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PubMed1988

Thermodynamic evaluation of activated charcoal as a poison antidote by high-performance liquid chromatography. I: Derivation and validation of an equation for Gibbs free energy of liquid-solid adsorption.

An in vitro method utilizing high-performance liquid chromatography (HPLC) was developed in order to investigate the adsorptive process between activated charcoal and various drugs and toxic chemicals by measuring their Gibbs free energy of adsorption from various acetonitrile:water mobile phases. This report details the derivation and validation of the equation for calculating the Gibbs free energy of liquid-solid adsorption via HPLC. The derived equation incorporates the following experimental parameters: specific surface area of the adsorbent, specific retention volume of the solute, molar volume of the mobile phase, and surface concentration of the solute in a predefined standard state. This equation was validated by means of a closed thermodynamic cycle composed of three segments. Each segment represents a different physical process: gas-solid adsorption of methyl iodide on activated charcoal, gas-liquid solution of methyl iodide in n-hexadecane, and liquid-solid adsorption of methyl iodide on activated charcoal from n-hexadecane. The Gibbs free energy for each of these thermodynamic processes was determined by the appropriate chromatographic technique. Since the cycle did not balance because it did not account for the interaction of n-hexadecane and activated charcoal, it was altered to include a gas-liquid-solid chromatographic technique. When the Gibbs free energies of solution and gas-solid adsorption determined by this chromatographic technique were incorporated into the cycle, the resulting imbalance was only 0.213 kJ/mol (1.1%), thereby validating the derived equation.

Antidotes↗
PubMed1993

A rapid method for the measurement of cholesterol thermodynamic activity in bile salt-lecithin-cholesterol solutions.

Earlier work from this laboratory suggested that the cholesterol (Ch) thermodynamic activity is a more meaningful measure of the degree of Ch supersaturation in human bile than the widely known cholesterol saturation index. An early version of a method for determining thermodynamic activity based on Ch uptake from bile salt (BS)-lecithin (LE) solutions into silicone polymer particles, but requiring 12-24 h for reaching equilibrium, was considered unsatisfactory because Ch nucleation and crystal formation frequently occurred within a few hours. The aim of the present work was to develop a method that would reduce equilibration times to the order of 1 h. Changing the thickness of the silicone film alone did not result in the desired reduction of equilibration times and it was soon deduced that the uptake of Ch by the silicone film from the BS-LE solution was a surface-controlled transport process involving the transport of Ch by negatively charged BS and BS-LE micelles at the interface. Three different approaches were tried to modify the silicone film to make its surface positively charged, thereby reducing and/or eliminating the presumed electrical repulsion barrier for the interfacial transport of Ch. The film was treated with different concentrations of aminopropyl methyl-dimethylsiloxane (AMDS) in cyclohexane, octadecyldimethyl-[3-(trimethoxysilyl)-propyl] ammonium chloride (ODTOP) in methanol, and octadecylamine solution in ethanol. Films treated with 1-1.5% ODTOP and 5-10% AMDS reduced the Ch equilibration times for model BS-LE solutions to < 1 h.

Bile Acids and Salts↗
PubMed1994

Thermodynamic characterization of drug binding to human serum albumin by isothermal titration microcalorimetry.

Binding sites on human serum albumin (HSA) for anionic drugs and fatty acids have been thermodynamically characterized by microcalorimetry. The binding and the thermodynamic parameters were directly computed from the calorimetric titration data at 37 degrees C in a phosphate buffer (pH 7.4) using one- and two-class binding models. From compensation analyses plotting the molar enthalpy change (delta Hm,i) versus those of the molar free energy (delta Gm,i) and molar entropy (delta Sm,i) for each class of binding sites, HSA binding sites were classified into groups S1, S2, and S3. Group S1 included high-affinity binding sites for site II-bound drugs, such as ibuprofen, flufenamic acid, and ethacrynic acid, and short- or medium-length alkyl-chain fatty acids; group S2 included low-affinity binding sites of site II-bound drugs and long-length alkyl-chain fatty acids; and group S3 contained the high-affinity binding sites for site I-bound drugs, such as phenylbutazone, oxphenbutazone, and warfarin, and long-length alkyl-chain fatty acids. High- and low-affinity bindings sites for salicylic acid and acetylaslicylic acid agreed with the regions of groups S3 and S2, respectively. Groups S1 and S2 were characterized by large negative values of delta Hm,i and delta Sm,i, reflecting van der Waals interaction and hydrogen-bonding formation in low dielectric media, and the main force to stabilize the binding complex in group S3 was a hydrophobic interaction, characterized by a small negative delta Hm,i and minor or positive values of delta Sm,i (entropy-driven).

