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PubMed1985

Geometric and thermodynamic restrictions for the self-assembly of glycosphingolipid-phospholipid systems.

The thermodynamic and geometrical features of possible self-assembled structures of a series of chemically related glycosphingolipids differing in the complexity of their polar headgroup, and of their mixture with phospholipids, have been predicted according to the theory of self-assembly of hydrocarbon amphiphiles of Israelachvili et al. ((1980) Q. Rev. Biophys. 13, 340-357). The type and number of carbohydrate residues in the oligosaccharide chain of the polar headgroup are of paramount importance to determine the characteristics and thermodynamic stability of the possible self-assembled structure. In single component systems, the general prediction of the theory is that smaller aggregates may form as the polar headgroup of the glycosphingolipid is more complex and as the lateral surface pressure is smaller. In noninteracting two-component glycosphingolipid-phospholipid systems, the thermodynamic stability and the overall geometry of the possible aggregate appear to be determined by the proportion and type of glycosphingolipid present. Large and abrupt changes of the possible free energy per molecule, radius of curvature, and predicted asymmetry ratio for a particular glycosphingolipid may be triggered by relatively small changes of the molecular parameters, lipid composition, lateral surface pressure or vice-versa. If intermolecular interactions are taken into account with respect to the predictions for an ideal, noninteracting system, the theory indicates that two-component bilayer vesicles of polysialoganglioside-phosphatidylcholine may be thermodynamically and geometrically more stable. On the other hand, for systems constituted by phosphatidylcholine and neutral glycosphingolipids or monosialogangliosides, the possible bilayer vesicle is predicted to be less stable than in the ideal, noninteracting case. The results emphasize the general validity of the theory as applied to glycosphingolipid-containing systems.

Glycosphingolipids↗
PubMed1991

Solid model compounds and the thermodynamics of protein unfolding.

Analysis of thermodynamic data on the dissolution of solid cyclic dipeptides into water in terms of group additivity provides a rationale for the enthalpy and entropy convergence temperatures observed for small globular protein denaturation and the dissolution of model compounds into water. Convergence temperatures are temperatures at which the extrapolated enthalpy or entropy changes for a series of related compounds take on a common value. At these temperatures (TH* and TS*) the apolar contributions to the corresponding thermodynamic values (delta H degrees and delta S degrees) are shown to be zero. Other contributions such as hydrogen bonding and configurational effects can then be evaluated and their quantitative effects on the stability of globular proteins assessed. It is shown that the denaturational heat capacity is composed of a large positive contribution from the exposure of apolar groups and a significant negative contribution from the exposure of polar groups in agreement with previous results. The large apolar contribution suggests that a liquid hydrocarbon model of the hydrophobic effect does not accurately represent the apolar contribution to delta H degrees of denaturation. Rather, significant enthalpic stabilizing contributions are found to arise from peptide groups (hydrogen bonding). Combining the average structural features of globular proteins (i.e. number of residues, fraction of buried apolar groups and fraction of hydrogen bonds) with their specific group contributions permits a first-order prediction of the thermodynamic properties of proteins. The predicted values compare well with literature values for cytochrome c, myoglobin, ribonuclease A and lysozyme. The major thermodynamic features are described by the number of peptide and apolar groups in a given protein.

Cytochrome c Group↗
PubMed1992

Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration.

Thermodynamic-cycle perturbation theory and molecular dynamics simulations were used to calculate the difference in the free energy of binding of the antiviral compound WIN53338 to the wild-type human rhinovirus 14 and to a drug-resistant mutant of the virus in which valine 188 of the viral protein 1 is mutated to leucine. Because of the difficulty of achieving adequate sampling of all of the rotational isomers of amino acid side-chains in molecular dynamics simulations, an explicit treatment of the effects of the existence of multiple rotational isomers of residue 188 on the calculated free energies was used. The rotamers of residue 188 were first mapped by steric and energetic techniques as described in the accompanying article. Thermodynamic integration was then carried out during simulations of the virus, both with and without the antiviral compound bound, by mutating residue 188 while restraining its side-chain to one conformation. The contributions of the other rotamers of residue 188 to the free-energy changes for this mutation were then added to those calculated by thermodynamic integration as correction factors. Binding of WIN53338 to the wild-type virus was calculated to be favored over binding to the mutant virus by 1.7(+/- 3.0) kcal/mol. This is consistent with experimental data which, if differences in activity are assumed to be due to differences in binding, indicate that the binding affinity of WIN53338 for the wild-type virus is at least 0.15 to 1.7 kcal/mol greater than for the mutant virus. Thermodynamic integration was also performed in the conventional manner without restraints and was found to give less accurate results.

