by 18 Da. The dominant reaction pathway, however, was Michael addition of the aldehyde to nucleophilic functional groups on the protein. The large number of Michael adducts relative to the one available cysteine requires that other amino acids, such as histidine and lysine, also be modified. The data suggest that methods for analysis of HNE that involve displacement of Schiff base groups from proteins will only recover a small fraction of HNE.

Aldehydes↗

PubMed1994

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy.

Understanding the relations between the conformation of the side-chains and the backbone geometry is crucial for structure prediction as well as for homology modelling. To attempt to unravel these rules, we have developed a method which allows us to predict the position of the side-chains from the co-ordinates of the main-chain atoms. This method is based on a rotamer library and refines iteratively a conformational matrix of the side-chains of a protein, CM, such that its current element at each cycle CM (ij) gives the probability that side-chain i of the protein adopts the conformation of its possible rotamer j. Each residue feels the average of all possible environments, weighted by their respective probabilities. The method converges in only a few cycles, thereby deserving the name of self consistent mean field method. Using the rotamer with the highest probability in the optimized conformational matrix to define the conformation of the side-chain leads to the result that on average 72% of chi 1, 75% of chi 2 and 62% of chi 1 + 2 are correctly predicted for a set of 30 proteins. Tests with six pairs of homologous proteins have shown that the method is quite successful even when the protein backbone deviates from the correct conformation. The second application of the optimized conformational matrix was to provide estimates of the conformational entropy of the side-chains in the folded state of the protein. The relevance of this entropy is discussed.

Amino Acids↗

PubMed1994

Carcinogenesis, genetic instability and genomic entropy: insight derived from malignant brain tumor age specific mortality rate dynamics.

Aging-related carcinogenesis has been attributed to inherent genetic instability, which manifests in a multistep fashion by activation of oncogenes and inactivation of tumor suppressor genes. Malignant brain tumor cells display multiple-characteristic acquired genetic abnormalities in oncogenes and tumor suppressor genes. Age-specific malignant brain tumor mortality rates in the United States from 1962 to 1988 were interpreted by longitudinal Gompertzian analysis. Utilizing a thermodynamic perspective of the Strehler-Mildvan modification of the Gompertz relationship between mortality and aging, a measure of the rate of increase in informational entropy for those genetic factors involved in the carcinogenesis of malignant brain tumor was determined. Aging-related carcinogenesis can be viewed as a natural consequence of increasing informational entropy of the genome.

Adult↗

PubMed1996

High statistics block entropy measures of DNA sequences.

We have used an improved block-entropy measure in order to gain some further insights into the short-range correlations present in whole chromosomes of S. cerevisiae, viruses and organelles and very large genomic regions of E. coli. Although DNA sequences are largely inhomogeneous and word frequencies are unevenly distributed, the comparison of entire chromosomes and large genomic regions show a "bulk" composition homogeneity. This property suggests that biases in selection, directional mutational pressure and recombination processes act in homogenizing the base composition of the DNA molecules within a genome but their mode of action, relative impact and direction may vary in different organisms. The most interesting results appear to be the differences between the SW (C,G/A,T) and RY (A,G/C,T) two-letter alphabet entropies. Deviations from randomness in E. coli and S. cerevisiae sequences particularly concern SW dinucleotide frequencies and RY tetranucleotide frequencies.

Base Sequence↗

PubMedDate not supplied

Entropy of the genetic information and evolution.

The entropy of the amino acid sequences coded by DNA is considered as a measure of diversity of variety of proteins, and is taken as a measure of evolution. The DNA or m-RNA sequence is considered as a stationary second-order Markov chain composed of four kinds of bases. Because of the biased nature of the genetic code table, increase of entropy of amino acid sequences is possible with biased nucleotide sequence. Thus the biased DNA base composition and the extreme rarity of the base doublet CpG of higher organisms are explained. It is expected that the amino acid composition was highly biased at the days of the origin of the genetic code table, and the more frequent amino acids have tended to get rarer, and the rarer ones more frequent. This tendency is observed in the evolution of hemoglobin, cytochrome C, fibrinopeptide, immunoglobulin and lysozyme, and protein as a whole.