Anions↗
PubMed1995

Inferring thermodynamic stability relationship of polymorphs from melting data.

This study investigates the possibility of inferring the thermodynamic stability relationship of polymorphs from their melting data. Thermodynamic formulas are derived for calculating the Gibbs free energy difference (delta G) between two polymorphs and its temperature slope from mainly the temperatures and heats of melting. This information is then used to estimate delta G, thus relative stability, at other temperatures by extrapolation. Both linear and nonlinear extrapolations are considered. Extrapolating delta G to zero gives an estimation of the transition (or virtual transition) temperature, from which the presence of monotropy or enantiotropy is inferred. This procedure is analogous to the use of solubility data measured near the ambient temperature to estimate a transition point at higher temperature. For several systems examined, the two methods are in good agreement. The qualitative rule introduced this way for inferring the presence of monotropy or enantiotropy is approximately the same as The Heat of Fusion Rule introduced previously on a statistical mechanical basis. This method is applied to 96 pairs of polymorphs from the literature. In most cases, the result agrees with the previous determination. The deviation of the calculated transition temperatures from their previous values (n = 18) is 2% on average and 7% at maximum.

Models, Theoretical↗
PubMed1988

CO2 and argon laser vascular welding: acute histologic and thermodynamic comparison.

CO2 and argon lasers have been used successfully for vascular welding in both experimental and clinical settings. This study compared the thermodynamics during CO2 and argon laser welding of 1-cm longitudinal arteriotomies in a canine model. Continuous recordings using an AGA 782 digital thermographic system with spatial and thermal resolution of +/-0.2 mm and +/-0.2 degree C, respectively, were analyzed. A HGM argon laser using a 300-microns optic fiber held at 1 cm from the vessel edges (spot diameter = 2.8 mm) with concomitant room temperature saline irrigation (1 drop/sec) was used for argon welds. Total exposure time was 150 sec/cm. CO2 welds were performed with a Sharplan CO2 laser (spot diameter = 0.22 mm) with no irrigation for total exposure time of 10 sec/cm. Thermodynamic results and laser parameters are summarized as follows: Argon-n = 20; power = 500 mW; energy fluence = 1,400 J/cm2; Tmax = 48.8 degrees C; T mean +/- S.D. = 45.1 +/- 2.7 degrees C; CO2-n = 20; power = 150 mW; energy fluence = 3,000 J/cm2; Tmax 84.0 degrees C; T mean +/- S.D. = 60.7 +/- 9.8 degrees C. There was a significant difference (P less than .05) in thermal measurements between successful CO2 and argon vascular welds. Temperature rise during the argon welds was limited by saline irrigation. In contrast, during CO2 laser welding, the temperature rose quickly to its maximum and was maintained at a relatively high level as the laser progressed (0.1 cm/sec) along the anastomosis.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1994

Interaction of the DNA-binding domain of Drosophila heat shock factor with its cognate DNA site: a thermodynamic analysis using analytical ultracentrifugation.

