SEARCH · PubMed Health

Results for “Entropy”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources

PubMed1998

Young child injury analysis by the classification entropy method.

The project 'The Register and Preventive Programs for Accidents and Injuries' enabled data collection on all the injured who sought medical aid in Koprivnica County (population 61,052), Croatia, since 1992. Children aged 1-4 years are 5.03% of the whole population of the district. Complex injury attributes were analysed. Binary attributes were classified as input: age, gender, place of injury; and output: severity of injury. A new application of information entropy was introduced and applied to the classification of injury-causes attributes. The information entropy was calculated for the classification of input attributes according to the minimum information content. The decision procedure is given as a sequential procedure separating important from unimportant causes of injury at each decision level. Thus a decision tree with increasing entropy, i.e. decreasing determinism, was obtained showing that age (0.5347 N), place (0.6062 N) and gender (0.6105 N) are measurable attributes in child injury ascertainment in a descending pattern. It was shown that this method is, at the same time, an optimal way of using an attribute decision process of injury causes classification.

Accidents↗

PubMed2003

Entropy loss in long-distance DNA looping.

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow us to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor in comparison to both k(B)T and typical bond energies in biopolymers, which has to be overcome by the released bond energy between the looping contact sites.

Binding Sites↗

PubMed1998

Entropy-driven intermediate steps of oxygenation may regulate the allosteric behavior of hemoglobin.

When the oxygen binding isotherms of human, bovine and fallow deer (Dama-Dama) hemoglobins are measured at different temperatures either by optical or calorimetric techniques, analyses according to the Adair's formalism show that at least one of the intermediate steps of ligation has a positive enthalpy change, i.e., absorbs rather than emitting heat, indicating that it is entropy rather than enthalpy driven (Bucci, E., et al. 1991. Biochemistry. 30:3195-3199; Bucci, E., et al. 1993. Biochemistry. 32:3519-3526; Johnson, C., et al. 1992. Biochemistry. 31:10074-10082; Johnson, C., et al. 1995. Biophys. Chem. 59:107-117). This phenomenon is confirmed in systems in which the beta82 lysines of human hemoglobin are covalently cross-linked by acylation with dicarboxylic acids of increasing length, namely the fumaryl (four-carbon-long), adipoyl (six-carbon-long), and sebacoyl (10-carbon-long) residues. Consistently in all of the systems here reported, the enthalpy excursions are masked by compensatory entropy changes, which keep the free energy of ligand binding constant for the first three steps of oxygenation. Furthermore, the cooperativity index and the overall oxygen affinity seem to be correlated to the positive enthalpy excursions of the intermediate steps of ligation. Fumaryl-Hb (hemoglobin cross-linked with a fumaryl residue, four carbons) with the lowest absorption of heat has the highest affinity and lowest cooperativity index. Adipoyl-Hb (hemoglobin cross-linked with an adipoyl residue, six carbons) has the highest absorption of heat and the highest cooperativity index. It appears that nonuniform heat release by the intermediates of oxygenation is part of the allosteric phenomena in hemoglobin systems. There is not enough information that would allow assigning these phenomena to the interplay of the various conformations described for hemoglobin besides the classic T (Fermi et al. 1984. J. Mol. Biol. 175:159-174) and R (Shanaan. 1983. J. Mol. Biol. 171:31-59), as listed at the end of the Discussion. The possibility cannot be excluded that entropy-driven steps characterize new conformational transitions still to be described.

Adipates↗

PubMed2003

Entropy convergence in hydrophobic hydration: a scaled particle theory analysis.

The occurrence of entropy convergence in hydrophobic hydration is verified from available experimental thermodynamic data for both noble gases and hydrocarbons. The entropy convergence phenomenon can be reproduced by means of the scaled particle theory, provided that a temperature-dependent hard sphere diameter is used for water molecules. The calculated work of cavity creation shows a non-monotonic temperature dependence with a flat maximum slightly above 100 degrees C, irrespective of the cavity size. The corresponding cavity entropy changes converge approximately 100 degrees C, in qualitative agreement with the experimental finding.

Entropy↗

PubMed1996

A two-dimensional extension of minimum cross entropy thresholding for the segmentation of ultrasound images.

Segmentation is often an important step in medical image analysis. The local entropy is a possible variable for segmenting ultrasound images containing fluid surrounded by a soft tissue. A commonly used tool for image segmentation is thresholding. Recently, a new thresholding technique, known as "minimum cross entropy thresholding" (MCE), has been proposed. We present a multivariate extension of MCE in which the segmented variable (gray level) is replaced by a weighted combination of several image parameters. We propose to use a bivariate extension of MCE, which uses a linear combination of the gray level and the local entropy. The results obtained are demonstrated for ultrasound images of ovarian cysts.

