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Side-chain entropy and packing in proteins.

What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is side-chain "freezing" or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.

Drug Stability↗

Alkyl chains acting as entropy reservoir in liquid crystalline materials.

The roles played by the conformational disordering of alkyl chains in determining the aggregation states of matter are reviewed for liquid crystalline materials from a thermodynamic perspective. Entropy, which is one of the most macroscopic concepts but which has a clear microscopic meaning, provides crucial microscopic information for complex systems for which a microscopic description is hard to establish. Starting from structural implication by absolute (third-law) entropy for crystalline solids, the existence of successive phase transitions caused by the successive conformational melting of alkyl chains in discotic mesogens is explained. An experimental basis is given for the "quasi-binary picture" of thermotropic liquid crystals, i.e., the highly disordered alkyl chains behave like a second component (solvent). A novel entropy transfer between the "components" of a molecule and the resulting "alkyl chains as entropy reservoir" mechanism are explained for cubic mesogens.

Journal Article↗

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

The association reaction of two molecules to form a single complex must overcome a large entropic barrier due to the loss of translational and rotational degrees of freedom; estimates of the T delta S term are of the order of 30 kcal/mol for proteins. The approach of Chandler and Pratt is used to provide a statistical mechanical formulation for the connection between the gas-phase and solution binding free energies. This makes possible a clear separation of the vibrational contribution to the gas-phase binding enthalpy and entropy from the solvation terms. Further, it suggests that the calculated gas-phase result, should be a good approximation in solution for many systems. To illustrate the formulation, a harmonic dynamics model is used to study the dimerization of insulin. The vibrational entropy increase in the dimer complex, relative to the two separate monomers, is 23 entropy units. This contributes -7.2 kcal/mol to the dimerization free energy. It is not possible to identify a small number of specific dimer modes that give rise to this entropy contribution. Instead, small alterations in the frequencies of many modes below 400 to 600 cm-1 are found to contribute. The relative importance of vibrational and other effects in macromolecule-macromolecule and macromolecule-small molecule associations is discussed.

Binding Sites↗

Role of main-chain electrostatics, hydrophobic effect and side-chain conformational entropy in determining the secondary structure of proteins.

The physiochemical bases of amino acid preferences for alpha-helical, beta-strand, and other main-chain conformational states in proteins is controversial. Hydrophobic effect, side-chain conformational entropy, steric factors, and main-chain electrostatic interactions have all been advanced as the dominant physical factors which determine these preferences. Many attempts to resolve the controversy have focused on small model systems. The disadvantage of such systems is that the amino acids in small molecules are largely exposed to the solvent. In proteins, however, the amino acids are in contact with the solvent to a different degree, causing a large variability of strengths of all interactions. The estimates of mean strengths of interactions in the actual protein environment are therefore essential to resolve the controversy. In this work the experimental protein structures are used to estimate the mean strengths of various interactions in proteins. The free energy contributions of the interactions are implemented into the Lifson-Roig theory to calculate the helix and strand free energy profiles. From the profiles the secondary structures of proteins and peptides are predicted using simple rules. The role of hydrophobic effect, side-chain conformational entropy, and main-chain electrostatic interactions in determining the secondary structure of proteins is assessed from the abilities of different models, describing stability of secondary structures, to correctly predict alpha-helices, beta-strands and coil in 130 proteins. The three-state accuracy of the model, which contains only the free energy terms due to the main-chain electrostatics with 40 coefficients, is 68.7%. This accuracy is approaching to the accuracy of currently the best secondary structure prediction algorithm based on neural networks (72%); however, many thousands of parameters have to be optimized during the training of the neural networks to reach this level of accuracy. The correlation coefficient between the calculated and the experimental helix contents of 37 alanine based peptides is 0.91. If the hydrophobic and the side-chain conformational entropy terms are included into the helix-coil transition parameters, the accuracy of the algorithm does not improve significantly. However, if the main-chain electrostatic interactions are excluded from the helix-coil and strand-coil transition parameters, the accuracy of the algorithm reaches only 59.5%. These results support the dominant role of the short-range main-chain electrostatics in determining the secondary structure of proteins and peptides. The role of the hydrophobic effect and the side-chain conformational entropy is small.