Antiviral Agents↗
PubMed1996

Binding thermodynamics at A1 and A2A adenosine receptors.

Only recently the binding equilibrium of a number of ligands at adenosine A1 and A2a receptors has been analyzed from a thermodynamic point of view. This approach presents the advantage, with respect to usual affinity constant measurements, of a greater capability to give information about the molecular mechanisms underlying the binding process. All available data agree in indicating that, for both A1 and A2a receptors, agonist binding of adenosine derivatives was totally entropy-driven, while xanthine antagonist binding was essentially enthalpy-driven. The differences in thermodynamic behaviour of A1 and A2a agonists and antagonists could be interpreted in terms of a simplified general model of drug-receptor interaction, which accounted for the role played by the ribose moiety and N6-substituents of adenosinic drugs in determining both affinity and intrinsic activity properties. In the frame of this model, measurements of thermodynamic parameters of N6-monosubstituted agonists allowed to hypothesize, for the first time, the existence of partial agonists to adenosine A1 receptors, as now confirmed experimentally. All thermodynamic data concerning the interaction of all ligands studied with A1 and A2a receptors are briefly discussed in terms of the enthalpy-entropy compensation phenomenon which appears to be widely determined by the reorganization of solvent molecules in the binding process.

Animals↗
PubMed1991

Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA.

The concentration and nature of the electrolyte are key factors determining (1) the equilibrium extent of binding of oligocations or proteins to DNA, (2) the distribution of bound protein between specific and nonspecific sites, and (3) the kinetics of association and dissociation of both specific and nonspecific complexes. Salt concentration may therefore be used to great advantage to probe the thermodynamic basis of stability and specificity of protein-DNA complexes, and the mechanisms of association and dissociation. Cation concentration serves as a thermodynamic probe of the contributions to stability and specificity from neutralization of DNA phosphate charges and/or reduction in phosphate charge density. Cation concentration also serves as a mechanistic probe of the kinetically significant steps in association and dissociation that involve cation uptake. In general, effects of electrolyte concentration on equilibrium constants (quantified by SKobs) and rate constants (quantified by Skobs) are primarily cation effects that result from the cation-exchange character of the interactions of proteins and oligocations with polyanionic DNA. The competitive effects of Mg2+ or polyamines on the equilibria and kinetics of protein-DNA interactions are interpretable in the context of the cation-exchange model. The nature of the anion often has a major effect on the magnitude of the equilibrium constant (Kobs) and rate constant (kobs) of protein-DNA interactions, but a minor effect on SKobs and Skobs, which are dominated by the cation stoichiometry. The order of effects of different anions generally follows the Hofmeister series and presumably reflects the relative extent of preferential accumulation or exclusion of these anions from the relevant surface regions of DNA-binding proteins. The question of which anion is most inert (i.e., neither accumulated nor excluded from the relevant regions of these proteins) remains unanswered. The characteristic effects of temperature on equilibrium constants and rate constants for protein-DNA interactions also serve as diagnostic probes of the thermodynamic origins of stability and specificity and of the mechanism of the interaction, since large changes in thermodynamic and activation heat capacities accompany processes with large changes in the amount of water-accessible nonpolar surface area.(ABSTRACT TRUNCATED AT 400 WORDS)

Anions↗
PubMed1996

The interaction of sodium dodecyl sulfate and urea with cat-fish collagen solutions in acetate buffer: hydrodynamic and thermodynamic studies.

