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PubMed2004

Distribution of GD3 in DPPC monolayers: a thermodynamic and atomic force microscopy combined study.

Gangliosides are the main component of lipid rafts. These microdomains, floating in the outer leaflet of cellular membrane, play a key role in fundamental cellular functions. Little is still known about ganglioside and phospholipid interaction. We studied mixtures of dipalmitoylphosphatidylcholine and GD3 (molar fraction of 0.2, 0.4, 0.6, 0.8) using complementary techniques: 1), thermodynamic properties of the Langmuir-Blodgett films were assessed at the air-water interface (surface tension, surface potential); and 2), three-dimensional morphology of deposited films on mica substrates were imaged by atomic force microscopy. Mixture thermodynamics were consistent with data in the literature. In particular, excess free energy was negative at each molar fraction, thus ruling out GD3 segregation. Atomic force microscopy showed that the height of liquid-condensed domains in deposited films varied with GD3 molar fraction, as compatible with a lipid aggregation model proposed by Maggio. No distinct GD3-rich domain was observed inside the films, suggesting that GD3 molecules gradually mix with dipalmitoylphosphatidylcholine molecules, confirming DeltaG data. Morphological analysis revealed that the shape of liquid-condensed domains is strongly influenced by the amount of GD3, and an interesting stripe-formation phenomenon was observed. These data were combined with the thermodynamic results and interpreted in the light of McConnell's model.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1969

Thermodynamics and the primary processes of photosynthesis.

Numerous discussions of the relationship of the thermodynamics of radiation to photosynthesis have been published, but the results are often in disagreement or at best difficult to compare with one another. The recent treatment of maximal photosynthetic efficiencies by Ross and Calvin is here shown to be directly related to the thermodynamic method of Duysens. A smooth connection between the light and dark conditions is derived, the case of polarized light is considered briefly, and a critique of some other thermodynamic treatments is presented.

Bacteria↗
PubMed1979

Network thermodynamic approach compartmental analysis. Na+ transients in frog skin.

We introduce a general network thermodynamic method for compartmental analysis which uses a compartmental model of sodium flows through frog skin as an illustrative example (Huf and Howell, 1974a). We use network thermodynamics (Mikulecky et al., 1977b) to formulate the problem, and a circuit simulation program (ASTEC 2, SPICE2, or PCAP) for computation. In this way, the compartment concentrations and net fluxes between compartments are readily obtained for a set of experimental conditions involving a square-wave pulse of labeled sodium at the outer surface of the skin. Qualitative features of the influx at the outer surface correlate very well with those observed for the short circuit current under another similar set of conditions by Morel and LeBlanc (1975). In related work, the compartmental model is used as a basis for simulation of the short circuit current and sodium flows simultaneously using a two-port network (Mikulecky et al., 1977a, and Mikulecky et al., A network thermodynamic model for short circuit current transients in frog skin. Manuscript in preparation; Gary-Bobo et al., 1978). The network approach lends itself to computation of classic compartmental problems in a simple manner using circuit simulation programs (Chua and Lin, 1975), and it further extends the compartmental models to more complicated situations involving coupled flows and non-linearities such as concentration dependencies, chemical reaction kinetics, etc.

Animals↗
PubMed1989

Thermodynamic parameters for the binding of divalent cations to gramicidin A incorporated into a lipid environment by Tl-205 nuclear magnetic resonance.

Thermodynamic parameters, enthalpy and entropy, for the binding of the divalent cations, Mg+2, Ca+2, Sr+2, Ba+2, and Cd+2, to gramicidin A, incorporated into lysophosphatidylcholine, have been determined using a combination of Tl-205 nuclear magnetic resonance spectroscopy and competition binding. The binding process is thermodynamically driven by the enthalpy and not the entropy. The enthalpy values are related to the process involving the transfer of cations from an aqueous environment to an amide environment. A comparison is made between the thermodynamic parameters for the binding of monovalent and divalent cations to gramicidin A to illustrate the channel blocking ability of the divalent cations with respect to monovalent cation transport.

Cations↗
PubMed1996

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study.