Agglutinins↗

A maximum entropy criterion of filtering and coding for stationary autoregressive signals: its physical interpretations and suggestions for its application to neural information transmission.

The operations of encoding and decoding in communication agree with filtering operations of convolution and deconvolution for Gaussian signal processing. In an analogy with power transmission in thermodynamics, an autoregressive model of information transmission is proposed for representing a continuous communication system which requires a pair of an internal noise source and a signal source to encode or decode a message. In this model transinformation (informational entropy) equals the increase in stationary nonequilibrium organization formed through the amplification of white noise by a positive feedback system. The channel capacity is finite due to the existence of inherent noise in the system. The maximum entropy criterion in information dynamics corresponds to the 2nd law of thermodynamics. If the process is stationary, the communication system is invertible, and has the maximum efficiency of transformation. The total variation in informational entropy is zero in the cycle of the invertible system, while in the noninvertible system the entropy of decoding is less than that of encoding. A noisy autoregressive coding which maximizes transinformation is optimum, but is also ideal.

Animals↗

Entropy as a factor in the binding of gamma-aminobutyric acid and nipecotic acid to the gamma-aminobutyric acid transport system.

Nipecotic acid is one of the most potent competitive inhibitors and alternative substrates for the high-affinity gamma-aminobutyric acid transport system in neurons, but the structural basis of this potency is unclear. Because gamma-aminobutyrate is a highly flexible molecule in solution, it would be expected to lose rotational entropy upon binding to the transport system, a change which does not favor binding. Nipecotic acid, in contrast, is a much less flexible molecule, and one would expect the loss of conformational entropy upon binding to be smaller thus favoring the binding of nipecotic acid over gamma-aminobutyric acid. To investigate this possibility, the thermodynamic parameters, delta G degrees, delta H degrees, and delta S degrees, were determined for the binding of gamma-aminobutyrate and nipecotic acid to the high affinity GABA transport system in synaptosomes. In keeping with expectations, the apparent entropy change for nipecotic acid binding (112 +/- 13 J.K-1) was more favorable than the apparent entropy change for gamma-aminobutyric acid binding (61.3 +/- 6.6 J.K-1). The results suggest that restricted conformation per se is an important contributory factor to the affinity of nipecotic acid for the high-affinity transport system for gamma-aminobutyric acid.

Animals↗

Rate of polymer formation and entropy production during competitive replication.

The rate of increase in the mean polymer formation rate constant during competitive replication by Qbeta RNA variants (Kramer et al., 1974) has been shown to agree statistically with the variance in their formation rate constants. This result demonstrates that Fisher's fundamental theorem of natural selection (Fisher, 1930) can define time variations in the mean rate of synthesis for a heterogeneous population of replicating polymers. It was also revealed that RNA replication, far from equilibrium, accompanied a progressive decrease in the order of the entropy production derivative, with respect to time, that reached a maximum (with the next higher order being zero). Maximization of entropy at equilibrium, in compliance with the second law of thermodynamics, therefore appears as a natural extension of the earlier non-equilibrium pattern of entropy production within the system. The order of the zero-valued entropy production derivative was shown to be determined by the chemical affinity, and its rate of decrease was specified by the mean polymer formation rate constant.

Biological Evolution↗

Pharmacokinetic parameter estimations by minimum relative entropy method.