Cat-fish collagen was extracted and characterized. Shrinkage temperature of cat-fish collagen is 54.5 degrees C. SDS-PAGE pattern indicated that the cat-fish collagen is Type I in nature. The ratio of proline and hydroxyproline is 1:2 and it suggests cat-fish collagen is vertebrate. The molecular weight of cat-fish collagen was determined by using molecular sieve chromatography and it was found to be 3 20,000 Da. The mutual interaction of cat-fish collagen with SDS and urea was studied at various temperatures. The results suggest that the aggregation of collagen is facilitated by the presence of SDS, whereas hindered by urea. The various thermodynamic parameters were estimated from viscosity measurements and the transfer of collagen into SDS micelles, urea and the reverse phenomenon was analysed. These transfer properties are temperature-dependent. Our thermodynamic results are also able to predict the exact denaturation temperature as well as the structural order of water in the collagen in various environments. The hydrated volumes, Vh of collagen in buffer, SDS, and urea environments using Simha-Einstein equation and intrinsic viscosity were also calculated. The low intrinsic viscosity [eta] and high Vh value of collagen in an SDS environment compared to buffer and other environments suggested a more workable system in cosmetic and dermatological preparations. The one and two-hydrogen-bonded models of this collagen in various environments have been analysed. The calculated thermodynamic parameters varied with the concentration of collagen as well as concentration of additives. The change of thermodyanamic parameters from coiled-coil to random-coil conformation upon denaturation of collagen were calculated from the amount of proline and hydroxyproline residues and compared with viscometric results. Denaturation enthalpy of the catfish collagen in buffer, SDS and urea environments has also been determined by differential scanning calorimetric (DSC) measurements, and the results are in good agreement with the viscosity-derived values. The assymmetry and molecular geometry of this collagen in buffer, SDS and urea environments are also computed. Overall, our hydrodynamic and thermodynamic results suggest that the stability of the collagen in the additive environments is in the following order: SDS > buffer > urea.

Acetates↗
PubMed1985

AMP interaction sites in glycogen phosphorylase b. A thermodynamic analysis.

The binding of AMP to activator site N and to inhibitor site I in glycogen phosphorylase b has been characterized by calorimetry, potentiometry and ultracentrifugation in the pH range 6.5-7.5 at 25 degrees C (mu = 0.1). Calorimetric titration data of phosphorylase b with adenosine 5'-phosphoramidate are also reported at pH 6.9 (T = 25 degrees C, mu = 0.1). Calorimetric curves have been analyzed on the basis of potentiometric and sedimentation velocity results to determine thermodynamic quantities for AMP binding to the enzyme. The comparison of calorimetric titration data of AMP and adenosine 5'-phosphoramidate at pH 6.9 supports the hypothesis previously suggested that the dianionic phosphate form of the nucleotide preferentially binds to the allosteric activator site. The thermodynamic parameters for AMP binding to site N are as follows: delta G0 = -22 kJ mol-1, delta H0 = -34 kJ mol-1 and delta S0 = -40 J mol-1 K-1. The binding of the nucleotide to site I was found to be strongly dependent on the pH. This behaviour may be explained in terms of coupled protonations of three groups having pKa values of 6.0, 6.0 and 6.1 in the unbound form and 7.0, 7.5 and 7.2 in the enzyme-nucleotide complex. The thermodynamic parameters for nucleotide binding to site I for the enzymatic form in which all the modified groups are completely deprotonated or protonated have been calculated to be: delta G0 = -7.7 kJ mol-1, delta H0 = -28 kJ mol-1 and delta S0 = -68 J mol-1 K-1 and delta G0 = -28 kJ mol-1, delta H0H = -10 kJ mol-1 and delta S0H = 61 J mol-1 K-1, respectively. These results suggest that attractive dispersion forces are of primary significance for AMP binding to activator site N, although electrostatic interactions act as a stabilizing factor in the nucleotide binding. The protonation states of those residues of which the pKa values are modified by AMP binding to site I highly influence the thermodynamic parameters for the nucleotide binding to this site.

Adenosine Monophosphate↗
PubMed1990

Kinetics and thermodynamics of metabolite transfer between enzymes.

Based on experimental evidence put forward by Bernhard and others, we explore the kinetics and thermodynamics of the proposed direct and diffusional transfer mechanisms of enzymatic catalysis. Data for transient transfer of NADH between two cognate dehydrogenases (E1 and E2) are combined with steady-state catalytic data to quantify the kinetics of the two transfer mechanisms. In order to rationalize these data we find: (1) that the rate constants for direct transfer of NADH from E1-NADH to E2 must be much larger when a reactive metabolite, M, is bound to E2, (2) that a significant amount of noncatalytic complex E1-E2-M must be formed, and (3) that dissociation constants of the order of 1 microM are required for the ternary complexes involved in direct transfer (E1-NADH-E2). Using values of rate parameters similar to those assumed in these calculations, we proceed to explore the kinetics and thermodynamics of a hypothetical two-enzyme segment of a metabolic pathway that involves direct and diffusional metabolite transfer operating in parallel. Under steady-state conditions, we conclude from our calculations: (1) that the flux through the direct transfer branch would be comparable to or greater than that through the diffusional transfer branch under physiological conditions, (2) that activity effects resulting from physiological concentrations of inert protein enhance the predominance of the direct transfer flux, (3) that significant concentrations of ternary transfer complexes are formed, (4) that changes in the catalytic mechanism involving the ternary complex have little effect, (5) that direct transfer significantly moderates the reduction in metabolic flux caused by protein complexation, and (6) that direct transfer greatly alters the thermodynamics and kinetics of our hypothetical pathways. We conclude, therefore, that direct transfer--when it exists--would have important kinetic, thermodynamic, and physiological consequences in vivo.

