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PubMed1995

Crystallographic and thermodynamic comparison of structurally diverse molecules binding to streptavidin.

Crystallographic structures and thermodynamic binding parameters are compared for three structural classes of streptavidin ligand including d-biotin, 2-[(4'-hydroxyphenyl)-azo] benzoate and the peptide NH(2)-Phe-Ser-His-Pro-Gln-Asn-Thr-COOH. Descriptions of these structural and thermodynamic observations emphasize the diversity of potential strategies for improving ligand affinity.

Journal Article↗
PubMed1987

Effect of calcium chloride on the conformation of proteins. Thermodynamic studies of some model compounds.

Partial molar heat capacities (CP2 degrees) and volumes (V2 degrees) for some amino acids and peptides were measured in 1 M aqueous calcium chloride solutions at 298.15 degrees K using a Picker flow microcalorimeter and an oscillating-tube digital density meter. Using the data for these amino acids and peptides in water, the corresponding partial molar heat capacities of transfer (CP2,tr degree) and volumes (V2,tr degree) from water to 1 M aqueous calcium chloride were deduced. These thermodynamic parameters are significantly positive, indicating that strong interactions occur between the ions of calcium chloride and the charged centres of these amino acids and peptides. A comparison has been made with a similar transfer of these compounds to sodium chloride solutions. The thermodynamic parameters of the transfer of peptide group (-CONH) are much more positive in calcium chloride than in sodium chloride solutions. The implication of this result for the ability of calcium chloride to act as a stronger destabilizer of protein conformation is discussed.

Amino Acids↗
PubMed2000

Thermodynamics of the size and shape of nanocrystals: epitaxial Ge on Si(001).

The growth and evolution of strained epitaxial Ge on a Si(001) surface provides a rich system for exploring the behavior of strongly interacting nanocrystals. In the temperature regime above 500 degrees C, there are two different (metastable) shapes of defect-free nanocrystals, termed pyramids and domes, that dominate the system depending on the temperature of the substrate during growth and the amount of Ge deposited. In contrast to the usual case considered in nucleation theory, the relaxation of the strain energy at the surface of the nanocrystals makes those surfaces stabilizing, i.e. the surface contribution to the free energy of the Ge nanocrystals is negative. Given that the edges of the nanocrystals are destabilizing (positive free energy), the interaction of the surfaces and edges of the nanocrystals in an ensemble renders an internal free energy for the system that has a local minimum with respect to the size (volume) of the nanocrystal. At finite temperatures, this free energy yields a size distribution with a characteristic centroid, width, and skewness for each nanocrystal shape. The smaller pyramids transform into domes when they grow to the point where they can surmount a kinetic energy barrier between the two structures. However, the Ge nanocrystals also effectively repel one another strongly via the strain fields that are produced in the Si substrate. This repulsive interaction makes the ensemble of Ge nanocrystals a highly nonideal thermodynamic system and, in turn, makes the free energies of the nanocrystals a function of their number density, or equivalently a function of the amount of Ge deposited. The interplay of the stabilizing effect of the nanocrystal surfaces and the destabilizing influence of their repulsive interactions yields a complex behavior for the nanocrystal-size distributions that can nonetheless be modeled using simple thermodynamic expressions.

Journal Article↗
PubMed2005

AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data.

AntiJen is a database system focused on the integration of kinetic, thermodynamic, functional, and cellular data within the context of immunology and vaccinology. Compared to its progenitor JenPep, the interface has been completely rewritten and redesigned and now offers a wider variety of search methods, including a nucleotide and a peptide BLAST search. In terms of data archived, AntiJen has a richer and more complete breadth, depth, and scope, and this has seen the database increase to over 31,000 entries. AntiJen provides the most complete and up-to-date dataset of its kind. While AntiJen v2.0 retains a focus on both T cell and B cell epitopes, its greatest novelty is the archiving of continuous quantitative data on a variety of immunological molecular interactions. This includes thermodynamic and kinetic measures of peptide binding to TAP and the Major Histocompatibility Complex (MHC), peptide-MHC complexes binding to T cell receptors, antibodies binding to protein antigens and general immunological protein-protein interactions. The database also contains quantitative specificity data from position-specific peptide libraries and biophysical data, in the form of diffusion co-efficients and cell surface copy numbers, on MHCs and other immunological molecules. The uses of AntiJen include the design of vaccines and diagnostics, such as tetramers, and other laboratory reagents, as well as helping parameterize the bioinformatic or mathematical in silico modeling of the immune system. The database is accessible from the URL: http://www.jenner.ac.uk/antijen.