For estimating pharmacokinetic parameters, we introduce the minimum relative entropy (MRE) method and compare its performance with least squares methods. There are several variants of least squares, such as ordinary least squares (OLS), weighted least squares, and iteratively reweighted least squares. In addition to these traditional methods, even extended least squares (ELS), a relatively new approach to nonlinear regression analysis, can be regarded as a variant of least squares. These methods are different from each other in their manner of handling weights. It has been recognized that least squares methods with an inadequate weighting scheme may cause misleading results (the "choice of weights" problem). Although least squares with uniform weights, i.e., OLS, is rarely used in pharmacokinetic analysis, it offers the principle of least squares. The objective function of OLS can be regarded as a distance between observed and theoretical pharmacokinetic values on the Euclidean space RN, where N is the number of observations. Thus OLS produces its estimates by minimizing the Euclidean distance. On the other hand, MRE works by minimizing the relative entropy which expresses discrepancy between two probability densities. Because pharmacokinetic functions are not density function in general, we use a particular form of the relative entropy whose domain is extended to the space of all positive functions. MRE never assumes any distribution of errors involved in observations. Thus, it can be a possible solution to the choice of weights problem. Moreover, since the mathematical form of the relative entropy, i.e., an expectation of the log-ratio of two probability density functions, is different from that of a usual Euclidean distance, the behavior of MRE may be different from those of least squares methods. To clarify the behavior of MRE, we have compared the performance of MRE with those of ELS and OLS by carrying out an intensive simulation study, where four pharmaco-kinetic models (mono- or biexponential, Bateman, Michaelis-Menten) and several variance models for distribution of observation errors are employed. The relative precision of each method was investigated by examining the absolute deviation of each individual parameter estimate from the known value. OLS is the best method and MRE is not a good one when the actual observation error magnitude conforms to the assumption of OLS, that is, error variance is constant, but OLS always behaves poorly with the other variance models. On the other hand, MRE performs better than ELS and OLS when the variance of observation is proportional to its mean. In contrast, ELS is superior to MRE and OLS when the standard deviation of observation is proportional to its mean. In either case the difference between MRE and ELS is relatively small. Generally, the performance of MRE is comparable to that of ELS. Thus MRE provides as reliable a method as ELS for estimating pharmacokinetic parameters.

Humans↗

Origin and destination entropies of U.S. 1965-70 age-sex-specific intercounty migration flows.

"Eight independent pairs of entropy-based rankings of 3,140 U.S. county-level units are obtained. The criteria employed are the homogeneities of the distribution of 1965-70 in- and out-migrants of each county--for eight age-sex-specific groups--over the other 3,139 counties. The most homogeneous counties for males of ages 19-39 in 1970 consistently have major military facilities." The results show that "for those 65 and over, Florida, Arizona and Texas counties have the broadest in-migration, while Northern metropolitan counties have dispersed out-migration. The cross-correlations of entropies--though all strongly positive--are lowest between those 19-39 and those 65 and over, and relatively weak, in general, between those 65 and over and other groups. In all eight demographic groups, destination entropies reach higher values than origin entropies."

Age Factors↗

Observations on maximum entropy processing of MR images.

A maximum entropy (MAXENT) criteria for MR image processing optimizations has previously shown poor performance, but this note observes that there are two entirely different kinds of "data transmission" applications which appear to have been intermixed. In the two cases, "image entropy" actually refers to different kinds of data variables. The previous literature formulations are for transfer of data in which pixel-locations are the transmitted variable, and these pixels may be neither uniform nor constant. The second application concerns the MRI data set for display. Its data variables are image pixel-values of magnetization intensity, and the data transfer mode has the sense of visual display. When MAXENT criteria are modified to address an array of pixel-value intensities, and use a pixel-value information entropy rather than pixel-locations entropy, then successful data processing results. Restoring display visualization from highly nonuniform surface coils for lumbar spine scans are demonstrated, as an example of MAXENT usefulness.

Image Processing, Computer-Assisted↗

Entropy balances of microbial product formation.

Considering the approach of Bermudez and Wagensberg (1986) devoted to the entropy balance of growing microorganisms some equations were developed which describe particularly the entropy balance of microbial product formation. The formula allows to determine the coefficients of resistance R(mn) and of coupling L(mn) according to rates of growth, product formation, maintenance metabolism and heat evolution assuming a linear relationship between thermodynamic fluxes and forces. In order to check the usefulness of the derived model appropriate experimental data of two microbial batch processes concerning production of L-lysine and the antibiotic nourseothricine were taken into account. The results showed similar courses of entropy balances despite different pathways of product formation which were characterized by an overshoot of entropy production at the beginning of biosynthesis of the primary and secondary metabolite. This fact was interpreted as a more general phenomenon for microorganisms under inbalanced nutritional conditions.

Journal Article↗

Investigating entropy changes during gas adsorption in ETS-4.

