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PubMed2006

Thermodynamic stability and crystal structures for polymorphs and solvates of formoterol fumarate.

Polymorph screening of formoterol fumarate was performed in 12 solvents, followed by evaluations of thermodynamic stability. Three anhydrates, a dihydrate, a diethanolate, a diisopropanolate, and a dibensylalcoholate were found. The crystal structure of three solvated modifications and of the most stable anhydrate was investigated. This indicated that solvation is needed to get a stable and well packed crystal structure. Thermodynamic testing suggests that five crystal modifications are thermodynamically stable, at different conditions, since they are all reversibly related to each other.

2-Propanol↗
PubMed2007

A calorimetric investigation of thermodynamic and molecular mobility contributions to the physical stability of two pharmaceutical glasses.

The purpose of this work was to investigate the contribution of thermodynamics and mobility to the physical stability of two pharmaceutical glasses with similar glass transition temperatures (Tg), by comparing configurational thermodynamic quantities and molecular relaxation time constants (tau) at temperatures below Tg. Ritonavir and nifedipine were chosen as model glasses because they show excellent and poor physical stability, respectively. Although ritonavir and nifedipine have similar Tg values (50 and 46 degrees C, respectively), amorphous ritonavir is quite stable while nifedipine has been reported to crystallize at temperatures as low as 40 degrees C below Tg. Modulated temperature differential scanning calorimetry (MTDSC) was used to characterize both crystalline phases and freshly prepared glasses. The glasses were then annealed at Tg-Ta = 25 degrees C while monitoring the extent of relaxation and heat capacity change as a function of time via MTDSC. Configurational thermodynamic quantities (Gc, Hc, and Sc) and molecular relaxation time constants, tau, were calculated from the calorimetric data. Interestingly, the Gibbs free energy driving force for crystallization was nearly identical for the two compounds. The largest differences were found in the configurational entropy (Sc) values for the fresh glasses and in the Sc values over time. Configurational entropy values were approximately 50% higher for ritonavir. The tau values of freshly prepared glasses indicated that both materials had similar initial mobility at the annealing temperatures and the temperature dependence of tau was approximately Arrhenius, regardless of age. Although initial tau values were similar, the tau values after 3 days annealing were approximately sixfold greater for ritonavir. The relatively poor physical stability of nifedipine compared to ritonavir is attributed to both the lower entropic barrier to crystallization for fresh and annealed glass, and higher molecular mobility in aged glasses of nifedipine. These observations below Tg are consistent with the previous work on physical stability of amorphous pharmaceuticals performed above Tg.

Calorimetry, Differential Scanning↗
PubMed1978

Kinetic and thermodynamic aspects of in vitro interphase transfer of tetracyclines I: influence of hydroxyl group substitution.

The influence of hydroxyl group substitution on the kinetic and thermodynamic aspects of the interphase transfer of three tetracycline derivatives was studied in a two-phase in vitro system composed of an aqueous pH 5.5 buffer and 1-octanol. Data are reported on the kinetic and thermodynamic parameters of activation, the net thermodynamic parameters for interphase transfer, and the contribution of hydroxyl group substituents to the energy changes associated with partitioning. For each derivative, deltaH, deltaS, T deltaS, and deltaF were positive with enthalpy dominating the entropic energy contribution. Introduction of a hydroxyl group at C-5 on the tetracycline nucleus promoted partitioning through an entropy-dominated decrease in the "apparent" free energy of partitioning, whereas shifting the hydroxyl group to C-6beta retarded partitioning due to an enthalpy-dominated gain in the apparent free energy.

Diffusion↗
PubMed1987

Sulfa drugs: thermodynamic proton-ligand and metal-ligand stability constants.

