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PubMed2004

Different binding thermodynamics of Ni2+, Cu2+, and Zn2+ to bacitracin A1 determined by capillary electrophoresis.

Thermodynamics of the binding of Ni(2+), Cu(2+) and Zn(2+) to bacitracin A(1) was studied by capillary electrophoresis measuring the peptide effective mobility at different pH in the presence of increasing concentration of the three ligands. The affinity follows the order Ni(2+) > Cu(2+) > Zn(2+), with association constant values of (2.3 +/- 0.1)x10(4), (4.9 +/- 0.2)x10(3), and (1.5 +/- 0.1)x10(3) M(-1), respectively. The only model able to rationalize mobility data implies that metal ion binds to the P(0) peptide form. Moreover, mobility values indicated a change of bacitracin A(1) acidic properties on Ni(2+) and Cu(2+) binding, with a shift of the pK(a) of N-terminal Ile-1 from 7.6 to about 5 and of the pK(a) of the delta-amino group of D-Orn-7 from 9.7 to about 7. Even though on Zn(2+) binding a shift of the N-terminal Ile-1 pK(a) was observed, restrictions in the pH range suitable for investigation, due to precipitation phenomena, did not allow establish if the shift of D-Orn-7 lateral chain pK(a) also occurred. Nonetheless, if present, the shift should be limited to the 7.8-9.7 range. Mobility data indicated that the Stokes radius of the complexes is ca. 3 A lower than that of the free peptide. The present results indicate that metal-ion binding to bacitracin A(1) is more complex than previously assumed.

Bacitracin↗

PubMed2005

Application of cyclodextrin-mediated capillary electrophoresis to determine the apparent binding constants and thermodynamic parameters of the alkylnaphthalene derivatives.

The separation and migration behavior of seven positional and structural neutral alkylnaphthalene derivatives in cyclodextrin-mediated capillary electrophoresis were systematically investigated. The effective separation conditions were to use 10 mM phosphate buffer with negatively charged carboxymethyl-beta-cyclodextrin (CM-beta-CD) at pH 6.0. The guest-host interactions with 1:1 or both 1:1 and 1:2 binding stoichiometries for various derivatives were evaluated by comparing their apparent binding constants. The results reveal that the substituent group(s) attached to the naphthalene ring significantly affected the inclusion stoichiometric behaviors. Alkylnaphthalene derivatives with the substituent(s) at the 1-position(s), such as 1-ethylnaphthalene, 1,4-dimethylnaphthalene, may undergo complexation with one and two CM-beta-CD molecules. The binding constants of these derivatives were consistent with the data obtained by a spectrophotometric method. The thermodynamic parameters were also calculated in order to improve our understanding of the interaction between the neutral alkylnaphthalene derivatives and CM-beta-CD at various temperatures. The positive entropy (deltaS degrees) values of the alkylnaphthalenes with the substituent(s) at the 2-position(s) indicate that the inclusion of the guest molecule into the cavity of CM-beta-CD is favored at all temperatures.

Electrophoresis, Capillary↗

PubMed2006

Capillary electrophoresis for thermodynamic and kinetic studies of peptidyl-proline isomerization by the theoretical plate height model.

The theoretical plate height model, extended to include reactive CE, is used to calculate equilibrium constants and rate constants for the reversible, first-order isomerization of proline dipeptides. This model is consistent with chromatographic theory and enables calculation of equilibrium constants from velocity and calculation of rate constants from plate height. Thermodynamic and kinetic parameters for isomerization of Ala-Pro and Phe-Pro are calculated by using the plate height model, and are shown to be in good agreement with literature values. Additionally, the efficacy of the plate height model is compared to ChromWin, an existing simulation method for calculating rate constants from zone profiles. It is shown that ChromWin and the plate height model are complementary methods. ChromWin is best used for calculating rate constants for reactions that are far from steady state, where the zone profiles exhibit plateau formation. On the other hand, the plate height model is best used for calculating rate constants for reactions that are at or near steady state, where the zone profiles exhibit a single zone containing both reacting species.

Dipeptides↗

PubMed1985

Thermodynamic compatibility of proteins in aqueous media. Part. I. Phase diagrams of some water--protein A--protein B systems.