The proton transfer activity of the light-driven proton pump, bacteriorhodopsin (bR) in the photochemical cycle might imply internal water molecules. The free energy of inserting water molecules in specific sites along the bR transmembrane channel has been calculated using molecular dynamics simulations based on a microscopic model. The existence of internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each hydrated model from molecular dynamics simulations of the creation of water molecules into specific protein-binding sites. A rigorous statistical mechanical formulation allowing the calculation of the free energy of transfer of water molecules from the bulk to a protein cavity is used to estimate the probabilities of occupancy in the putative bR proton channel. The channel contains a region lined primarily by nonpolar side-chains. Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permitted. The column forms a continuous hydrogen-bonded chain over 12 A between a proton donor, Asp 96, and the retinal Schiff base acceptor. The presence of two water molecules in direct hydrogen-bonding association with the Schiff base is found to be strongly favorable thermodynamically. The implications of these results for the mechanism of proton transfer in bR are discussed.

Amino Acid Sequence↗
PubMed1996

Atomic-scale analysis of the solvation thermodynamics of hydrophobic hydration.

Molecular dynamics simulations are used to model the transfer thermodynamics of krypton from the gas phase into water. Extra long, nanosecond simulations are required to reduce the statistical uncertainty of the calculated "solvation" enthalpy to an acceptable level. Thermodynamic integration is used to calculate the "solvation" free energy, which together with the enthalpy is used to calculate the "solvation" entropy. A comparison series of simulations are conducted using a single Lennard-Jones sphere model of water to identify the contribution of hydrogen bonding to the thermodynamic quantities. In contrast to the classical "iceberg" model of hydrophobic hydration, the favorable enthalpy change for the transfer process at room temperature is found to be due primarily to the strong van der Waals interaction between the solute and solvent. Although some stabilization of hydrogen bonding does occur in the solvation shell, this is overshadowed by a destabilization due to packing constraints. Similarly, whereas some of the unfavorable change in entropy is attributed to the reduced rotational motion of the solvation shell waters, the major component is due to a decrease in the number of positional arrangements associated with the translational motions.

Calorimetry↗
PubMed1996

"Adaptive" behavior of ligand-gated ion channels: constraints by thermodynamics.

The calcium-induced calcium release channel of the cardiac sarcoplasmic reticulum has been reported to inactivate in a novel manner (termed "adaptation"), which permits reactivation by exposure to successively higher concentrations of calcium. I examined the limitations placed by thermodynamics on the possible kinetic mechanisms for such behavior. The mechanism suggested by Gyorke and Fill, in which the affinity of a calcium-binding site decreases during adaptation, is not thermodynamically feasible for a passive system, but requires an external input of free energy. Possible sources of such energy are 1) metabolic energy, which is excluded by the fact that adaptation was observed in isolated channels in the absence of ATP, or 2) coupling of ion permeation to gating, for which there is currently no evidence. I derived a general limit on the thermodynamic feasibility of a sequence of channel activations and adaptations, irrespective of channel kinetics, from the requirement that the free energy must decrease during the spontaneous evolution of the system from the state existing immediately after a step increase in [Ca2+] to the state of maximum open probability that follows. The opening of the channel must involve an increase in free energy, which must be compensated by the free energy released by the incremental binding of calcium. This requirement leads to a complicated system of inequalities, which was simplified and manipulated algebraically into the form of a linear programming problem. Numerical solution of this problem showed that the sequence of adaptations of the SR channel observed by Gyorke and Fill requires the presence of at least 10 calcium-binding sites on the channel if it is to occur in the absence of exogenous sources of free energy. This indicates either that a large number of calcium-binding sites participate in the regulation of the SR calcium release channel, or that the existing data are significantly flawed with respect to the low open probability in the resting state, the importance of "calcium spike" artifacts from flash photolysis, or both.

Adaptation, Physiological↗
PubMed1997

Thermodynamics of the hydrolysis and cyclization reactions of alpha-, beta-, and gamma-cyclodextrin.