The thermodynamic proton-ligand stability constants of sulfa drugs have been determined in different mole fractions of dioxane (0.083-0.174) at 25 and 35 +/- 0.1 degrees C. Empirical corrections to pH meter readings in mixed aqueous media have been applied. The pKa varies linearly with the mole fraction of dioxane. Numerical equations expressing this linear relationship have been obtained using the method of least squares, and relevant correlation coefficients have been calculated. The thermodynamic parameters delta G degrees, delta H degrees, and delta S degrees are calculated. The effect of solvent and the change in free energy from mixed aqueous media, delta, is discussed. The thermodynamic metal-ligand stability constants of Cu(II), Pd(II), and Ce(IV) with sulfa drugs in 50% aqueous dioxane at 35 +/- 0.1 degrees C have been determined. The effect of basicity of the ligand and the order of the stability constant is discussed.

Chemical Phenomena↗
PubMed1988

Silicone polymer uptake method for determination of cholesterol thermodynamic activity in model bile systems.

Cholesterol in bile has been linked to the incidence of gallstone disease through the concept of supersaturation as measured by the cholesterol saturation index (CSI). The latter is a linear function of cholesterol concentration and is based on the assumption that all cholesterol in bile is solubilized and transported in bile salt-lecithin (BS-L) mixed micelles, as well as in bile salt simple micelles. In light of the discovery of the cholesterol-lecithin vesicles as significant cholesterol carriers, there is a need to re-evaluate this old concept. This study examined the feasibility of the silicone polymer uptake method for the direct determination of the cholesterol thermodynamic activity (AT) in model bile systems. In cases of unsaturation and near saturation, a linear relationship was observed between CSP,Eq, the cholesterol concentration in the silicone polymer at equilibrium, and CAq,Eq/Cs,Aq for taurocholate (TC), taurochenodeoxycholate (TCDC), and tauroursodeoxycholate (TUDC) systems either containing or not containing lecithin. Here, CAq,Eq is the cholesterol concentration in the aqueous micellar solution at equilibrium, and Cs,Aq is the cholesterol monohydrate solubility of the same medium. In TC-L solutions supersaturated with cholesterol, the linear relationship continued to hold up to the point where vesicles started to form. Vesicle formation initiated a negative deviation from linearity. At constant lecithin concentration, the CSP,Eq value, or the cholesterol thermodynamic activity at which vesicle formation began, was a function of the TC:L ratio; the larger the TC:L ratio, the higher the cholesterol thermodynamic activity for the onset of vesicle formation.(ABSTRACT TRUNCATED AT 250 WORDS)

Bile↗
PubMed1994

Thermodynamics of barnase unfolding.

The thermodynamics of barnase denaturation has been studied calorimetrically over a broad range of temperature and pH. It is shown that in acidic solutions the heat denaturation of barnase is well approximated by a 2-state transition. The heat denaturation of barnase proceeds with a significant increase of heat capacity, which determines the temperature dependencies of the enthalpy and entropy of its denaturation. The partial specific heat capacity of denatured barnase is very close to that expected for the completely unfolded protein. The specific denaturation enthalpy value extrapolated to 130 degrees C is also close to the value expected for the full unfolding. Therefore, the calorimetrically determined thermodynamic characteristics of barnase denaturation can be considered as characteristics of its complete unfolding and can be correlated with structural features--the number of hydrogen bonds, extent of van der Waals contacts, and the surface areas of polar and nonpolar groups. Using this information and thermodynamic information on transfer of protein groups into water, the contribution of various factors to the stabilization of the native structure of barnase has been estimated. The main contributors to the stabilization of the native state of barnase appear to be intramolecular hydrogen bonds. The contributions of van der Waals interactions between nonpolar groups and those of hydration effects of these groups are not as large if considered separately, but the combination of these 2 factors, known as hydrophobic interactions, is of the same order of magnitude as the contribution of hydrogen bonding.

Bacterial Proteins↗
PubMed1994

Thermodynamic characterization of an equilibrium folding intermediate of staphylococcal nuclease.

