Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Applicability of Butler's equation in interpreting the thermodynamic behavior of surfaces and adsorption in Fe-S-O melts

Expressions for various second-order derivatives of surface tension with respect to composition at infinite dilution in terms of the interaction parameters of the surface and those of the bulk phases of dilute ternary melts have been presented. A method of deducing the parameters, which consists of repeated differentiation of Butler's equations with subsequent application of the appropriate boundary conditions, has been developed. The present investigation calculates the surface tension and adsorption functions of the Fe-S-O melts at 1873 and 1923 K using the modified form of Butler's equations and the derived values for the surface interaction parameters of the system. The calculated values are found to be in good agreement with those of the experimental data of the system. The present analysis indicates that the energetics of the surface phase are considerably different from those of the bulk phase. The present research investigates a critical compositional range beyond which the surface tension increases with temperature. The observed increase in adsorption of sulfur with consequent desorption of oxygen as a function of temperature above the critical compositional range has been ascribed to the increase of activity ratios of oxygen to sulfur in the surface relative to those in the bulk phase of the system.

A thermodynamic criterion for selection of gas compositions for diamond deposition

Isoactivity lines for carbon with respect to diamond as the standard state have been calculated in the ternary system C-H-O at 1223 K to identify the diamond deposition domain. The gas composition is calculated by suppressing the formation of all condensed forms of carbon using the SOLGASMIX free-energy minimization program. Thirty six gas species were included in the calculation. From the gas composition, isoactivity lines are computed using recent data on the Gibbs energy of diamond. Except for activities less than 0.1, the isoactivity lines are almost linear on the C-H-O ternary diagram. Gas compositions which generate activity of diamond ranging from 1 to 100 at 1223 K fall inside a narrow wedge originating from the point representing CO. This wedge is very similar to the revised lens-shaped diamond growth domain identified by Bachman et al., using inputs from experiment. The small difference between the calculated and observed domains may be attributed to variation in the supersaturation required for diamond deposition with gas composition. The diamond solubility in the gas phase along the isoactivity line for a(di)=100 and P=6.7 kPa exhibits a minimum at 1280 K, which is close to the optimum temperature found experimentally. At higher supersaturations, non-diamond forms of carbon, including amorphous varieties, are expected. The results suggest that thermodynamic calculations can be useful for locating diamond growth domains in more complex CVD systems containing halogens, for which very little experimental data is available.

Integral treatment for the representation of thermodynamic properties in multicomponent systems using interaction parameters

The partial thermodynamic functions of the solvent component of a ternary system have been deduced in terms of the interaction parameters by integration of several series which emerge from the Maclaurin infinite series based on the integral property of the system and subjected to appropriate boundary conditions. The series integration shows that the resulting partial functions are suitable for interpreting the thermodynamic properties of the system and are independent of compositional paths. In the present analysis, the higher order terms of these series are found to make insignificant contributions.

Verifying scalings for bending rigidity of bilayer membranes using mesoscale models

The bending rigidity kappa of bilayer membranes was studied with coarse grained soft repulsive potentials using dissipative particle dynamics (DPD) simulations. Using a modified Andersen barostat to maintain the bilayers in a tensionless state, the bending rigidity was obtained from a Fourier analysis of the height fluctuations. From simulations carried out over a wide range of membrane thickness, the continuum scaling relation kappa proportional to d(2) was captured for both the L-alpha and L-beta phases. For membranes with 4 to 6 tail beads, the bending rigidity in the L-beta phase was found to be 10-15 times higher than that observed for the L-alpha phase. From the quadratic scalings obtained, a six fold increase in the area stretch modulus, k(A) was observed across the transition. The magnitude of increase in both kappa and k(A) from the L-alpha to the L-beta phase is consistent with current experimental observations in lipid bilayers and to our knowledge provides for the first time a direct evaluation of the mechanical properties in the L-beta phase.