Heat shock transcription factor (HSF) mediates the activation of heat shock genes by binding to its cognate sites with high affinity and specificity. The high-affinity binding of HSF is dependent on the formation of an HSF homotrimer, which interacts specifically with the heat shock response element (HSE), comprised of 3 inverted repeats of the 5-bp sequence NGAAN. In order to investigate the thermodynamic basis of the interaction between HSF and HSE, we have overexpressed and purified a polypeptide (dHSF(33-163)) encompassing only the DNA-binding domain of HSF from Drosophila and analyzed its binding to DNA by equilibrium analytical ultracentrifugation using a multiwavelength scan technique. We demonstrate that dHSF(33-163) can bind as a monomer with 1:1 stoichiometry to a synthetic 13-bp DNA containing a single NGAAN sequence. The values of the thermodynamic parameters obtained from the temperature dependence of the equilibrium binding constants indicate that the changes of free energy for the binding of dHSF(33-163) to the wild-type site and a mutant DNA site are predominantly characterized by substantial negative changes of enthalpy. Binding to the wild-type DNA is characterized by a significant positive change of entropy, whereas binding to the mutant DNA is distinguished by a negative change of entropy of comparable magnitude. The binding to the mutant DNA was also highly sensitive to increasing salt concentrations, indicating a dominance of ionic interactions. The sequence-specific, 1:1 binding of dHSF(33-163) to the NGAAN sequence provides a basis for the analysis of higher order interactions between HSF trimers and the HSE.

Animals↗
PubMed1996

Water-mediated protein-DNA interactions: the relationship of thermodynamics to structural detail.

The elucidation of a relationship between the thermodynamic parameters and the structural changes accompanying biomolecular interactions could lead to predictive algorithms. For example, based on some knowledge of the structure of a target molecule the affinities of ligands could be determined with obvious implications for the pharmaceutical industry. In attempting to relate the thermodynamic and structural changes on formation of a protein-DNA complex, the correlation between change in heat capacity and burial of surface area has proved successful. However, this correlation appears to break down when water molecules are included in the binding interface. Here we present data that support the hypothesis that bound water molecules have to be considered as contributing to the change in heat capacity and could, thus, be used in ligand design.

Bacterial Proteins↗
PubMed2003

Simple two-state protein folding kinetics requires near-levinthal thermodynamic cooperativity.

Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with an apparent two-state description of equilibrium thermodynamics. This phenomenon is hereby recognized as a nontrivial heteropolymer property capable of providing fundamental insight into protein energetics. Many current protein chain models, including common lattice and continuum Gō models with explicit native biases, fail to reproduce this generic protein property. Here we show that simple two-state kinetics is obtainable from models with a cooperative interplay between core burial and local conformational propensities or an extra strongly favorable energy for the native structure. These predictions suggest that intramolecular recognition in real two-state proteins is more specific than that envisioned by common Gō-like constructs with pairwise additive energies. The many-body interactions in the present kinetically two-state models lead to high thermodynamic cooperativity as measured by their van't Hoff to calorimetric enthalpy ratios, implying that the native and denatured conformational populations are well separated in enthalpy by a high free-energy barrier. It has been observed experimentally that deviations from Arrhenius behavior are often more severe for folding than for unfolding. This asymmetry may be rationalized by one of the present modeling scenarios if the effective many-body cooperative interactions stabilizing the native structure against unfolding is less dependent on temperature than the interactions that drive the folding kinetics.

Algorithms↗
PubMed2005

Binding of recombinant PrPc to human plasminogen: kinetic and thermodynamic study using a resonant mirror biosensor.

Transmissible spongiform encephalopathies are a class of sporadic, genetic and transmissible neurodegenerative diseases that affect both humans and animals. Propagation of these diseases is thought to be due to the misfolding of a neuronal glyco-protein, PrP(c), into a pathological insoluble conformer, PrP(Sc). In earlier works, some serum components were identified as exclusive PrP(Sc)-interacting proteins (Fisher et al., Nature 2000;408:479), and thus those macromolecules were thought to represent a potential diagnostic endogenous factor discriminating between normal and pathological prion proteins. In contrast, in agreement with a recent work (Kornblatt et al., Biochem Biophys Res Commun 2003;305:518), in this paper we present a detailed thermodynamic and kinetic characterization of the interaction between recombinant bovine PrP(c 25-242) and the human serum component plasminogen, measured using a resonant mirror technique: our results reveal a high-affinity interaction between the two binding partners. For comparison, the complex obtained from the purified full-length PrP(c) and human plasminogen was also studied: both prion proteins (the recombinant bovine PrP(c 25-242) and the purified full-length PrP(c)) are able to bind human plasminogen. Both kinetic and thermodynamic parameters are affected by the modulation exerted by the H(+) ions in solution. Moreover, the analysis of binding, according to canonical linkage relationships, suggests the involvement of a His residue, consistent with the interaction between other serine (pro)enzymes and their ligands.