Algorithms↗

PubMed2002

Entropy and complexity of finite sequences as fluctuating quantities.

The paper is devoted to the analysis of digitized sequences of real numbers and discrete strings, by means of the concepts of entropy and complexity. Special attention is paid to the random character of these quantities and their fluctuation spectrum. As applications, we discuss neural spike-trains and DNA sequences. We consider a given sequence as one realization of finite length of certain random process. The other members of the ensemble are defined by appropriate surrogate sequences and surrogate processes. We show that n-gram entropies and the context-free grammatical complexity have to be considered as fluctuating quantities and study the corresponding distributions. Different complexity measures reveal different aspects of a sequence. Finally, we show that the diversity of the entropy (that takes small values for pseudorandom strings) and the context-free grammatical complexity (which takes large values for pseudorandom strings) give, nonetheless, consistent results by comparison of the ranking of sample sequences taken from molecular biology, neuroscience, and artificial control sequences.

Action Potentials↗

PubMed1999

Using entropies of reaction to predict changes in protein stability: tyrosine-67-phenylalanine variants of rat cytochrome c and yeast Iso-1 cytochromes c.

Using the voltammetric method of square-wave voltammetry, a direct electrochemical examination was made of the wild type and Tyr67Phe mutant of both rat cytochrome c and yeast iso-1-cytochrome c. In addition to determining the equilibrium reduction potential (E0') for each cytochrome, the entropy of reaction, deltaS0'(Rxn)(deltaS0'(Rxn) = S0'(Red) - S0'(Ox)), for the reduction process was determined via the non-isothermal method. Having determined deltaS0'(Rxn) and E0', deltaH0' was calculated. For rat cytochrome c, it was found that deltaS0'(Rxn) = -43 J mol(-1) K(-1) for the wild type and -53 J mol(-1) K(-1) for the Tyr67Phe variant, with the deltaH0' for both the wild type and variant nearly identical, indicating that the changes in reduction potential and probably stability are due to changes in deltaS0'(Rxn). In contrast the measured deltaS0'(Rxn) for yeast iso-1-cytochrome c demonstrated significant changes in both entropic and enthalpic contributions in going from wild type to mutant cytochrome c. The entropy of reaction provides information regarding the relative degree of solvation, and very likely the degree of compactness, of the oxidized state versus the reduced state of the redox protein. A thermodynamic scheme and stability derivation are presented that show how the entropies of reaction of wild type versus variant cytochromes contribute to and predict changes in stability in going from oxidized to reduced protein. For yeast iso-1-cytochrome c, the thermodynamically predicted change in stability was very close to the experimentally observed value, based on previous differential scanning calorimetric stability measurements. While such data is not available for rat cytochrome c, consideration of the enormously increased local stability of the rat oxidized cytochrome c variant predicts that the reduced rat variant will be even more stable than the already stabilized oxidized variant.

Algorithms↗

PubMed2001

H-BloX: visualizing alignment block entropies.

H-BloX is a web-based JavaScript application that allows the calculation and visualization of Shannon information content or relative entropy (Kullback-Leibler 'distance') within sequence alignment blocks. The application was designed for use in both teaching and research. Amino acid, nucleic acid sequences, or any other type of aligned chemical structures may serve as the input. Various interpretations of the meaning of 'entropy' or 'information content' are possible, including treatment as a chemical diversity measure or the degree of feature conservation. For analysis of numerical data by H-BloX, values must be converted to a user-defined character alphabet before computation of entropy or information content. H-BloX was successfully applied to feature identification in Escherichia coli signal peptides and their cleavage sites. Characteristics known features became visible, e.g., the hydrophobic core region and the well-known '-3,-1' cleavage site pattern. Based on the H-BloX analysis, the hydrophobic core is centered at amino acid residue position 13, counting from the N-terminal end of the protein precursor sequence. This result was obtained by using a built-in feature of H-BloX that enables conversion of amino acid sequences to a different alphabet that is based on hydrophobicity assignments. H-BloX can be accessed online or downloaded as HTML/JavaScript at http://bopwww.biologie.uni-freiburg.de/~bioinfo/HBloX/html/index.html.

Bacterial Proteins↗

PubMed2004

Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins.

A protein molecule exists in either a compact folded state or a variable and open unfolded state. Since the unfolded state is favored by chain entropy, restricting its entropy is an attractive mechanism for shifting the equilibrium toward the folded state. A number of entropy-based strategies have been engineered or used by natural proteins to increase the folding stability: (a) shortening of loop lengths, (b) covalent linkage of dimeric proteins, (c) backbone cyclization, (d) catenation, (e) spatial confinement, and (f) macromolecular crowding. Theoretical analyses demonstrate the importance of accounting for consequences on the folded as well as the unfolded state and provide guidance for further exploitation of these stabilization strategies.