Field evaluation of unsaturated hydraulic conductivity models and parameter estimation from retention data

Predictions of two popular closed-form models for unsaturated hydraulic conductivity (K) are compared with in situ measurements made in a sandy loam field soil. Whereas the Van Genuchten model estimates were very close to field measured values, the Brooks-Corey model predictions were higher by about one order of magnitude in the wetter range. Estimation of parameters of the Van Genuchten soil moisture characteristic (SMC) equation, however, involves the use of non-linear regression techniques. The Brooks-Corey SMC equation has the advantage of being amenable to application of linear regression techniques for estimation of its parameters from retention data. A conversion technique, whereby known Brooks-Corey model parameters may be converted into Van Genuchten model parameters, is formulated. The proposed conversion algorithm may be used to obtain the parameters of the preferred Van Genuchten model from in situ retention data, without the use of non-linear regression techniques.

Interaction of sheep liver apo-serine hydroxymethyltransferase with pyridoxal-5'-phosphate: A physicochemical, kinetic, and thermodynamic study

Sheep liver serine hydroxymethyltransferase (EC 2.1.2.1) is a homotetramer of M(r) 213,000 requiring pyridoxal-5'-phosphate (PLP) as cofactor, Removal of PLP from the holoenzyme converted the enzyme to the apo form which, in addition to being inactive, was devoid of the characteristic absorption spectrum. Upon the addition of PLP to the apoenzyme, complete activity was restored and the visible absorption spectrum with a maximum at 425 nm was regained. The interaction of PLP with the apoenzyme revealed two phases of reaction with pseudo-first-order rate constants of 20 +/- 5 s(-1) and 12.2 +/- 2.0 x 10(-3) s(-1), respectively. However, addition of PLP to the apoenzyme did not cause gross conformational changes as evidenced by circular dichroic and fluorescence spectroscopy. Although conformationally apoenzyme and holoenzyme were indistinguishable, they had distinct apparent melting temperatures of 51 +/- 2 and 58 +/- 2 degrees C, respectively, and the reconstituted holoenzyme was thermally as stable as the native holoenzyme. These results suggested that there was no apparent difference in the secondary structure of holoenzyme, apoenzyme, and reconstituted holoenzyme, However, sedimentation analysis of the apoenzyme revealed the presence of two peaks of S-20,S-w values of 8.7 +/- 0.5 and 5.7 +/- 0.3 S, respectively. A similar pattern was observed when the apoenzyme was chromatographed on a calibrated Sephadex G-150 column. The first peak corresponded to the tetrameric form (M(r) 200,000 +/- 15,000) while the second peak had a M(r) of 130,000 +/- 10,000. Reconstitution experiments revealed that only the tetrameric form of the apoenzyme could be converted into an active holoenzyme while the dimeric form could not be reconstituted into an active enzyme. These results demonstrate that PLP plays an important role in maintaining the structural integrity of the enzyme by preventing the dissociation of the enzyme into subunits, in addition to its function in catalysis. (C) 1996 Academic Press, Inc.

Critical earthquake input power spectral density function models for engineering structures

The problem of determining optimal power spectral density models for earthquake excitation which satisfy constraints on total average power, zero crossing rate and which produce the highest response variance in a given linear system is considered. The solution to this problem is obtained using linear programming methods. The resulting solutions are shown to display a highly deterministic structure and, therefore, fail to capture the stochastic nature of the input. A modification to the definition of critical excitation is proposed which takes into account the entropy rate as a measure of uncertainty in the earthquake loads. The resulting problem is solved using calculus of variations and also within linear programming framework. Illustrative examples on specifying seismic inputs for a nuclear power plant and a tall earth dam are considered and the resulting solutions are shown to be realistic.

Representation of thermodynamic properties of ternary systems and its application to the system silver-gold-copper at 1350 K

The article presents a generalized analytical expression for description of the integral excess Gibbs free energy of mixing of a ternary system. Twelve constants of the equation are assessed by the least mean squares regressional analysis of the experimental integral excess data of the constituent binaries; three ternary parameters are evaluated by a regressional analysis based on the partial experimental data of a component of the ternary system. The assessed values of the ternary parameters describe the nature of the ternary interaction in the system. Activities and isoactivities of the components in the Ag-Au-Cu system at 1350 K are calculated and found to be in good agreement with the experimental data. This analytical treatment is particularly useful to ternary systems where the thermodynamic data are available from different sources.