Enzymes↗
PubMed2004

Thermodynamics of alpha-lactalbumin-DL-alpha-dipalmitoylphosphatidylcholine interactions and effect of the antioxidant nicotinamide on these interactions.

Differential scanning calorimetry has been used to understand the thermodynamics of the interactions of dl-alpha-dipalmitoylphosphatidylcholine (DPPC) with alpha-lactalbumin and the effect of the antioxidant nicotinamide on these interactions. Nicotinamide decreases the thermal transition temperature of both the lipid and the protein at high concentrations. The thermal unfolding transitions of the protein were two state and calorimetrically reversible. There was no significant change in the shape and thermodynamic parameters accompanying the lipid endotherms, suggesting that nicotinamide did not penetrate the lipid bilayer. The thermal unfoldings of alpha-lactalbumin in the presence of DPPC as cosolute also adhered to two-state reversible mechanism. The changes in the thermodynamic parameters accompanying the thermal transitions were small, indicating no significant interaction of alpha-lactalbumin with DPPC. The changes in the thermodynamic parameters indicate that the lipid bilayer organization, as well as the partitioning of the extrinsic protein alpha-lactalbumin into the bilayer, is not affected in the entire studied concentration range of the lipid. It is observed that the presence of increasing concentration of nicotinamide (as high as 1.0 mol dm(-3)) in the lipid-protein mixture does not affect its partitioning into the lipid bilayer, although nicotinamide preferentially interacts with alpha-lactalbumin. The change in the effect of nicotinamide on lipid transition temperature in the mixture and literature report suggests that nicotinamide may be forming a hydrogen-bonded complex with the protein through its amide functionality. The surface tension data of aqueous nicotinamide in combination with the thermal denaturation results of protein in presence of nicotinamide confirmed that surface tension effect does not have any significant contribution to the effect of nicotinamide on protein.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2004

Reversed-phase retention thermodynamics of pure-water mobile phases at ambient and elevated temperature.

The use of pure water at superheated temperatures, between 100 and 200 degrees C, as a mobile phase for reversed-phase separations is explored. The thermodynamics of the retention process at low temperature (15-55 degrees C) are compared to the thermodynamics at elevated temperature (125-175 degrees C). Significant differences in the enthalpy of the retention process are observed between the two temperature ranges. This is possibly due to changes in the hydrogen-bond network of the pure-water mobile phase, which would change the solvation, and therefore retention, of non-polar solutes. The change in thermodynamic values between the two temperature regions invalidates extrapolation of retention as a function of temperature between the two temperature regions for the prediction of room-temperature pure-water retention factors. The thermodynamic changes observed as the temperature is increased are similar to those seen when mobile phase composition is changed (by adding organic modifier) at constant temperature.

Hydrogen Bonding↗
PubMed2006

A thermodynamic view of networks.

Networks can be described by the frequency distribution of the number of links associated with each node (the degree of the node). Of particular interest are the power law distributions, which give rise to the so-called scale-free networks, and the distributions of the form of the simplified canonical law (SCL) introduced by Mandelbrot, which give what we shall call the Mandelbrot networks. Many dynamical methods have been obtained for the construction of scale-free networks, but no dynamical construction of Mandelbrot networks has been demonstrated. Here we develop a systematic technique to obtain networks with any given distribution of the degrees of the nodes. This is done using a thermodynamic approach in which we maximise the entropy associated with degree distribution of the nodes of the network subject to certain constraints. These constraints can be chosen systematically to produce the desired network architecture. For large networks we therefore replace a dynamical approach to the stationary state by a thermodynamical viewpoint. We use the method to generate scale-free and Mandelbrot networks with arbitrarily chosen parameters. We emphasise that this approach opens the possibility of insights into a thermodynamics of networks by suggesting thermodynamic relations between macroscopic variables for networks.