A thermodynamic investigation of the hydrolysis and cyclization reactions of cyclomaltohexa-, hepta-, and octa-ose (alpha-, beta-, and gamma-cyclodextrins) has been performed using microcalorimetry and high-performance liquid-chromatography. The calorimetric measurements lead to standard molar enthalpy changes delta rHm0 (T = 298.15 K, KH2PO4 buffer (m = 0.10 mol kg-1), pH = 4.58 to 5.15) for the following reactions: alpha-cyclodextrin(aq) + 6H2O(l) = 6 D-glucose(aq), beta-cyclodextrin(aq) + 7H2O(l) = 7 D-glucose(aq), gamma-cyclodextrin(aq) + 8H2O(l) = 8 D-glucose(aq). Equilibrium constants were determined for the following generalized cyclization reactions (T = 329.6 K, 0.005 mol kg-1 K2HPO4 buffer adjusted to pH = 5.55 with H3PO4) catalyzed by cyclomaltodextrin glucanotransferase: Gu(aq) = alpha-cyclodextrin(aq) + G(u-6)(aq), Gv(aq) = beta-cyclodextrin(aq) + G(v-7)(aq), Gw(aq) = gamma-cyclodextrin(aq) + G(w-8)(aq). Here, G1 is D-glucose and the Gn's (n is a positive integer) are linear maltodextrins; u, v, and w are, respectively, integers > or = 7, > or = 8, and > or = 9. Values of the equilibrium constants, standard molar Gibbs energy change delta rGm0, standard molar enthalpy change delta rHm0, standard molar entropy change delta rSm0, and standard molar heat-capacity change delta rCp,m0 are tabulated for the above reactions at T = 298.15 K. The values of delta rGm0 and delta rSm0 for the first three above-mentioned reactions rely upon an estimated value of delta rSm0 for the hydrolysis reaction of maltose to D-glucose. The thermodynamics of the disproportionation reaction Gm(aq) + Gn(aq) = Gm-1(aq) + Gn+1(aq) is also discussed. Values of the quantities delta rHm0/N, delta rGm0/N, delta rSm0/N, and delta rCp,m0/N for the three above-mentioned hydrolysis reactions where N is the number of (1-->4)-alpha-D-glucosidic bonds broken in each of these reactions, have been calculated and compared with thermodynamic quantities for the similar hydrolysis reaction of a linear oligosaccharide.

Calorimetry↗
PubMed1997

Prediction of the thermodynamic properties of aqueous metal complexes to 1000 degrees C and 5 kb.

A large number of aqueous metal complexes contribute significantly to hydrothermal, metamorphic, and magmatic processes in the crust of the Earth. Nevertheless, relatively few thermodynamic data other than dissociation constants (K) for a few dozen of these complexes have been determined experimentally at elevated temperatures and pressures. The calculations summarized below are intended to supplement these experimental data by providing interim predictions of the thermodynamic properties of supercritical aqueous metal complexes using the revised HKF (Helgeson et al., 1981) equations of state for aqueous species (Tanger and Helgeson, 1988; Shock et al., 1992) and correlations among equations of state parameters and standard partial molal properties at 25 degrees C and 1 bar (Shock and Helgeson, 1988, 1990; Shock et al., 1989). These equations and correlations permit retrieval of the conventional standard partial molal entropies (mean S0), volumes (mean V0), and heat capacities (mean C0P) of aqueous metal complexes at 25 degrees C and 1 bar from published values of log K in the supercritical region and the limited number of experimental dissociation constants available in the literature over relatively short ranges of elevated temperature at PSAT (PSAT and SAT are used in the present communication to refer to pressures corresponding to liquid-vapor equilibrium for the system H2O except at temperatures <100 degrees C, where they refer to the reference pressure of 1 bar). The standard partial molal properties computed in this way can then be used to generate corresponding values of delta mean S0, delta mean V0, and delta mean C0P of association, which for similar complexes correlate linearly with mean S0, mean V0 and mean C0P, respectively, of the constituent cations and ligands at 25 degrees C and 1 bar. Generalizing these correlations and combining them with the equations of state permits prediction of the temperature and pressure dependence of log K and other thermodynamic properties of a large number of aqueous metal complexes. As a consequence, it is possible to retrieve values of log K at 25 degrees C and 1 bar from the results of hydrothermal experiments at higher temperatures and pressures or to predict values of log K at hydrothermal conditions when no experimental data are available at temperatures and pressures above 25 degrees C and 1 bar. Such predictions can be made for temperatures and pressures from 0 degrees C and 1 bar to 1000 degrees C and 5000 bars.

Algorithms↗
PubMed2003

Thermodynamics and kinetics of solute transfer in reversed-phase liquid chromatography.