Sibling rivalry between seeds within a fruit: Some population genetic models

Competition between seeds within a fruit for parental resources is described using one-locus-two-allele models. While a �normal� allele leads to an equitable distribution of resources between seeds (a situation which also corresponds to the parental optimum), the �selfish� allele is assumed to cause the seed carrying it to usurp a higher proportion of the resources. The outcome of competition between �selfish� alleles is also assumed to lead to an asymmetric distribution of resources, the �winner� being chosen randomly. Conditions for the spread of an initially rare selfish allele and the optimal resource allocation corresponding to the evolutionarily stable strategy, derived for species with n-seeded fruits, are in accordance with expectations based on Hamilton�s inclusive fitness criteria. Competition between seeds is seen to be most intense when there are only two seeds, and decreases with increasing number of seeds, suggesting that two-seeded fruits would be rarer than one-seeded or many-seeded ones. Available data from a large number of plant species are consistent with this prediction of the model.

Spatially dependent zero-frequency response functions and correlation functions in the Kondo model

We present the details of a formalism for calculating spatially varying zero-frequency response functions and equal-time correlation functions in models of magnetic and mixed-valence impurities of metals. The method is based on a combination of perturbative, thermodynamic scaling theory [H. R. Krishna-murthy and C. Jayaprakash, Phys. Rev. B 30, 2806 (1984)] and a nonperturbative technique such as the Wilson renormalization group. We illustrate the formalism for the spin-1/2 Kondo problem and present results for the conduction-spin-density�impurity-spin correlation function and conduction-electron charge density near the impurity. We also discuss qualitative features that emerge from our calculations and discuss how they can be carried over to the case of realistic models for transition-metal impurities.

Thermodynamic modelling of absorption-resorption heating cycles with some new working pairs

This paper presents the results of a thermodynamic cycle analysis of single stage resorption heat pump (RHP) and resorption heat transformer (RHT) cycles with the new working pairs R22-NMP and R22-DMA. The coefficients of performance (COP) are correlated with the low grade source temperature, temperature at which useful heat is obtained and ambient temperature. The COPs are in the range 1.20–1.60 for the RHP mode and 0.25–0.45 for the RHT mode. Absorber temperatures (useful temperatures) as high as 50°C in the RHP mode and 87°C in the RHT mode have been obtained. It is observed that absorption-resorption systems are inflexible in their range of operating temperature and necessitate a higher pump work as compared with simple single-stage absorption heating systems. However, single stage RHTs show higher temperature boosts than simple absorption heat transformers.

Phase Relations in the System La-Rh-O and Thermodynamic Properties of LaRhO3

Phase relations in the system La-Rh-O at 1223 Ii have been determined by examination of equilibrated samples by optical and scanning electron microscopy, powder X-ray diffraction (XRD), and energy-dispersive analysis of X-rays (EDAX). Only one ternary oxide, LaRhO3, with distorted orthorhombic perovskite structure (Pbnm, a = 0.5525, b = 0.5680, and c = 0.7901 nm) was identified. The alloys and intermetallics along the La-Rh binary are in equilibrium with La2O3. The thermodynamic properties of LaRhO3 were determined in the temperature range 890 to 1310 K, using a solid-state cell incorporating yttria-stabilized zirconia as the electrolyte. A new four-compartment design of the emf cell was used to enhance the accuracy of measurement. For the reaction 1/2La(2)O(3) + 1/2Rh(2)O(3) --> LaRhO3, Delta G degrees = - 70 780 + 4.89T (+/- 90) J.mol(-1) The compound decomposes on heating to a mixture of La2O3, Ph and O-2. The calculated decomposition temperatures are 1843 (+/- 5) K in pure O-2 and 1728 (+/- 5) K in air at a pressure of 1.01 x 10(5) Pa. The phase diagrams for the system La-Rh-O at different partial pressures of oxygen are calculated from the thermodynamic information.