Amino Acid Sequence↗

PubMed1981

Entropy measures of signal in the presence of noise: evidence for 'byte' versus 'bit' processing in the nervous system.

A method for detecting signal in the presence of noise in a highly specific way is described. Using action potential interval data from 12 neurons in rat cerebellum, we have demonstrated that the sequential ordering of spike intervals contains both noise and signal. We have identified and quantified the magnitude of relative entropy (uncertainty) of specified sets of interval patterns, ranging in length from 3-5 successive intervals. Some of these sets have exceptionally low entropy and thus seem to be especially meaningful as a set ('word') to the brain.

Action Potentials↗

PubMed1985

Comparison of the entropy-driven polymerization reactions of E66 and vulgare tobacco mosaic virus proteins.

The effects of temperature (T), ionic strength (mu), and pH on the polymerization of the coat protein of the E66 strain of tobacco mosaic virus (TMV) from the 4 S form (A), a trimer of the polypeptide chain, to the 20 S form (D) were investigated by the method of sedimentation velocity. Interpretations of thermodynamic parameters were based on only those data obtained in experiments for which reversibility could be demonstrated both by lowering temperature and by lowering concentration. E66 protein differed from vulgare TMV in that, in position 140, lysine replaced asparagine. Thus, E66 protein should be less hydrophobic than vulgare protein and K's, the salting-out constant, should be less. The charge on unpolymerized E66 protein was -3 proton units per polypeptide chain, compared to -4 for vulgare protein. The electrical work contribution, delta W*el, for E66 protein should be (-3/-4)2, or 0.5625 that for vulgare. The results were that delta W*el at pH 6.7, 15 degrees C, and mu = 0.1 was 0.700 kcal/mol for E66 protein compared to 1.22 for vulgare. The experimental ratio was 0.574; K's = 2.16 for E66 compared to 4.93 for vulgare. Hydrogen ions (1.5) were bound per A unit, or 0.5 per polypeptide chain, in the formation of D from A. delta H*, the enthalpy change per mole of A, was 33 kcal at pH 6.7 and 36 at pH 6.9, compared to 30 at both pH values for vulgare protein. delta S*, the entropy change per mole of A, was +132.1 e.u. for E66 compared to 127.4 for vulgare. Entropy-driven processes are found in dynamic biological situations. Ready reversibility at biological temperatures is a requirement, yet the polymer structures must be strong and well ordered. This is achieved through a large number of weak bonds between subunits, combined with ready reversibility under slightly changed conditions. The significant role of water is to facilitate depolymerization by binding to subunits.

Biopolymers↗

PubMed1992

Alcohol interaction with high entropy states of macromolecules: critical temperature hypothesis for anesthesia cutoff.

Nerve excitation generates heat and decreases the entropy (review by Ritchie and Keynes (1985) Q. Rev. Biophys. 18, 451-476). The data suggest the existence of at least two thermodynamically identifiable states: resting and excited, with a thermotropic transition between the two. We envision that nerve excitation is a transition between the two states of the excitation machinery consisting of proteins and lipids, rather than the sodium channel protein alone. Presumably, both proteins and lipids change their conformation at excitation. We proposed (Kaminoh et al. (1991) Ann. N.Y. Acad. Sci. 625, 315-317) that anesthesia occurs when compounds have a higher affinity to the resting state than to the excited state of excitable membranes, and that there is a critical temperature above which the affinity to the excited state becomes greater than to the resting state. When the temperature exceeds this critical level, compounds lose their anesthetic potency. We used thermotropic phase-transition of macromolecules as a model for the excitation process. Anesthetic alcohols decreased the main transition temperature of dipalmitoylphosphatidylcholine (DPPC) membranes and also the temperature of the alpha-helix to beta-sheet transition of poly(L-lysine). The affinity of alcohols to the high- and low-temperature states of the DPPC membranes were separately estimated. The difference in the affinity of n-alcohols to the liquid (high-temperature) and solid (low-temperature) states correlated with their anesthetic potency. It is not the total number of bound anesthetic molecules that determines the anesthesia, rather, the difference in the affinity between the higher and lower entropy states determines the effects. The critical temperatures of the long-chain alcohols were found to be lower than those of the short-chain alcohols. Cutoff occurs when the critical temperature of long-chain alcohols is below the physiological temperature, such that the anesthetic potency is not manifested in the experimental temperature range.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1978