Journal Article↗
PubMed2006

Physicochemical attack against solid tumors based on the reversal of direction of entropy flow: an attempt to introduce thermodynamics in anticancer therapy.

BACKGROUND: There are many differences between healthy tissue and growing tumor tissue, including metabolic, structural and thermodynamic differences. Both structural and thermodynamic differences can be used to follow the entropy differences in cancerous and normal tissue. Entropy production is a bilinear form of the rates of irreversible processes and the corresponding "generalized forces". Entropy production due to various dissipation mechanisms based on temperature differences, chemical potential gradient, chemical affinity, viscous stress and exerted force is a promising tool for calculations relating to potential targets for tumor isolation and demarcation. METHODS: The relative importance of five forms of entropy production was assessed through mathematical estimation. Using our mathematical model we demonstrated that the rate of entropy production by a cancerous cell is always higher than that of a healthy cell apart from the case of the application of external energy. Different rates of entropy production by two kinds of cells influence the direction of entropy flow between the cells. Entropy flow from a cancerous cell to a healthy cell transfers information regarding the cancerous cell and propagates its invasive action to the healthy tissues. To change the direction of entropy flow, in addition to designing certain biochemical pathways to reduce the rate of entropy production by cancerous cells, we suggest supplying external energy to the tumor area, changing the relative rate of entropy production by the two kinds of cells and leading to a higher entropy accumulation in the surrounding normal cells than in the tumorous cells. CONCLUSION: Through the use of mathematical models it was quantitatively demonstrated that when no external force field is applied, the rate of entropy production of cancerous cells is always higher than that of healthy cells. However, when the external energy of square wave electric pulses is applied to tissues, the rate of entropy production of normal cells may exceed that of cancerous cells. Consequently, the application of external energy to the body can reverse the direction of the entropy current. The harmful effect brought about by the entropy flow from cancerous to healthy tissue can be blocked by the reversed direction of entropy current from the irradiated normal tissue around the tumor.

Journal Article↗
PubMed1987

Enhancement of transdermal delivery by superfluous thermodynamic potential. II. In vitro-in vivo correlation of percutaneous nifedipine transport.

Nifedipine was selected as a representative compound to investigate a method for improving transdermal bioavailability. The general strategy explored to improve the percutaneous transport of nifedipine was the manipulation of thermodynamics of the drug substance by the use of volatile/nonvolatile systems as vehicles. To investigate the potential of the strategy, diffusion studies were conducted using an ethylene-vinyl acetate copolymer (EVA) membrane and full-thickness excised abdominal skin of rats. Little penetration through EVA membrane or rat skin was found either from the volatile solvent ethanol (EtOH) or from the nonvolatile solvent diethyl sebacate (DES). When the vehicle was changed to a mixed solvent containing both EtOH and DES in a volume ratio of 75:25, penetration through EVA membrane or rat skin was increased up to 3 to 4 times, compared with those values for DES. The increase in the penetration was accounted for by the increase in the thermodynamic activity of the drug in the nonvolatile vehicle caused by the evaporation of the volatile component. The bioavailability of percutaneous nifedipine in rats was determined from the drug solutions containing different proportions of EtOH and DES. Once again, the highest bioavailability was achieved from the mixed solvent containing EtOH and DES in a volume ratio of 75:25. The area under the plasma nifedipine concentration-time curve for the mixed solvent was higher by about 4 times than that for DES.

Administration, Cutaneous↗
PubMed2004

Thermodynamics of complexation of dimethyl esters of tere-, iso-, and phthalic acids with alpha- and beta-cyclodextrins.