Computer Simulation↗
PubMed2005

Isothermal titration calorimetry method for determination of cyclodextrin complexation thermodynamics between artemisinin and naproxen under varying environmental conditions.

A novel isothermal titration calorimetry method was used to determine the complexation thermodynamics for hydroxypropyl-beta-cyclodextrin with artemisinin and naproxen at varying temperature and pH. The new method is very useful for studying complexation reactions between cyclodextrin and drugs with poor solubility and all the thermodynamic parameters of the cyclodextrin complexation were determined. The analysis of the thermodynamic data reveals involvement of hydrophobic bonding in the cyclodextrin complexes studied. The data also reveals the presence of enthalpy-entropy compensation in the system and provide information as to the orientation of the drug molecule inside the cyclodextrin cavity. From the thermodynamic parameters for dissociation of HPBCD complexes of artemisinin and naproxen at pH 2 it is concluded that the complexation is primarily driven by enthalpy with entropic assistance at all temperatures studied. From the dissociation studies of HPBCD complexes of naproxen at pH 10 it is concluded that the complexation is predominantly driven by entropy and moderately by enthalpy at lower temperatures and by enthalpy with entropic assistance at higher temperatures.

Artemisinins↗
PubMed2005

Protein evolution in viral quasispecies under selective pressure: a thermodynamic and phylogenetic analysis.

The evolution of RNA viruses under antiviral pressure is characterized by high mutation rates and strong selective forces that induce extremely rapid changes of protein sequences. This makes the course of molecular evolution directly observable on time scales of months. Here we study the interplay between selection for drug resistance and selection for thermodynamic stability in the protease (PR) and the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) clones extracted from two patients with complex treatment histories. This analysis shows that folding thermodynamic properties may fluctuate very strongly in the course of quasispecies evolution under selective pressure. For the first case, our data suggest that folding efficiency of the RT is sacrificed at the advantage of drug resistance, while the corresponding PR seems to undergo selection for thermodynamic stability in the absence of substitutions associated to resistance. The PR of the second case is not submitted to antiviral pressure during the period analyzed and seems to initiate random fluctuations that lead to the accidental increase of its folding efficiency. In summary, joint consideration of sequence evolution and thermodynamic parameters can represent a more comprehensive approach for the study of the evolution of RNA viruses.

Anti-HIV Agents↗
PubMed2004

Thermodynamic dissection of the binding energetics of proline-rich peptides to the Abl-SH3 domain: implications for rational ligand design.

The inhibition of the interactions between SH3 domains and their targets is emerging as a promising therapeutic strategy. To date, rational design of potent ligands for these domains has been hindered by the lack of understanding of the origins of the binding energy. We present here a complete thermodynamic analysis of the binding energetics of the p41 proline-rich decapeptide (APSYSPPPPP) to the SH3 domain of the c-Abl oncogene. Isothermal titration calorimetry experiments have revealed a thermodynamic signature for this interaction (very favourable enthalpic contributions opposed by an unfavourable binding entropy) inconsistent with the highly hydrophobic nature of the p41 ligand and the Abl-SH3 binding site. Our structural and thermodynamic analyses have led us to the conclusion, having once ruled out any possible ionization events or conformational changes coupled to the association, that the establishment of a complex hydrogen-bond network mediated by water molecules buried at the binding interface is responsible for the observed thermodynamic behaviour. The origin of the binding energetics for proline-rich ligands to the Abl-SH3 domain is further investigated by a comparative calorimetric analysis of a set of p41-related ligands. The striking effects upon the enthalpic and entropic contributions provoked by conservative substitutions at solvent-exposed positions in the ligand confirm the complexity of the interaction. The implications of these results for rational ligand design are discussed.

Amino Acid Sequence↗
PubMed2005

Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases.