Animals↗

PubMed2003

Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics.

All-atom, explicit water molecular dynamics simulations of calcium-loaded calmodulin complexed with a peptide corresponding to the smooth muscle myosin light chain kinase target were carried out at 295 and 346 K. Amide and side chain methyl angular generalized order parameters were calculated and analyzed in the context of the protein's structure and dynamics. The agreement between amide order parameters measured by NMR and those from the simulations was found to be good, especially at the higher temperature, indicating both better convergence for the latter and excellent transferrability of the CHARMM parameters to the higher temperature. Subtle dynamical features such as helix fraying were reproduced. A large range of order parameters for the nine calmodulin methionines was observed in the NMR, and reproduced quite well in the simulations. The major determinant of the methionine order parameter was found to be the proximity to side chains of aromatic residues. An upper bound estimate of the difference in backbone entropy between loop and helical regions was extracted from the order parameters using a model of motion in an effective potential. Although loop regions are more flexible than helical regions, it was found that the entropy loss per residue upon folding was only approximately 20% less for loops than for helices. Pairwise correlated motions, which could significantly lower entropy estimates obtained from order parameter analysis alone, were found to be largely absent.

Amides↗

PubMed1997

Entropy-driven interactions of anesthetics with membrane proteins.

Thermodynamic analysis of anesthetic effects on Ca2+-ATPase activity was performed to evaluate the feasibility of anesthetic binding and gain insight into the molecular events underlying the anesthetic-enzyme interactions. The Ca2+-ATPases, integral membrane proteins vital in cellular Ca2+ regulation, are suitable models for investigation of the mechanism of anesthetic action on membrane proteins that are targeted by the anesthetics. Ca2+-ATPase of plasma membrane, PMCA, and SERCA1 in the intracellular sarcoplasmic reticulum membrane were used to study two general anesthetics: halothane, a halogenated two-carbon alkane; and propofol, an intravenous, strongly lipophilic-substituted phenol. Interactions of both anesthetics result in a negative Gibbs free energy change, which in both enzymes is more favorable for the more lipophilic propofol than halothane. Temperature dependence (more negative change in Gibbs free energy at increased temperature) is in agreement with predominantly nonpolar interactions. The interactions are entropy-driven, characterized by positive enthalpy which is overcompensated by positive entropy changes. This is in contrast to the reported in literature enthalpy-driven anesthetic binding to soluble proteins. The possible contributions to the observed positive entropy change are discussed including displacement of ordered water molecules by anesthetic binding in nonpolar cavities in the membrane proteins and subtle structural rearrangements.

Anesthetics↗

PubMedDate not supplied

Distinguishing between natural products and synthetic molecules by descriptor Shannon entropy analysis and binary QSAR calculations.

Molecular descriptors were identified by Shannon entropy analysis that correctly distinguished, in binary QSAR calculations, between naturally occurring molecules and synthetic compounds. The Shannon entropy concept was first used in digital communication theory and has only very recently been applied to descriptor analysis. Binary QSAR methodology was originally developed to correlate structural features and properties of compounds with a binary formulation of biological activity (i.e., active or inactive) and has here been adapted to correlate molecular features with chemical source (i.e., natural or synthetic). We have identified a number of molecular descriptors with significantly different Shannon entropy and/or "entropic separation" in natural and synthetic compound databases. Different combinations of such descriptors and variably distributed structural keys were applied to learning sets consisting of natural and synthetic molecules and used to derive predictive binary QSAR models. These models were then applied to predict the source of compounds in different test sets consisting of randomly collected natural and synthetic molecules, or, alternatively, sets of natural and synthetic molecules with specific biological activities. On average, greater than 80% prediction accuracy was achieved with our best models. For the test case consisting of molecules with specific activities, greater than 90% accuracy was achieved. From our analysis, some chemical features were identified that systematically differ in many naturally occurring versus synthetic molecules.

Algorithms↗

PubMed2001

An enthalpic component in cooperativity: the relationship between enthalpy, entropy, and noncovalent structure in weak associations.

Attempts to quantify binding interactions of noncovalent complexes in aqueous solution have been stymied by complications arising from enthalpy-entropy compensation and cooperativity. We have extended work detailing the relationship between noncovalent structure and free energy of binding to include the roles of enthalpy and entropy of association. On the basis of van't Hoff measurements of the dimerization of vancomycin type antibiotics, we demonstrate that positive cooperativity manifests itself in a more favorable enthalpy of association and a partially compensating less favorable entropy of association. Finally, we extend these results to rationalize thermodynamic observations in unrelated systems.