Thermodynamics of inclusion of alpha- and beta-cyclodextrins (CDs) with three diester precursors of polyesters, dimethyl terephthalate (DMT), dimethyl isophthalate (DMI), and dimethyl phthalate (DMP) were studied with different fluorescence spectroscopy techniques. The stoichiometry, association constants, and other thermodynamics parameters were investigated from the fluorescence intensity decrease that takes place upon CD addition and temperature changes. Apart from DMP, which did not form a complex with alphaCD, all other systems showed 1:1 stoichiometry complexes with different stabilities. The complexes formed with the DMT guest are the most stable, whereas the stability constant for DMP:betaCD is the lowest. Binding constants are also larger for complexes formed with betaCD than for those formed with alphaCD. Fluorescence polarization, quenching, and lifetime measurements provide information about the structure of the complexes formed. This geometry explains the values of enthalpy and entropy changes during complexation. Van der Waals interactions seem to be involved in the formation of these complexes.

Journal Article↗
PubMed1997

Thermodynamic Stability of Hen Egg White Lysozyme and Its Mutants by Site-directed Mutagenesis.

The folding transition thermodynamics parameters and activity of hen egg white lysozyme and its mutants, R21E, A31V, I55L, S91A, D101A, SIS, TIT, SVS, TVS by site-directed mutagenesis in urea solutions of various concentration were measured. The values of free energy of stabilization (delta G(T)(H(2)O)) are 16.87-28.67 kJ/mol at 25 degrees, and those at midpoint of urea concentration for folding transition [C](1/2) are 4.89-6.24 M for the mutants, respectively. The possible folding transition mechanism in urea solution, the change of transition thermodynamic stability induced by site-directed mutagenesis, and the contribution of hydrophobic interaction and the volume change of amino acid residues to protein stability were discussed.

Journal Article↗
PubMed1999

[The thermodynamic molar absorptivity of coordination color reaction of indium(III) with 4,5-dihydroxybenzene-1,3-disufornic acid].

The thermodynamic molar absorptivity of complex formed by 1:1 coordination color reaction of tiron with highly charged cation In3+ has been measured spectrophotometrically at 20.0+/-0.1 degrees C, using NaClO4 as supporting electrolyte. The influence of å on linear relation between molar absorptivity and ionic strength has been investigated. At å = 6.5, the thermodynamic molar absorptivity lg epsilon(o) was found to be 3.69.

English Abstract↗
PubMed1964

THERMODYNAMIC EQUILIBRIA IN PREBIOLOGICAL ATMOSPHERES.

The concentrations of a large number of compounds of biological interest which would be present in the atmosphere at thermodynamic equilibrium were computed under many combinations of temperature, pressure, and elemental composition. These computations revealed a possible mechanism for the abiological formation of asphaltic tar and an oxidative threshold at which all but the simplest compounds disappear.

Atmosphere↗
PubMed1998

Is the molten globule a third thermodynamic state of protein? The example of alpha-lactalbumin.

Thermal and denaturant-induced transitions of the acid molten globule state of bovine alpha-lactalbumin (acid [A] state) are analyzed by scanning calorimetry, titration calorimetry, viscosimetry, and derivative spectroscopy. A denaturant-induced heat effect of the A state is shown by a calorimetric difference titration of the A-state versus unfolded (reduced) alpha-lactalbumin. However, changes of viscosity and derivative spectra do not parallel the heat effect. At thermal denaturation monitored by derivative spectroscopy and scanning microcalorimetry the presence of a gradual transition in alpha-lactalbumin A state is shown. The results are consistent with the existence of tertiary interactions in the A state and the absence of a cooperative unfolding transition of the molten globule. The results do not support the idea that the molten globule is a third thermodynamic state.

Animals↗
PubMed1999

Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations.

The thermodynamics of folding and unfolding of a beta-heptapeptide in methanol solution has been studied at four different temperatures, 298 K, 340 K, 350 K, and 360 K, by molecular dynamics simulation. At each of these temperatures, the 50-ns simulations were sufficient to generate an equilibrium distribution between a relatively small number of conformations (approximately 10(2)), showing that, even above the melting temperature (approximately 340 K), the peptide does not randomly sample conformational space. The free energy of folding and the free energy difference between pairs of conformations have been calculated from their relative populations. The experimentally determined folded conformation at 298 K, a left-handed 3(1)-helix, is at each of the four temperatures the predominant conformation, with its probability and average lifetime decreasing with increasing temperature. The most common intermediates of folding and unfolding are also the same at the four temperatures. Paths and rates of interconversion between different conformations have been determined. It has been found that folding can occur through multiple pathways, not necessarily downhill in free energy, although the final step involves a reduced number of intermediates.