Energetic heterogeneity has been investigated for Engelhard titanium silicate Na-ETS-4 adsorbent and its Sr-exchanged variant, Sr-ETS-4. Na-ETS-4 was nearly homogeneous, while Sr exchange seemed to induce some degree of energetic heterogeneity in the sample, which diminished upon dehydration at higher temperature. Analysis of the entropy change during adsorption showed that the adsorbate molecules at low as well as moderate loading possess entropy greater than that predicted by the 2-D mobile film model, the excess being attributed to vibrational freedom. The wavelength of this vibration decreased with increasing coverage, as expected. For oxygen, the observed entropy drops in Na-ETS-4 and in Sr-ETS-4 are comparable, whereas, for nitrogen and methane, Sr exchange resulted in a greater entropy drop than in Na-ETS-4, suggesting greater restriction to movement in the Sr-exchanged sample. This study presents a simplistic yet effective understanding of the energetic behavior of the adsorbed molecules in ETS-4 adsorbent. This is vital to a thorough energetic characterization and study of the adsorption phenomenon in these new, promising adsorbents.

Journal Article↗

Measuring diversity from dissimilarities with Rao's quadratic entropy: are any dissimilarities suitable?

Rao has developed quadratic entropy to measure diversity in a set of entities divided up among a fixed set of categories. This index depends on a chosen matrix of dissimilarities among categories and a frequency distribution of these categories. With certain choices of dissimilarities, this index could be maximized over all frequency distributions by eliminating several categories. This unexpected result is radically opposite to those obtained with usual diversity indices. We demonstrate that the elimination of categories to maximize the quadratic entropy depends on mathematical properties of the chosen dissimilarities. In particular, when quadratic entropy is applied to ultrametric dissimilarities, all categories are retained in order to reach its maximal value. Three examples, varying from simple one-dimensional to ultrametric dissimilarity matrices, are provided. We conclude that, as far as diversity measurement is concerned, quadratic entropy is most relevant when applied to ultrametric dissimilarities.

Animals↗

Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted.

Circular versions of a large number of proteins have been designed by connecting the N and C termini via peptide linkers. A motivation for these designs is the assumed enhancement in folding stability, because backbone cyclization reduces the chain entropy of the unfolded state. Here, it is recognized that backbone cyclization also reduces the chain entropy of a flexible peptide linker in the folded state. Specifically, the end-to-end distance of the linker is restricted to fluctuations around the average displacement between the N and C termini of the folded protein. The balance of the chain-entropy reductions in the folded and unfolded states is used to predict the change in the unfolding free energy, deltadeltaG(cycl), by backbone cyclization. Predicted values of deltadeltaG(cycl) are in quantitative agreement with results of a careful study on cyclizing the 34 residue PIN1 WW domain by linkers with two to seen residues. The experimental results of an optimal linker length l=4 and a maximum stabilization of 1.7 kcal/mol are reproduced. Calculations of deltadeltaG(cycl) for a broad selection of circular proteins suggest that the stabilizing effect of backbone cyclization is modest, reflecting entropy reductions in both the unfolded and the folded states.

Animals↗

Seizure anticipation in pediatric epilepsy: use of Kolmogorov entropy.

The purpose of this paper is to demonstrate feasibility of using trends in Kolmogorov entropy to anticipate seizures in pediatric patients with intractable epilepsy. Surface and intracranial recordings of preseizure and seizure activity were obtained from five patients and subjected to time series analysis using Kolmogorov entropy. This metric was compared with correlation dimension and power indices, both known to predict seizures in some adult patients. We used alarm levels and introduced regression analysis as a quantitative approach to the analysis of trends. Surrogate time series evaluated data nonlinearity, as a precondition to the use of nonlinear measures. Seizures were anticipated before clinical or electrographic seizure onset for three of the five patients from the intracranial recordings, and in two of five patients from the scalp recordings. Anticipation times varied between 2 and 40 minutes. This is the first report in which simultaneous surface and intracranial recording are used for seizure prediction in children. We conclude that the Kolmogorov entropy and power indices were as effective as the more commonly used correlation dimension in anticipating seizures. Further, regression analysis of the Kolmogorov entropy time series is feasible, making the analysis of data trends more objective.

Adolescent↗

Maximum entropy method for frequency-domain fluorescence lifetime analysis. 2. Timing, mismatched intensity, and reference lifetime errors.