Animals↗
PubMed1993

Novel mechanism-based substrates of dihydrofolate reductase and the thermodynamics of ligand binding: a comparison of theory and experiment for 8-methylpterin and 6,8-dimethylpterin.

Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of the designed mechanism-based pterins, 8-methylpterin and 6,8-dimethylpterin, to dihydrofolate reductase (DHFR), with cofactor nicotinamide adenine dinucleotide phosphate (NADPH). The calculated free energy differences suggest that DHFR.NADPH.6,8-dimethylpterin is thermodynamically more stable than DHFR.NADPH.8-methylpterin by 2.4 kcal/mol when the substrates are protonated and by 1.3 kcal/mol when neutral. The greater binding strength of 6,8-dimethylpterin may be attributed largely to hydration effects. In terms of an appropriate model for the pH-dependent kinetic mechanism, these differences can be interpreted consistently with experimental data obtained from previous kinetic studies, i.e., 6,8-dimethylpterin is a more efficient substrate of vertebrate DHFRs than 8-methylpterin. The kinetic data suggest a value of 6.6 +/- 0.2 for the pKa of the active site Glu-30 in DHFR.NADPH. We have also used experimental data to estimate absolute values for thermodynamic dissociation constants of the active (i.e., protonated) forms of the substrates: these are of the same order as for the binding of folate (0.1-10 microM). The relative binding free energy calculated from the empirically derived dissociation constants for the protonated forms of 8-methylpterin and 6,8-dimethylpterin is 1.4 kcal/mol, a value which compares reasonably well with the theoretical value of 2.4 kcal/mol.

Computer Simulation↗
PubMed1993

Thermodynamic elucidation of structural stability of deuterated biological molecules: deuterated phospholipid vesicles in H2O.

Thermodynamic studies of deuterated phospholipids in H2O were conducted using deuterated lipid bilayer vesicles prepared from aqueous dispersions of 1,2-dimyristoyl-d54-, 1,2-dipalmitoyl-d62-, and 1,2-distearoyl-d70-phosphatidylcholines. The results obtained in combination with those previously reported in D2O made possible the evaluation of deuterium solvent and deuterium alkyl-chain substitution effects in deuterated phospholipids. These effects included the temperature (delta tm), the enthalpy (delta delta H), the free energy (delta delta G), the entropy (delta delta S), and the cooperative melting unit (delta n) of the main lipid phase transition from the gel to the liquid-crystalline phase. To supplement thermodynamic observations, fluorescence steady-state polarization measurements were also performed. The results were examined to elucidate the nature of interactions in deuterated compounds. The deuterium solvent effect increases the structural stability of deuterated lipid vesicles, due to an enhancement of hydrophobic interaction in D2O. This observation is contrary to that previously reported for deuterated proteins, phycocyanins, where structural stability is reduced in D2O solvent. These findings therefore support the proposal that an alteration in hydrophobic interactions in deuterated proteins due to deuterium substitution is not likely to play a significant role in contributing to the structural instability of proteins.

Calorimetry, Differential Scanning↗
PubMed2001

Inhibitors to the Src SH2 domain: a lesson in structure--thermodynamic correlation in drug design.

Src homology 2 (SH2) domains play a key role in many tyrosine kinase-mediated intracellular signal transduction pathways. Aberrancies in the interaction of these domains can lead to a range of disease states. As a result, the pharmaceutical industry has made a large temporal and financial investment in the development of specific inhibitors to these domains. Focusing on the interactions of the SH2 domain from the protein Src, we report how the correlation of structural and thermodynamic data allows an assessment of the process of drug design. The binding site of the protein includes two pockets; one interacts with phosphotyrosine groups on cognate ligands, and the other accommodates an aliphatic hydrophobic side chain. The interaction with cognate ligands is also mediated by a network of water molecules. Thermodynamic data from isothermal titration calorimetric studies suggest that modification of the interactions in the SH2 binding site has been largely unsuccessful in producing high-affinity inhibitors. Furthermore, it appears that compounds that disrupt the interfacial water pay the price for the loss of the contribution to the free energy from a network of hydrogen bonds.