In this study, the thermodynamic and kinetic behavior of a homologous series of fatty acids is examined using a polymeric octadecylsilica stationary phase and a methanol mobile phase. The zone profiles are evaluated as the temperature is varied from 20 to 60 degrees C and the average pressure from 400 to 4570 p.s.i. (1 p.s.i.=6894.76 Pa). The rate constant for solute transfer from mobile to stationary phase (k(ms)) appears to be relatively constant with carbon number. In contrast, the rate constant from stationary to mobile phase (k(sm)) decreases logarithmically with increasing carbon number. This suggests that the mass transport processes become progressively slower, owing to the smaller diffusion coefficients of the larger solutes in the stationary phase. The activation energy decreases slightly in the mobile phase and increases slightly in the stationary phase with increasing carbon number. The activation energy in the stationary phase ranges from 41.6 to 55.9 kcal/mol, while the thermodynamic change in internal energy ranges from -9.8 to -29.0 kcal/mol for C10 to C22, respectively (1 cal=4.184 J). The activation volume increases with increasing carbon number in both the mobile and stationary phase. The activation volume in the stationary phase ranges from 31.7 to 211 cm3/mol, while the thermodynamic change in molar volume ranges from -27.1 to -104 cm3/mol for C10 to C22, respectively. These large changes in activation energy and volume suggest that the solutes do not enter and leave the stationary phase in a single step, but in a stepwise or progressive manner.

Chromatography, High Pressure Liquid↗
PubMed2002

Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange.

We report a native-state hydrogen-exchange (HX) method to simultaneously obtain both thermodynamic and kinetic information on the formation of multiple excited states in a folding energy landscape. Our method exploits the inherent dispersion and pH dependence of the intrinsic HX rates to cover both the EX2 (thermodynamic) and EX1 (kinetic) regimes. At each concentration of denaturant, HX measurements are performed over a range of pH values. Using this strategy, we dissected Borrelia burgdorferi OspA, a predominantly beta-sheet protein containing a unique single-layer beta-sheet, into five cooperative units and postulated excited states predominantly responsible for HX. More importantly, we determined the interconversion rates between these excited states and the native state. The use of both thermodynamic and kinetic information from native-state HX enabled us to construct a folding landscape of this 28kDa protein, including local minima and maxima, and to discriminate on-pathway and off-pathway intermediates. This method, which we term EX2/EX1 HX, should be a powerful tool for characterizing the complex folding mechanisms exhibited by the majority of proteins.

Animals↗
PubMed1991

A thermodynamic and biomechanical theory of cell adhesion. Part I: General formulism.

The equilibrium thermodynamics calculus of cell adhesion developed by Bell et al. (1984, Biophys. J. 45, 1051-1064) has been extended to the general non-equilibrium case. In contrast to previous models which could only compute the end results of equilibrium states, the present theory is able to calculate the kinetic process of evolution of adhesion, which may or may not approach towards equilibrium. Starting from a basic constitutive hypothesis for Helmholtz free energy, equations of balance of normal forces, energy balance at the edge of the contact area and rate of entropy production are derived using an irreversible thermodynamics approach, in which the restriction imposed by the Second Law of Thermodynamics takes the place of free energy minimization used by Bell et al. (1984). An explicit expression for adhesion energy density is derived for the general transient case as the difference of the usable work transduced from chemical energy liberation from bond formation of specific crosslinking molecules and the repulsive potential of non-specific interactions. This allows the energy balance to be used as an independent boundary equation rather than a practical way of computing the adhesion energy. Jump conditions are obtained from the conservation of crosslinking molecules across the edge of adhesion region which is treated as a singular curve. The bond formation and lateral motion of the crosslinking molecules are assumed to obey a set of reaction-diffusion equations. These equations and the force balance equation within the contact area, plus the jump conditions and the energy balance equation at the edge form a well-posed moving boundary problem which determines the propagation of the adhesion boundary, the separation distance between the two cell membranes over the contact area as well as the distributions of the crosslinking molecules on the cell surfaces. The behavior of the system depends on the relative importance of virtual convection, lateral diffusion and bond formation of the crosslinking molecules at the edge of the adhesion region, according to which two types of rate limiting cases are discussed, viz, reaction-limited and diffusion-limited processes.

Animals↗
PubMed1985

Thermodynamics and the conceptual structure of evolutionary theory.

Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another. The point of this paper is to consider some qualitative ways in which thermodynamics can enrich both the theory and epistemology of evolution. The "autonomy of biology" posture in evolutionary theory hangs on the supposed uniqueness of why-questions in biology. With this posture, and with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms. Thermodynamics provides for a two-tiered hierarchy of causation in nature in which the why-question is rendered not only legitimate materialistically, but essential to understanding the evolutionary process in its totality--from the emergence of life to the branching of lineages in speciation.