High-sensitivity differential scanning calorimetry and CD spectroscopy have been used to probe the structural stability and measure the folding/unfolding thermodynamics of a Pro117-->Gly variant of staphylococcal nuclease. It is shown that at neutral pH the thermal denaturation of this protein is well accounted for by a 2-state mechanism and that the thermally denatured state is a fully hydrated unfolded polypeptide. At pH 3.5, thermal denaturation results in a compact denatured state in which most, if not all, of the helical structure is missing and the beta subdomain apparently remains largely intact. At pH 3.0, no thermal transition is observed and the molecule exists in the compact denatured state within the 0-100 degrees C temperature interval. At high salt concentration and pH 3.5, the thermal unfolding transition exhibits 2 cooperative peaks in the heat capacity function, the first one corresponding to the transition from the native to the intermediate state and the second one to the transition from the intermediate to the unfolded state. As is the case with other proteins, the enthalpy of the intermediate is higher than that of the unfolded state at low temperatures, indicating that, under those conditions, its stabilization must be of an entropic origin. The folding intermediate has been modeled by structural thermodynamic calculations. Structure-based thermodynamic calculations also predict that the most probable intermediate is one in which the beta subdomain is essentially intact and the rest of the molecule unfolded, in agreement with the experimental data. The structural features of the equilibrium intermediate are similar to those of a kinetic intermediate previously characterized by hydrogen exchange and NMR spectroscopy.

Calorimetry, Differential Scanning↗
PubMed1998

Thermodynamics of the reconstitution of tuna cytochrome c from two peptide fragments.

Two peptide fragments from tuna cytochrome c (cyt c), N-fragment (residues 1-44 containing the heme) and C-fragment (residues 45-103), combine to form a 1:1 fragment complex. This was clearly proved by ion-spray mass spectrometry. It was found from CD and NMR spectra that the structure of the fragment complex formed is similar to that of an intact cyt c, although each isolated fragment itself is unstructured. Binding constants and enthalpies upon the complex formation were directly observed by isothermal titration calorimetry. Thermodynamic parameters (deltaG(o)b, deltaHb, deltaS(o)b, and deltaC(b)p)) associated with the complex formation were determined at various pHs and temperatures. DeltaHb was found to be almost independent of pH values. The change in heat capacity accompanying the complex formation (deltaC(b)p) was directly determined from the temperature dependence of deltaHb. In addition, the change in heat capacity and enthalpy upon tuna cyt c unfolding were determined by differential scanning calorimetry. Thermodynamic parameters for the unfolding/dissociation process of the fragment complex were compared with those for cyt c unfolding at pH 3.9 and 303 K. In a comparison of two unfolding processes, the heat capacity change of each was very close to the other, while both the unfolding enthalpy and entropy of the fragment complex were larger than those of tuna cyt c. These thermodynamic data suggest that the internal interactions between polar groups (hydrogen bonding) and nonpolar groups (van der Waals interactions) are preserved in the fragment complex as well as in the native state of cyt c.

Animals↗
PubMed1993

Thermodynamic nonideality in macromolecular solutions: interpretation of virial coefficients.

Consideration is given to the interpretation of virial coefficients reflecting thermodynamic nonideality in incompressible solutions of a single macromolecular species for which there is no volume change on mixing. Expressions are presented for the concentration dependence of thermodynamic activity under conditions where either the chemical potential of solvent or the pressure is fixed, these two conditions being mutually exclusive. For the former situation, which applies to partition equilibrium procedures, the thermodynamic activity is most conveniently defined on the molar scale because the coefficients in polynomial expansions for the osmotic pressure and the activity coefficient in terms of molarity are then related to each other without the inclusion of partial molar volume terms. Under conditions of constant pressure a similar situation prevails provided that the osmotic pressure and the corresponding activity coefficient are expanded in powers of molality. In either case conversion of the virial expansions to the other concentration scale is possible, but requires the introduction of partial molar volume terms into the virial coefficients. The implications of these findings are discussed in relation to results obtained by osmometry, isopiestic measurements, equilibrium dialysis, gel chromatography, and sedimentation equilibrium.

Chromatography, Gel↗
PubMed1993

In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo.