Amino Acid Motifs↗
PubMed1995

Thermodynamic analysis of tetracycline-mediated induction of Tet repressor by a quantitative methylation protection assay.

We describe a method for quantitative detection and thermodynamic interpretation of tetracycline (tc)-mediated induction of the Tn10 encoded Tet repressor (TetR). Binding of dimeric TetR to the tet operator (tetO) was quantitated by protection of DNA from methylation as a function of te concentration. A thermodynamic scheme covering all single reactions relevant for TetR induction was used to interpret the data. The equilibrium association constants of the TetR-[Mg-tc]+ and TetR-[Mg-tc]2+ complexes to tetO were determined at different NaCl and TetR concentrations. Variation of total TetR concentration from 0.2 to 1.1 x 10(-7) M yielded identical results. A strong salt dependency of TetR-tetO binding was verified between 2.5 and 100 mM NaCl, whereas [Mg-tc]+ binding to TetR is independent of the ionic strength. The TetR-tetO binding constant drops 10(2)- to 10(3)-fold upon binding of the first and further 10(4)- to 10(7)-fold by binding of the second [Mg-tc]+. This apparent cooperativity of tc-mediated induction indicates that each [Mg-tc]+ interacts with both TetR monomers.

DNA Transposable Elements↗
PubMed1998

Low-affinity binding determined by titration calorimetry using a high-affinity coupling ligand: a thermodynamic study of ligand binding to protein tyrosine phosphatase 1B.

A competition-based method is used for the determination of the thermodynamic parameters for a low-affinity ligand binding reaction by isothermal titration calorimetry. This method is based on the coupling of a high-affinity ligand to the binding of the low-affinity ligand. Results are presented for the binding of a nonhydrolyzable phosphotyrosine analog phosphonodifluoromethyl phenylalanine (F2Pmp)-containing peptide (Ac-Asp-Ala-Asp-Glu-F2Pmp-Leu-NH2), arsenate, and inorganic phosphate to the intracellular human protein tyrosine phosphatase 1B(PTP1B). The binding constants are 3.3 x 10(6), 4.3 x 10(3), and 48 M-1 for the F2Pmp-containing peptide, arsenate, and inorganic phosphate, respectively. The binding of arsenate and inorganic phosphate to PTP1B is enthalpy driven. This is in contrast to the binding of the F2Pmp-containing peptide which is mainly driven by entropy. The calorimetrically determined binding constants are in agreement with the Ki values determined by enzyme inhibition studies. This demonstrates that isothermal titration calorimetry can be used to quantitatively determine the thermodynamic parameters for the interactions between proteins and low-affinity ligands if a proper coupling ligand can be identified.

Amino Acid Sequence↗
PubMed2002

Thermodynamic quantities of surface formation of aqueous electrolyte solutions. V. Aqueous solutions of aliphatic amino acids.

The surface tension of aqueous solutions of glycine, L-alanine, L-valine, and L-leucine has been observed using the drop volume method as a function of temperature and concentration. The L-leucine molecules form an adsorbed film, while glycine affects the water surface in accordance with simple salts which dissociate into cations and anions completely. The surface tension data have been analyzed in view of K. Motomura's thermodynamic treatment (J. Colloid Interface Sci.64, 348 (1978)), and the thermodynamic quantities relevant to the surface have been shown systematically.

Adsorption↗
PubMed1993

Thermodynamic studies of the collagen-like region of human subcomponent C1q. A water-containing structural model.

Thermal transitions of Clq were investigated by methods of differential scanning calorimetry, circular dichroism and fluorescence. The melting curves of Clq display two pronounced heat absorption peaks with enables determination of the thermodynamic parameters characterizing each transition. The low temperature peak was assigned to melting of the Clq collagenous part. Analysis of the data has revealed unusual, as compared with the monomeric collagen molecules, thermodynamic features of the Clq collagenous part: (1) higher thermal stability strongly dependent on pH; (2) less linear co-operative regions; and (3) a noticeable change in the partial specific heat capacity (delta Cp) in contrast to both the monomeric collagen and the collagen fibrils. This unusually large delta Cp value suggested a conclusion that the fibril-like endpiece of Clq may have a cavity filled with ice-like ordered water molecules.