Adaptation, Biological↗
PubMed1989

Linkage thermodynamics of individual site binding phenomena.

The principles of linkage thermodynamics are extended to the analysis of individual site binding phenomena in biological macromolecules. A group of thermodynamic potentials is introduced for the description of linkage among the sites. These potentials are isomorphic with Wyman's linkage potentials derived for the description of the mutual interference of different ligands. Thermodynamic stability principles are used to show how they affect individual site binding phenomena and give rise to possible paradoxes.

Animals↗
PubMed2002

DNA thermodynamic pressure: a potential contributor to genome evolution.

Codon usage bias is a feature of living organisms. The origin of this bias might be explained not only by external factors but also by the nature of the structure of deoxyribonucleic acid (DNA) itself. We have developed a point mutation simulation program of coding sequences, in which nucleotide replacement follows thermodynamic criteria. For this purpose we calculated the hydrogen bond-like and electrostatic energies of non-canonical base pairs in a 5 bp neighbourhood. Although the rate of non-canonical base pair formation is extremely low, such pairs occur with a preference towards a guanine (G) or cytosine (C) rather than an adenine (A) or thymine (T) replacement due to thermodynamic considerations. This feature, according to the simulation program, should result in an increase in the GC content of the genome over evolutionary time. In addition, codon bias towards a higher GC usage is also predicted. DNA sequence analysis of genes of the Trypanosomatidae lineage supported the hypothesis that DNA thermodynamic pressure is a driving force that impels increases in GC content and GC codon bias.

Algorithms↗
PubMed2000

Thermodynamic, kinetic and structural studies on the ternary palladium(II) complexes of thioether ligands.

Potentiometric, calorimetric, NMR and stopped-flow kinetic studies were performed on the palladium(II) complexes of thioether and/or nitrogen donor ligands. The ternary systems always contained a tridentate ligand (dien, terpy and dianions of dipeptides, GlyGly, GlyAla and GlyMet) and a monodentate thioether (AcMet). The stability constants of thioether complexes were obtained by indirect potentiometric measurements using uridine as a competitive ligand. The thermodynamic parameters revealed that selectivity of palladium(II) for thioether binding can be significantly influenced by the other donor atoms around the metal ion. [Pd(terpy)]2+ and [Pd(GlyMet)] had the lowest affinity for thioether binding and it was explained by steric and electronic effects. Ternary complexes of nitrogen donors have higher thermodynamic stability constants than the thioether complexes, but rate constants of the substitution reactions revealed that formation of thioether complexes is the faster reaction. As a consequence, the thermodynamic equilibrium state of a multicomponent system is characterized by the coordination of N-donors, which are formed via the existence of thioether-bonded intermediates.

Calorimetry↗
PubMed1997

Thermodynamics in biochemical engineering.

Equilibrium aspects in biotechnology and thermodynamics as the main theory underlying them have thus far received relatively little attention. As a consequence, design and development of biotechnological processes is still carried out today in an relatively empirical way. For this situation to improve, a wider and more systematic use of the thermodynamic aspects pertaining to biotechnology must be encouraged. Recognizing this need, the ESF program on Process Integration in Biotechnology developed an intensive advanced course which was held twice so far. The present contribution uses the course structure in order to give a short overview of the field and to identify research needs. The development of a rigorous thermodynamic description, for the exceedingly complex world of biotechnology, is indeed one of the major challenges today in establishing the scientific basis for rational efficient, and fast bioprocess development and design.

Biotechnology↗
PubMed2000

Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures II. Unfolded proteins.

Equations of state for completely unfolded proteins have been generated from group additivity algorithms and the revised Helgeson-Kirkham-Flowers (HKF) equations of state to compute the standard molal thermodynamic properties of these molecules at elevated temperatures and pressures. The requisite equations of state parameters were computed from those of groups retrieved by regression of experimental calorimetric and densimetric data reported in the literature. This approach permits calculation of the standard molal thermodynamic properties as a function of temperature and pressure for any completely unfolded protein for which the amino acid sequence is known. Calculations of this kind have been carried out for 11 thermophilic proteins. The thermodynamic properties reported below can be combined with those for protein unfolding to compute the corresponding properties of completely folded (i.e. native) proteins.

Algorithms↗