A strong-binding primary (O1) lac operator located 100 to 200 base-pairs (bp) upstream from a lac promoter control region reduces expression from a lac promoter controlled by a weaker-binding (Oc) lac operator between 3 and 20-fold on a multicopy plasmid in E. coli. We attribute this effect to loop formation in which a thermodynamically stable complex is formed between bidentate lac repressor tetramers and the O1 and Oc operators. A thermodynamic model for repression is developed to interpret these data in terms of the composite effects of free lac repressor concentration and of local repressor concentration (from looping) at the Oc site. The local repressor concentration is found to vary periodically with the distance in base-pairs between the O1 and the Oc operators, ranging from 2 to 20-fold larger than the free concentration (i.e. the bulk thermodynamic activity) of repressor in this F'Iq overproducing strain (estimated to be approximately less than 0.5 microM). The amplitude of the periodic variation in expression and in local concentration appears to decrease with increasing interoperator distance in the range examined. Quantitative analysis of the looping data provides estimates of the physical properties of the intervening DNA region in vivo. For distances in the range 127 to 197 bp, the periodicity of modulation is uniformly 11.28(+/- 0.04) bp, which we interpret as the helical repeat of this region of supercoiled plasmid DNA in vivo. Possible origins of this altered helical repeat include the global linking deficit of the supercoiled DNA and any local linking deficit induced by divergent transcription from promoters bracketing the interoperator region. DNA cyclization analysis yields an apparent in vivo persistence length of this interoperator region of 64(+/- 26) A (which is approximately 15% of the in vivo result) and an in vivo torsional rigidity constant of 1.1(+/- 0.1) x 10(-19) erg cm, which is at the lower end of the range of values found in vitro.

DNA, Bacterial↗
PubMed1994

Thermodynamic partitioning model for hydrophobic binding of polypeptides by GroEL. I. GroEL recognizes the signal sequences of beta-lactamase precursor.

From equilibrium measurements with urea we found a three-state thermodynamic and kinetic folding behavior for the precursor and mature form of Escherichia coli beta-lactamase TEM2. The thermodynamic intermediate H of Escherichia coli beta-lactamase and its precursor had no enzymatic activity, and a quenched tryptophan fluorescence intensity, but a native-like wavelength of maximum intensity. State H of mature beta-lactamase was 8.7 kcal mol-1 less stable than the native state N and about 4.2 kcal mol-1 more stable than the unfolded state U, extrapolated to absence of urea. In contrast, state H of precursor beta-lactamase was even more stable than N by about 0.5 kcal mol-1 and about 6.9 kcal mol-1 more stable than U. Native pre-beta-lactamase could be stabilized by lowering the pH value from 7.0 to 5.5, probably by protonating a histidine residue leading to an improved solubility of the signal sequence. Synthetic peptides, containing 23 or 38 N-terminal amino acid residues of pre-beta-lactamase, were unable to compete with pre-beta-lactamase for binding to GroEL. However, GroEL prevented the inactivation of mature beta-lactamase by p38, consistent with competition between GroEL and mature beta-lactamase for binding to p38. The equilibrium constant for dissociation KD of the complex between GroEL and p23, a peptide containing exclusively the signal sequence of pre-beta-lactamase, was measured with the BIAcore instrument to be in the range 10(-7) to 10(-8) M. Our results are consistent with co-operative binding of GroEL to the mature part and to the signal sequence of pre-beta-lactamase. We suggest a thermodynamic partitioning model for hydrophobic binding of polypeptides by GroEL.

Amino Acid Sequence↗
PubMed1994

Thermodynamic partitioning model for hydrophobic binding of polypeptides by GroEL. II. GroEL recognizes thermally unfolded mature beta-lactamase.