Anti-Bacterial Agents↗

PubMed2006

Importance of entropy in the conformational equilibrium of phenylalanine: a matrix-isolation infrared spectroscopy and density functional theory study.

The conformational behavior and infrared spectrum of l-phenylalanine were studied by matrix-isolation infrared spectroscopy and DFT [B3LYP/6-311++G(d,p)] calculations. The fourteen most stable structures were predicted to differ in energy by less than 10 kJ mol(-1), eight of them with abundances higher than 5% at the temperature of evaporation of the compound (423 K). Experimental results suggest that six conformers contribute to the spectrum of the isolated compound, whereas two conformers (IIb(3) and IIIb(3)) relax in matrix to a more stable form (IIb(2)) due to low energy barriers for conformational isomerization (conformational cooling). The two lowest-energy conformers (Ib(1), Ia) differ only in the arrangement of the amino acid group relative to the phenyl ring; they exhibit a relatively strong stabilizing intramolecular hydrogen bond of the O-H...N type and the carboxylic group in the trans configuration (O=C-O-H dihedral angle ca. 180 degrees ). Type II conformers have a weaker H-bond of the N-H...O=C type, but they bear the more favorable cis arrangement of the carboxylic group. Being considerably more flexible, type II conformers are stabilized by entropy and the relative abundances of two conformers of this type (IIb(2) and IIc(1)) are shown to significantly increase with temperature due to entropic stabilization. At 423 K, these conformers are found to be the first and third most abundant species present in the conformational equilibrium, with relative populations of ca. 15% each, whereas their populations could be expected to be only ca. 5% if entropy effects were not taken into consideration. Indeed, phenylalanine can be considered a notable example of a molecule where entropy plays an essential role in determining the relative abundance of the possible low-energy conformational states and then, the thermodynamics of the compound, even at moderate temperatures. Upon UV irradiation (lambda > 235 nm) of the matrix-isolated compound, unimolecular photodecomposition of phenylalanine is observed with production of CO(2) and phenethylamine.

Carbon Dioxide↗

PubMed2006

Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates.

Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model should reproduce the thermodynamic and structural properties of the corresponding AL model after mapping to the lower-resolution scale. In the present work, two such models are investigated: (i) the classical GROMOS atomic-level model; (ii) a CG model recently proposed by Marrink et al., which maps approximately four non-hydrogen atoms to one bead [J. Phys. Chem. B 2004, 108, 750]. The study is restricted to n-alkanes whose aliphatic fragments are abundantly found in lipids of biological interest. Additionally, cis-9-octadecene is included, as a template chain of the lipid dioleoylphosphatidylcholine (DOPC). The two representations of molecules in the liquid phase are compared in terms of average molecular structures, extent of configurational space sampled, and single-molecule entropies. An approximate method is used to estimate the rotational contributions to the absolute configurational entropy. Good correspondence between the AL and CG representations is found. The loss in configurational entropy due to the reduction in degrees of freedom upon coarse-graining of the model is estimated.

Algorithms↗

PubMed2006

Entropy of water in the hydration layer of major and minor grooves of DNA.

Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex are known to be different from those in the bulk. Here, we use a recently developed theoretical scheme to compute the entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. The scheme requires as input both translational and rotational velocity autocorrelation function (C(V)(t) and C(omega)(t), respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulation of a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy of water at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and that in the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS value is 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TDeltaS) of transferring a minor groove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is 0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We also calculate the energy of interaction of each water molecule with the rest of the atoms in the system and hence calculate the chemical potential (Helmholtz free energy per water molecule, A = E - TS) in the different domains. The identical free energy value of water molecules in the different domains proves the robustness of the scheme. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or microviscosity) of water molecules in a given domain.

Biophysics↗

PubMed2002

A new method based on entropy theory for genomic sequence analysis.

We have refined entropy theory to explore the meaning of the increasing sequence data on nucleic acids and proteins more conveniently. The concept of selection constraint was not introduced, only the analyzed sequences themselves were considered. The refined theory serves as a basis for deriving a method to analyze non-coding regions (NCRs) as well as coding regions. Positions with maximal entropy might play the most important role in genome functions as opposed to positions with minimal entropy. This method was tested in the well-characterized coding regions of 12 strains of Classical Swine Fever Virus (CSFV) and non-coding regions of 20 strains of CSFV. It is suitable to analyze nucleic acid sequences of a complete genome and to detect sensitive positions for mutagenesis. As such, the method serves to formulate the basis for elucidating the functional mechanism.

Algorithms↗

PubMed2002

The consequences of translational and rotational entropy lost by small molecules on binding to proteins.

When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.

Binding Sites↗