Thermodynamic studies of the interaction of alpha-chymotrypsin with water. II. Statistical analyses of the enthalpy-entropy compensation effect.

Differential enthalpies (deltaH) and entropies (deltaS) of the interaction of water with a high and low temperature conformer of alpha-chymotrypsin were determined previously by multitemperature sorption measurements. The changes in (deltaH) and (deltaS) with water content of the protein were found to show a pronounced compensation pattern. It is known that van 't Hoff data may exhibit enthalpy-entropy compensation, which is entirely due to statistical error propagation. To discriminate between artifactual and significant compensation, the experimental results are analyzed by statistical methods. The results of two different statistical analyses show that a linear, chemically caused compensation effect can be established for the interaction of water with both chymotrypsin conformers. The compensation temperature beta = deltaH/deltaS was found to be 433 +/- 22 K. The compensation effect is detectable only in the water content range above the monolayer volume (upsilonm), computed by the Brunauer, Emmett and Teller equation. This result is discussed in terms of a monolayer hydration mechanism, formulated on the basis of previous thermodynamic results: The interaction of the first water monolayer with the charged and polar surface area of the dry protein, largely stabilizes its tertiary structure. Further water addition then occurs to a practically invariable protein surface. According to this mechanism (which ensures a maximum of conformational stability with a minimum of hydration water), large conformational changes can be expected to occur mainly in the monolayer water content range. This expectation is confirmed by extra-thermodynamic data (infrared and X-ray measurements). The thermodynamic quantities of the sorption process are thus governed by conformational effects below upsilonm. Above the monolayer water content range, however, the water binding process per se strongly predominates. The deltaH/deltaS compensation effect established for this water content range, is thus attributable to phase transitions of water molecules from the gas (or liquid) phase to the protein-bound state (or vice versa). A possible relationship between the linear compensation effect established in this study, and the compensation phenomenon observed in reactions in aqueous solution is discussed.

Calorimetry↗

PubMed1978

Thermodynamic studies of the interaction of alpha-chymotrypsin with water. I. Determination of the isosteric enthalpies and entropies of water binding to the native enzyme.

The enthalpies (deltaH) and entropies (deltaS) of the interaction of water with alpha-chymotrypsin were evaluated from multitemperature sorption isotherms in the temperature range 283--313 K, determined in a fully automatized, computer controlled sorption apparatus. The temperature dependence of deltaH and deltaS shows a marked anomaly in the temperature range 295--298 K. The experimental results are interpreted by a phase transition of the enzyme protein, and by the existence of a low- and high-temperature conformer of alpha-chymotrypsin below and above the transition region. The two conformers differ significantly in their water binding energetics, as proved by two F-tests based on analyses of variance. The deltaH and deltaS versus water content functions of the high and low temperature conformer show markedly different anomalies at and below 70 mol H2O per mol protein. This water content corresponds closely to the monolayer volume vm, (as defined by Brunauer, Emmett and Teller). The protein surface covered by one water-monolayer, agrees well with the polar and charged surface area of chymotrypsin, computed from X-ray data. The experimental results suggest that the interaction of the first water-monolayer with the protein surface induces major conformational changes. The energetic contributions of these structural changes dominate the deltaH and deltaS terms below vm, giving rise to the anomalies observed. Above this water content, their influence is drastically reduced, and the isosteric quantities are predominantly determined by the water binding process per se. This process is possibly related to the pronounced enthalphy-entropy compensation pattern exhibited by the deltaH and deltaS terms. A more detailed analysis and discussion of this compensation effect will be given.

Calorimetry↗