By thermal equilibrium measurements we found a three-state folding behavior of mature Escherichia coli beta-lactamase TEM2. The thermodynamically stable intermediate H had no enzymatic activity, but a native-like secondary structure. State H was 9 kcal mol-1 less stable than the native state N and 4 kcal mol-1 more stable than the totally unfolded state U, which is consistent with urea equilibrium measurements of mature beta-lactamase measured under similar conditions. Between 38 degrees C and 50 degrees C there was a decrease in the apparent equilibrium constant for dissociation K'D of the complex between GroEL and mature beta-lactamase, at least partially caused by a decrease in the thermodynamic stability of the native form of mature beta-lactamase. GroEL-bound beta-lactamase was released either after addition of ATP, or in the presence of a competing substrate (i.e. a single-chain antibody), or after lowering the temperature. Whereas at 10 degrees C the folding reaction of mature beta-lactamase was rate limiting, at 37 degrees C the release reaction was the rate-determining step for the regain of beta-lactamase activity, consistent with a decrease of the equilibrium constant for dissociation KD of the complex with temperature. A temperature dependent behavior of GroEL was also observed, when measuring the anilinonaphthalene sulfonic acid (ANS) fluorescence of the chaperone. Similar to all other substrate proteins studied so far, the maximal tryptohan fluorescence of GroEL-bound beta-lactamase was observed at 342 nm. Our results are compatible with a hydrophobic binding pocket of GroEL and confirm the suggested thermodynamic partitioning model for hydrophobic binding of polypeptides by GroEL.

Bacterial Proteins↗
PubMed1995

Thermodynamics of RNA unfolding: stabilization of a ribosomal RNA tertiary structure by thiostrepton and ammonium ion.

RNAs with interesting secondary and tertiary structures tend to melt in several broad and overlapping transitions over a wide temperature range, and it has been consequently difficult to resolve the thermodynamics of individual unfolding steps. In the case that a ligand selectively binds a single folded state of the RNA, it is possible to obtain reliable thermodynamic parameters for both RNA unfolding and RNA-ligand binding simply from the hyperchromicity of RNA denaturation. The analysis procedure involves fitting a three-dimensional surface to absorbance data collected as a function of both temperature and ligand concentration. Analysis of the unfolding of a fragment of the large subunit ribosomal RNA (Escherichia coli sequence 1051 to 1109) is presented; both an antibiotic (thiostrepton) and ammonium ion specifically stabilize a tertiary structure within this RNA. A consistent set of thermodynamic parameters (delta H and tm) for the first two sequentially linked unfolding transitions is obtained from the experiments, and the binding constants obtained for the two ligands are consistent with other independent measurements. The approach is applicable to a variety of RNAs that specifically bind proteins, antibiotics, ions or other ligands.

Ammonia↗
PubMed1999

Thermodynamics of the alpha-helix-coil transition of amphipathic peptides in a membrane environment: implications for the peptide-membrane binding equilibrium.

Amphipathic alpha-helices are the membrane binding motif in many proteins. The corresponding peptides are often random coil in solution but are folded into an alpha-helix upon interaction with the membrane. The energetics of this ubiquitous folding process are still a matter of conjecture. Here, we present a new method to quantitatively analyze the thermodynamics of peptide folding at the membrane interface. We have systematically varied the helix content of a given amphipathic peptide when bound to the membrane and have correlated the thermodynamic binding parameters determined by isothermal titration calorimetry with the alpha-helix content obtained by circular dichroism spectroscopy. The peptides investigated were the antibiotic magainin 2 amide and three analogs in which two adjacent amino acid residues were substituted by their d-enantiomers. The thermodynamic parameters controlling the alpha-helix formation were found to be linearly related to the helicity of the membrane-bound peptides. Helix formation at the membrane surface is characterized by an enthalpy change of DeltaH(helix) approximately -0.7 kcal/mol per residue, an entropy change of DeltaS(helix) approximately -1.9 cal/molK residue and a free energy change of DeltaG(helix)=-0.14 kcal/mol residue. Helix formation is a strong driving force of peptide insertion into the membrane and accounts for about 50 % of the free energy of binding. An increase in temperature entails an unfolding of the membrane-bound helix. The temperature dependence can be described with the Zimm-Bragg theory and the enthalpy of unfolding agrees with that deduced from isothermal titration calorimetry.

Calorimetry↗
PubMed2000

Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus.