Models, Molecular↗
PubMed1996

Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation.

Monte Carlo simulations are employed to investigate the thermodynamics of the first transition in writhe of a circular model filament corresponding to a 468 base-pair DNA. Parameters employed in these simulations are the torsional rigidity, C = 2.0 x 10(-19) dyne cm2, and persistence length, P = 500 A. Intersubunit interactions are modeled by a screened Coulomb potential. For a straight line of subunits this accurately approximates the nonlinear Poisson-Boltzmann potential of a cylinder with the linear charge density of DNA. Curves of relative free energy vs writhe at fixed linking difference (delta l) exhibit two minima, one corresponding to slightly writhed circles and one to slightly underwrithed figure-8's, whenever delta l lies in the transition region. The free energies of the two minima are equal when delta lc = 1.35, which defines the midpoint of the transition. At this midpoint, the free energy barrier between the two minima is found to be delta Gbar = (0.20) kBT at 298 K. Curves of mean potential energy vs writhe at fixed linking difference similarly exhibit two minima for delta l values in the transition region, and the two minimum mean potential energies are equal when delta l = 1.50. At the midpoint writhe, delta lc = 1.35, the difference in mean potential energy between the minimum free energy figure-8 and circle states is (1.3) kBT, and the difference in their entropies is 1.3 kB. Thus, the entropy of the minimum free energy figure-8 state significantly exceeds that of the circle at the midpoint of the transition. The first transition in writhe is found to occur over a rather broad range of delta l values from 0.85 to 1.85. The twist energy parameter (ET), which governs the overall free energy of supercoiling, undergoes a sigmoidal decrease, while the translational diffusion coefficient undergoes a sigmoidal increase, over this same range. The static structure factor exhibits an increase, which reflects a decrease in radius of gyration associated with the circle to figure-8 transition.

Chemical Phenomena↗
PubMed1996

Molecular modeling of closed circular DNA thermodynamic ensembles.

Many modeling studies of supercoiled DNA are based on equilibrium structures from theoretical calculations or energy minimization. Since closed circular DNAs are flexible, it is possible that errors are introduced by calculating properties from a single minimum energy structure, rather than from a complete thermodynamic ensemble. We have investigated this question using molecular dynamics simulations on a low resolution molecular mechanics model in which each base pair is represented by three points (a plane). This allows the inclusion of sequence-dependent variations of tip, inclination, and twist. Three kinds of sequences were tested: (1) homogeneous DNA, in which all base pairs have the helicoidal parameters of an ideal, average B-DNA; (2) random sequence DNA; and (3) curved DNA. We examined the rate of convergence of various structural parameters. Convergence for most of these is slowest for homogeneous sequences, more rapid for random sequences, and most rapid for curved sequences. The most slowly converging parameter is the antipodes profile. In a plasmid with N base pairs (bp), the antipodes distance is the distance dij from base pair i to base pair j halfway around the plasmid, j = i + N/2. The antipodes profile at time tau is a plot of dij over the range i = 1, N/2. In a homogeneous plasmid, convergence requires that the antipodes profile averaged over time must be flat. Even in the small plasmids examined here, the average properties of the ensembles were found to differ from those of static equilibrium structures. These effects will be even more dramatic for larger plasmids. Further, average and dynamic properties are affected by both plasmid size and sequence.

Chemical Phenomena↗
PubMed1997

Measuring the thermodynamics of RNA secondary structure formation.

The thermodynamics of RNA secondary structure formation in small model systems provides a database for predicting RNA structure from sequence. Methods for making these measurements are reviewed with emphasis on optical methods and treatment of experimental errors. Analysis of experimental results in terms of simple nearest-neighbor models is presented. Some measured sequence dependences of non-Watson-Crick motifs are discussed.

Base Composition↗
PubMed1997

Binding of basic amphipathic peptides to neutral phospholipid membranes: a thermodynamic study applied to dansyl-labeled melittin and substance P analogues.