Calorimetry, Differential Scanning↗
PubMed1995

Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions.

We have characterized thermodynamically the melting transitions of a DNA 31-mer oligonucleotide (5'-GAAGAGGTTTTTCCTCTTCTTTTTCTTCTCC-3') which is designed to fold into an intramolecular triple helix. The first 19 residues fold back on themselves to form an antiparallel Watson-Crick hairpin duplex with a T5 loop. The 3'-terminal seven residues, which are connected to the Watson-Crick hairpin duplex by a second T5 loop, form Hoogsteen interactions in the major groove of the Watson-Crick hairpin. From ultraviolet (UV) melting studies we find that the 31-mer exhibits either one or two transitions, depending on solution conditions. We use pH- and temperature-dependent circular dichroism (CD) to assign the initial and final states associated with each transition. We find that the disruption of the Hoogsteen hairpin is accompanied by a release of protons and an uptake of sodium ions while the disruption of the Watson-Crick hairpin is accompanied by a release of sodium ions with no change in protonation state. From these data, we construct a phase diagram for this intramolecular DNA triple helix as a function of pH, sodium ion concentration, and temperature. We characterize the energetics of each transition using a van't Hoff analysis and differential scanning calorimetry (DSC). Significantly, the DSC data provide a model-independent thermodynamic characterization of the thermally induced transitions of this triplex. By combining the spectroscopic and calorimetric data, we develop a semi-empirical model which describes the state of the 31-mer as a function of pH, sodium ion concentration, and temperature. With this model we successfully predict characteristics of the 31-mer, which are beyond the data which are used in establishing the model (for example, the salt dependence of the apparent pKa of the Hoogsteen strand). This semi-empirical model may serve as a prototype for developing a method to predict the phase diagrams of intramolecular triple helix systems.

Base Sequence↗
PubMed1995

Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin.

The discovery that the protease from the human immunodeficiency virus (HIV) belongs to the aspartic protease family has generated renewed interest in this class of proteins. In this paper, the interactions of endothiapepsin, an aspartic proteinase from the fungus Endothia parasitica, with the inhibitor pepstatin A have been studied by high-sensitivity calorimetric techniques. These experiments have permitted a complete characterization of the temperature and pH-dependence of the binding energetics. The binding reaction is characterized by negative intrinsic binding enthalpy and negative heat capacity changes. The association constant is maximal at low pH (2 x 10(9) M-1 at pH 3) but decreases upon increasing pH (8.1 x 10(6) M-1 at pH 7). The binding of the inhibitor is coupled to the protonation of one of the aspartic moieties in the Asp dyad of the catalytic site of the protein. This phenomenon is responsible for the decrease in the apparent affinity of the inhibitor for the enzyme upon increasing pH. The experimental results presented here indicate that the binding of the inhibitor is favored both enthalpically and entropically. While the favorable enthalpic contribution is intuitively expected, the favorable entropic contribution is due to the large gain in solvent-related entropy associated with the burial of a large hydrophobic surface, that overcompensates the loss in conformational and translational/rotational degrees of freedom upon complex formation. The characteristics of the molecular recognition process have been evaluated by means of structure-based thermodynamic analysis. Three regions in the protein contribute significantly to the free energy of binding: the residues surrounding the Asp dyad (Asp32 in the N-terminal lobe and Asp215 in the C-terminal domain) and the flap region (Ile73 to Asp77). In addition, the rearrangement of residues that are not in immediate contact with the inhibitor provides close to 40% of the protease contribution to the binding free energy. On the other hand, the two statine residues provide more than half of the inhibitor contributions to the total free energy of binding. It is demonstrated that a previously developed empirical structural parametrization of the thermodynamic parameters that define the Gibbs energy, accurately accounts for the binding energetics and its temperature and pH-dependence.

Aspartic Acid Endopeptidases↗