To elucidate early nucleation stages in protein folding, multi-probed thermodynamic characterization was applied to the beta-hairpin structural formation of G-peptide, which is a C-terminal fragment of the B1 domain of streptococcal protein G. The segment corresponding to the sequence of G-peptide is believed to act as a nucleus during the folding process of the B1 domain. In spite of the broad thermal transition of G-peptide, nuclear magnetic resonance (NMR) melting measurements combined with our original analytical theory enabled us to obtain the thermodynamic properties of the beta-hairpin formation with considerable accuracy. Additionally, all the thermodynamic properties determined by every NMR probe on both the main-chain and the side-chains were quite similar, and also comparable to the values that were independently determined by calorimetric analysis of G-peptide. These results demonstrate that G-peptide folds cooperatively throughout the molecule. In other words, the formation of the beta-hairpin is interpreted as the fashion of a first-order phase transition between two states without any distinguishable intermediates. This cooperative formation of the short linear peptide consisting of only 16 residues provides insight into not only the first folding events of the B1 domain, but also the general principles of proteins in terms of structural hierarchy, stability and folding mechanism.

Bacterial Proteins↗
PubMed2000

The thermodynamic stability of the proteins of the ccd plasmid addiction system.

The two opponents, toxin (CcdB, LetB or LetD, protein G, LynB) and antidote (CcdA, LetA, protein H, LynA), in the plasmid addiction system ccd of the F plasmid were studied by different biophysical methods. The thermodynamic stability was measured at different temperatures combining denaturant and thermally induced unfolding. It was found that both proteins denature in a two-state equilibrium (native dimer versus unfolded monomer) and that CcdA has a significantly lower thermodynamic stability. Using a numerical model, which was developed earlier by us, and on the basis of the determined thermodynamic parameters the concentration dependence of the denaturation transition temperature was obtained for both proteins. This concentration dependence may be of physiological significance, as the concentration of both ccd addiction proteins cannot exceed a certain limit because their expression is controlled by autoregulation. The influence of DNA on the thermal stability of the two proteins was probed. It was found that cognate DNA increases the melting temperature of CcdA. In the presence of non-specific DNA the thermal stability was not changed. The melting temperature of CcdB was not influenced by the applied double-stranded oligonucleotides, neither cognate nor unspecific.

Bacterial Proteins↗
PubMed1994

Let there be life. Thermodynamic reflections on biogenesis and evolution.

The question of how life emerged from inanimate matter is closely related to the more fundamental question, namely: What is life? Both issues yield novel insights when discussed in the light of thermodynamics. The model proposed here is based on a simple assumption, namely, that life began with the accidental assembly of a self-replicating molecule. From this assumption the emergence of life naturally follows, enabling a new understanding of evolution as a whole. The evolution of any type of self-replicating systems, even the simplest ones, is shown to be highly efficient in extracting, recording and processing information about the environment. A variety of related issues yield some surprising conclusions when discussed in the thermodynamic context. New processes of order-increase are pointed out, a novel measure of information is proposed, and Lamarckianism is proved to be inconsistent with thermodynamics. Recent works on biogenesis and evolution are critically reviewed.

Animals↗
PubMed2001

Local thermodynamic stability scores are well represented by a non-central student's t distribution.

Local folding in mRNAs is closely associated w ith biological functions. In this study, we reveal the whole distribution of local thermodynamic stability in the complete genome of the poliovirus P3/Leon/37 and the single-stranded RNA sequences that corresponds to the nucleotide sequence of the complete genome sequence (1 667 867 bp) of Helicobacter pylori (H. pylori) strain 26695. Local thermodynamic stability in the RNA sequences is measured by two standard z -scores, significance score and stability score. To estimate the distribution of thermodynamic stability, a model based on the non-central Student's t distribution has been developed. Significant patterns of extremes that are either much more stable or unstable than expected by chance are detected. Our results indicate that the highly stable and statistically more significant folding regions are predominantly in non-coding sequences in the two genome sequences. Moreover, the highly unstable folding regions, on the contrary, are predominantly in the protein coding sequences of H. pylori. The observed differences across the complete genomic sequences are statistically very significant by a chi2-test. These extreme patterns may be useful in searching for target sequences for long-chain antisense RNA and for locating potential RNA functional elements involved in the regulation of gene expression including translation, mRNA localization and metabolism.

Animals↗