Alpha-lytic protease (alpha LP) and Streptomyces griseus protease B (SGPB) are two extracellular serine proteases whose folding is absolutely dependent on the existence of their companion pro regions. Moreover, the native states of these proteins are, at best, marginally stable, with the apparent stability resulting from being kinetically trapped in the native state by large barriers to unfolding. Here, in an effort to understand the physical properties that distinguish kinetically and thermodynamically stable proteins, we study the temperature-dependences of the folding and unfolding kinetics of alpha LP and SGPB without their pro regions, and compare their behavior to a comprehensive set of other proteins. For the folding activation thermodynamics, we find some remarkable universal behaviors in the thermodynamically stable proteins that are violated dramatically by alpha LP. Despite significant variations in deltaC(P,F)++, the maximal folding speed occurs within the narrow biological temperature range for all proteins, except for alpha LP, with its maximal folding speed shifted lower by 200 K. This implies evolutionary pressures on folding speed for typical proteins, but not for alpha LP. In addition, the folding free energy barrier in the biological temperature range for most proteins is predominantly enthalpic, but purely entropic for alpha LP. The unfolding of alpha LP and SGPB is distinguished by three properties: a remarkably large deltaC(P,U)++, a very high deltaG(U)++, and a maximum deltaG(u)++ at the optimal growth temperature for the organism. While other proteins display each of these traits to some approximation, the simultaneous optimization of all three occurs only in the kinetically stable proteins, and appears to be required to maximize their unfolding cooperativity, by suppressing local unfolding events, and slowing the rate of global unfolding. Together, these properties extend the lifetime of these enzymes in the highly proteolytic extracellular environment. Attaining such functional properties seems possible only through the gross perturbation of the folding thermodynamics, which in turn has required the co-evolution of pro regions as folding catalysts.

Bacterial Proteins↗
PubMed1998

Binding thermodynamics at the human neuronal nicotine receptor.

The thermodynamic parameters deltaGo (standard free energy), deltaHo (standard enthalpy) and deltaSo (standard entropy) of the binding equilibrium of eleven ligands (six agonists and five antagonists) to the neuronal nicotinic receptor were determined by affinity measurements carried out on human thalamus membranes at six different temperatures (0, 10, 20, 25, 30, 35 degrees) and deltaG vs. T plot analysis. Affinity constants were obtained by saturation experiments for [3H]-cytisine, a ganglionic nicotinic agonist, or its displacement in inhibition assays for the other compounds. The deltaG vs T plots appeared to be reasonably linear in the full temperature range for most of the compounds investigated (equilibrium heat capacity change,deltaCo(p) approximately 0), with the exception of the three agonists cytisine, nicotine and methylcarbachol (deltaCo(p) of the order of -720 / -1610 J mol(-1) K(-1)). Thermodynamic parameters were in the range -53.3 < or =deltaHo < or = -28.9 kJ mol(-1) and -41 < or = deltaSo < or = 69 J mol(-1) K(-1) for agonists, and 8.7 < or = deltaHo < or = 68.2 kJ mol(-1) and 99 < or = deltaSo < or = 311 J mol(-1) K(-1) for antagonists, indicating that agonistic binding was both enthalpy- and entropy-driven, while antagonistic binding was totally entropy-driven. Agonists and antagonists were, therefore, thermodynamically discriminated. Experimental results were discussed with particular regard to the following points: 1) reasons why membrane receptors displayed unusually low values of deltaCo(p); 2) possible reasons for the phenomenon of thermodynamic discrimination between agonists and antagonists particularly in connection with ligand-gated ion channel receptors; and 3) the origin of the recurrent phenomenon of enthalpy-entropy compensation which has been observed for neuronal nicotinic receptor ligands as well as for all membrane receptors studied thus far.

Binding, Competitive↗
PubMed1993

Thermodynamics and dynamics of phosphatidylcholine-cholesterol mixed model membranes in the liquid crystalline state: effects of water.