A thermodynamic approach is proposed to quantitatively analyze the binding isotherms of peptides to model membranes as a function of one adjustable parameter, the actual peptide charge in solution z(p)+. The main features of this approach are a theoretical expression for the partition coefficient calculated from the molar free energies of the peptide in the aqueous and lipid phases, an equation proposed by S. Stankowski [(1991) Biophysical Journal, Vol. 60, p. 341] to evaluate the activity coefficient of the peptide in the lipid phase, and the Debye-Hückel equation that quantifies the activity coefficient of the peptide in the aqueous phase. To assess the validity of this approach we have studied, by means of steady-state fluorescence spectroscopy, the interaction of basic amphipathic peptides such as melittin and its dansylcadaverine analogue (DNC-melittin), as well as a new fluorescent analogue of substance P, SP (DNC-SP) with neutral phospholipid membranes. A consistent quantitative analysis of each binding curve was achieved. The z(p)+ values obtained were always found to be lower than the physical charge of the peptide. These z(p)+ values can be rationalized by considering that the peptide charged groups are strongly associated with counterions in buffer solution at a given ionic strength. The partition coefficients theoretically derived using the z(p)+ values were in agreement with those deduced from the Gouy-Chapman formalism. Ultimately, from the z(p)+ values the molar free energies for the free and lipid-bound states of the peptides have been calculated.

Amino Acid Sequence↗
PubMed1997

Thermodynamic model of secondary structure for alpha-helical peptides and proteins.

A thermodynamic model describing formation of alpha-helices by peptides and proteins in the absence of specific tertiary interactions has been developed. The model combines free energy terms defining alpha-helix stability in aqueous solution and terms describing immersion of every helix or fragment of coil into a micelle or a nonpolar droplet created by the rest of protein to calculate averaged or lowest energy partitioning of the peptide chain into helical and coil fragments. The alpha-helix energy in water was calculated with parameters derived from peptide substitution and protein engineering data and using estimates of nonpolar contact areas between side chains. The energy of nonspecific hydrophobic interactions was estimated considering each alpha-helix or fragment of coil as freely floating in the spherical micelle or droplet, and using water/cyclohexane (for micelles) or adjustable (for proteins) side-chain transfer energies. The model was verified for 96 and 36 peptides studied by 1H-nmr spectroscopy in aqueous solution and in the presence of micelles, respectively ([set 1] and [set 2]) and for 30 mostly alpha-helical globular proteins ([set 3]). For peptides, the experimental helix locations were identified from the published medium-range nuclear Overhauser effects detected by 1H-nmr spectroscopy. For sets 1, 2, and 3, respectively, 93, 100, and 97% of helices were identified with average errors in calculation of helix boundaries of 1.3, 2.0, and 4.1 residues per helix and an average percentage of correctly calculated helix-coil states of 93, 89, and 81%, respectively. Analysis of adjustable parameters of the model (the entropy and enthalpy of the helix-coil transition, the transfer energy of the helix backbone, and parameters of the bound coil), determined by minimization of the average helix boundary deviation for each set of peptides or proteins, demonstrates that, unlike micelles, the interior of the effective protein droplet has solubility characteristics different from that for cyclohexane, does not bind fragments of coil, and lacks interfacial area.

Enzymes↗
PubMed1997

1H-NMR determination of the thermodynamics of drug complexation with single-stranded and double-stranded oligonucleotides in solution: ethidium bromide complexation with the deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA).

The thermodynamical parameters (free energy, enthalpy, and entropy) of complex formation between ethidium bromide and single-stranded and double-stranded tetranucleotides of different base sequence [5-d(TpGpCpA), 5-d(ApCpGpT), and 5-d(ApGpCpT) have been determined from the temperature dependencies of 500 MHz proton nmr chemical shifts. The analysis enables the contributions to be differentiated for the formation of different types of complexes (1:1, 2:1, 1.2 and 2:2) in aqueous solution. The results have been interpreted in terms of the main types of intermolecular interactions responsible for formation of the different complexes; van der Waals and electrostatic interactions are important for formation of complexes of ethidium bromide with single-stranded tetranucleotides, whereas van der Waals and hydrophobic interactions play a significant role in the binding of the dye to the tetramer duplexes.

Base Composition↗