The maximum entropy method (MEM) provides a robust and unbiased solution to fluorescence lifetime data through the use of a broad window of decay terms fit by simultaneous minimization of the chi 2 goodness-of-fit parameter and maximization of a statistical entropy function. This work investigated the effects of three systematic errors, common in frequency-domain measurements, on fluorescence lifetime recovery by MEM. Through real and simulated data, the expression of the systematic errors in lifetime distributions recovered by MEM was compared to that in standard nonlinear least-squares (NLLS) analysis. Reference lifetime errors in the presence of random noise had similar effects on both MEM and NLLS results. Characteristic changes in the recovered lifetimes, fractional intensities, and peak shapes were related to the identification of the true reference lifetime. Compared to NLLS, MEM afforded significant improvements for the recovery of lifetimes and fractional intensities from data containing timing or mismatched intensity errors. These improvements are linked to the dynamic, self-modeling approach of MEM and the direction provided by the entropy criterion. These results speak to the utility of the maximum entropy approach in frequency-domain fluorescence lifetime recovery as well as in other applications.

Fluorescence↗

Allosteric effects of carbamoyl phosphate synthetase from Escherichia coli are entropy-driven.

When catalyzing the formation of MgATP and carbamate from MgADP and carbamoyl phosphate, Escherichia coli carbamoyl phosphate synthetase (CPS) binds MgADP with a large negative change in heat capacity. The magnitude of this heat capacity change is not appreciably altered by the presence of a saturating concentration of either the allosteric activator ornithine or the inhibitor UMP despite the substantial and opposing effects these ligands have on the binding affinity for MgADP. By contrast, no detectable change in heat capacity is associated with the thermodynamic coupling between MgADP and either ornithine or UMP. The sign of the apparently constant enthalpic and entropic contributions to the coupling free energy for each of these ligands is opposite that of the coupling free energy, indicating that the observed allosteric phenomenology is in net opposed by the enthalpy of the interaction and instead arises from a change in entropy of the system. IMP produces only a very small allosteric effect as indicated by a near-zero value for the MgADP-IMP coupling free energy. However, the enthalpic and entropic contributions are individually larger in absolute value for the IMP coupling than for those pertaining to the other allosteric ligands, and entropy dominates the coupling free energy above 36 degrees C, causing IMP to become an activator at high temperature. In addition, the sign of the coupling enthalpy and entropy for IMP has the same sign as the coupling enthalpy and entropy produced by ornithine, suggesting that IMP and ornithine may similarly influence the enzyme at a molecular level despite binding to different allosteric sites on the enzyme. The data are consistent with a model in which the actions of the allosteric ligands arise primarily from changes in the conformational degeneracy introduced by each ligand. With this model, one can also rationalize the failure of these allosteric ligands to substantially influence kcat.

Adenosine Diphosphate↗

Standard absolute entropy, S degrees 298 values from volume or density. 1. Inorganic materials.

Standard absolute entropies of many inorganic materials are unknown; this precludes a full understanding of their thermodynamic stabilities. It is shown here that formula unit volume, V(m)(), can be employed for the general estimation of standard entropy, S degrees 298 values for inorganic materials of varying stoichiometry (including minerals), through a simple linear correlation between entropy and molar volume. V(m)() can be obtained from a number of possible sources, or alternatively density, rho, may be used as the source of data. The approach can also be extended to estimate entropies for hypothesized materials. The regression lines pass close to the origin, with the following formulas: For inorganic ionic salts, S degrees 298 /J K(-)(1) mol(-)(1) = 1360 (V(m)()/nm(3) formula unit(-)(1)) + 15 or = 2.258 [M/(rho/g cm(-)(3))] + 15. For ionic hydrates, S degrees 298 /J K(-)(1) mol(-)(1) = 1579 (V(m)()/nm(3) formula unit(-)(1)) + 6 or = 2.621 [M/(rho/g cm(-)(3))] + 6. For minerals, S degrees 298 /J K(-)(1) mol(-)(1) = 1262 (V(m)()/nm(3) formula unit(-)(1)) + 13 or = 2.095 [M/(rho/g cm(-)(3))] + 13. Coupled with our published procedures, which relate volume to other thermodynamic properties via lattice energy, the correlation reported here complements our development of a predictive approach to thermodynamics and ultimately permits the estimation of Gibbs energy data. Our procedures are simple, robust, and reliable and can be used by specialists and nonspecialists alike.

Journal Article↗