A method for obtaining the thermodynamic activity of each membrane component in phosphatidylcholine (PC)/cholesterol mixtures, that is based upon ESR spin labeling is examined. The thermodynamic activity coefficients, gamma PC and gamma chol, for the PC and cholesterol, respectively, are obtained from the measured orientational order parameters, SPC and S(chol), as a function of cholesterol content for a spin-labeled PC and the sterol-type cholestane spin probe (CSL), respectively, and the effects of water concentration are also considered. At water content of 24 weight%, the thermodynamics of DMPC/cholesterol/water mixtures in the liquid-crystalline state may be treated as a two-component solution ignoring the water, but at lower water content the role of water is important, especially at lower cholesterol concentrations. At lower water content (17 wt%), gamma chol decreases with increasing cholesterol content which implies aggregation. However, at higher water content (24 wt%), gamma chol is found initially to increase as a function of cholesterol content before decreasing at higher cholesterol content. This implies a favorable accommodation for the cholesterol in the membrane at high water and low cholesterol content. Good thermodynamic consistency according to the Gibbs-Duhem equation was obtained for gamma PC and gamma chol at 24 wt% water. The availability of gamma chol (and gamma PC) as a function of cholesterol concentration permits the estimate of the boundary for phase separation. The rotational diffusion coefficients of the labeled PC and of CSL were also obtained from the ESR spectra. A previously proposed universal relation for the perpendicular component of the rotational diffusion tensor, R perpendicular, for CSL in PC/cholesterol mixtures (i.e., R perpendicular = R0 perpendicular exp(-AS2chol/RT)) is confirmed. A change in composition of cholesterol or of water for DMPC/cholesterol/water mixtures affects R perpendicular only through the dependence of S(chol) on the composition. In particular, the amount of water affects the membrane fluidity, monitored by R perpendicular for CSL, solely by the structural changes it induces in the membrane for the compositions studied. Rotational diffusion for the labeled PC is found to be more complex, most likely due to the combined action of the internal modes of motion of the flexible chain and of the overall molecular reorientation.

Biophysical Phenomena↗
PubMed1997

Thermodynamic and structural analysis of microtubule assembly: the role of GTP hydrolysis.

Different models have been proposed that link the tubulin heterodimer nucleotide content and the role of GTP hydrolysis with microtubule assembly and dynamics. Here we compare the thermodynamics of microtubule assembly as a function of nucleotide content by van't Hoff analysis. The thermodynamic parameters of tubulin assembly in 30-100 mM piperazine-N,N'-bis(2-ethanesulfonic acid), 1 mM MgSO4, 2 mM EGTA, pH 6.9, in the presence of a weakly hydrolyzable analog, GMPCPP, the dinucleotide analog GMPCP plus 2 M glycerol, and GTP plus 2 M glycerol were obtained together with data for taxol-GTP/GDP tubulin assembly (GMPCPP and GMPCP are the GTP and GDP nucleotide analogs where the alpha beta oxygen has been replaced by a methylene, -CH2-). All of the processes studied are characterized by a positive enthalpy, a positive entropy, and a large, negative heat capacity change. GMPCP-induced assembly has the largest negative heat capacity change and GMPCPP has the second largest, whereas GTP/2 M glycerol- and taxol-induced assembly have more positive values, respectively. A large, negative heat capacity is most consistent with the burial of water-accessible hydrophobic surface area, which gives rise to the release of bound water. The heat capacity changes observed with GTP/2 M glycerol-induced and with taxol-induced assembly are very similar, -790 +/- 190 cal/mol/k, and correspond to the burial of 3330 +/- 820 A2 of nonpolar surface area. This value is shown to be very similar to an estimate of the buried nonpolar surface in a reconstructed microtubule lattice. Polymerization data from GMPCP- and GMPCPP-induced assembly are consistent with buried nonpolar surface areas that are 3 and 6 times larger. A linear enthalpy-entropy and enthalpy-free energy plot for tubulin polymerization reactions verifies that enthalpy-entropy compensation for this system is based upon true biochemical correlation, most likely corresponding to a dominant hydrophobic effect. Entropy analysis suggests that assembly with GTP/2 M glycerol and with taxol is consistent with conformational rearrangements in 3-6% of the total amino acids in the heterodimer. In addition, taxol binding contributes to the thermodynamics of the overall process by reducing the delta H degree and delta S degree for microtubule assembly. In the presence of GMPCPP or GMPCP, tubulin subunits associate with extensive conformational rearrangement, corresponding to 10% and 26% of the total amino acids in the heterodimer, respectively, which gives rise to a large loss of configurational entropy. An alternative, and probably preferable, interpretation of these data is that, especially with GMPCP-tubulin, additional isomerization or protonation events are induced by the presence of the methylene moiety and linked to microtubule assembly. Structural analysis shows that GTP hydrolysis is not required for sheet closure into a microtubule cylinder, but only increases the probability of this event occurring. Sheet extensions and sheet polymers appear to have a similar average length under various conditions, suggesting that the minimum cooperative unit for closure of sheets into a microtubule cylinder is approximately 400 nm long. Because of their low level of occurrence, sheets are not expected to significantly affect the thermodynamics of assembly.

Animals↗