The thermodynamic compatibility of proteins belonging to different classes according to Osborne has been investigated in aqueous media. Phase equilibrium for water--ovalbumin--soybean globulin fraction, water--ovalbumin--casein, water--casein--gliadin and water--casein--soybean globulin fraction systems has been investigated. The data obtained were analysed according to the theoretical concepts of Scott, Patterson and Prausnitz concerning the effect of polymer molar masses and the solvent quality on the phase equilibrium in similar systems. The analysis performed indicates that these concepts can be applied to the water--protein A--protein B systems. The phase equilibrium in water--protein A--protein B systems has some distinctive features as compared to that in systems containing two synthetic polymers in the single solvent. Firstly, proteins are usually compatible in a broader concentration range as compared to common polymers. Moreover, the separation of water--protein A--protein B systems into two phases often results in a considerable concentration of one of the protein components. Apparently, the latter fact can be associated with the marked difference in the interaction parameter of proteins belonging to different classes with the solvent, and, hence, with the marked difference in the hydrophilicity of the proteins investigated.

Animals↗

PubMed1991

Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA.

The functional relevance of a hairpin II-containing structure of viroid RNA was studied by site-directed mutagenesis, thermodynamic calculations, experimental denaturation curves and infectivity tests. Hairpin II is formed during thermal denaturation of circular viroids or as part of a metastable structure during synthesis of viroid replication intermediates. In potato spindle tuber viroid (PSTVd), eight single-site mutations were generated in the segments which form hairpin II. From the mutated viroid cDNA clones, linear RNA transcripts of PSTVd unit length were synthesized. The relevance of hairpin II for the mechanism of denaturation was confirmed quantitatively by optical denaturation curves and temperature-gradient gel electrophoresis. Infectivity tests showed that the mutations in the core region of hairpin II reverted to the wild type sequence whereas the mutations in the peripheral regions of hairpin II remained genetically stable. These data are in accordance with the natural variance of hairpin II in other viroids of the PSTVd class. Thus, the integrity of the core of hairpin II is critical for infectivity. Hairpin II exhibits a strong similarity in sequence as well as in three-dimensional structure to certain DNA GC-clusters found in the 5'-upstream regions of some genes in man, animals, viruses and plants. A hypothesis about a function of hairpin II as a binding site for host cell transcription factors is proposed.

Base Composition↗

PubMed1980

Kinetic and thermodynamic aspects of platelet adhesion from suspension to various substrates.

Kinetics of platelet adhesion from suspension to various substrates leads to Langmuir isotherm types of curves, both for suspensions in which the platelets were isolated by means of gel filtration as well as by centrifuging and washing. The level of platelet adhesion increases with increasing surface tension of the substrate. These results cannot be explained on the basis of the theoretical transport model of Ruckenstein et al. The plot of the platelet adhesion at equilibrium vs. gamma SV brings the observations in yet closer agreement with thermodynamic predictions based on free energy calculations than was found previously for the adhesion of platelets after short contact times between platelet suspension and substrate.

Animals↗

PubMed2002

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

Noncovalent association of proteins to specific target sites on DNA--a process central to gene expression and regulation--has thus far proven to be idiosyncratic and elusive to generalizations on the nature of the driving forces. The spate of structural information on protein--DNA complexes sets the stage for theoretical investigations on the molecular thermodynamics of binding aimed at identifying forces responsible for specific macromolecular recognition. Computation of absolute binding free energies for systems of this complexity transiting from structural information is a stupendous task. Adopting some recent progresses in treating atomic level interactions in proteins and nucleic acids including solvent and salt effects, we have put together an energy component methodology cast in a phenomenological mode and amenable to systematic improvements and developed a computational first atlas of the free energy contributors to binding in approximately 40 protein-DNA complexes representing a variety of structural motifs and functions. Illustrating vividly the compensatory nature of the free energy components contributing to the energetics of recognition for attaining optimal binding, our results highlight unambiguously the roles played by packing, electrostatics including hydrogen bonds, ion and water release (cavitation) in protein-DNA binding. Cavitation and van der Waals contributions without exception favor complexation. The electrostatics is marginally unfavorable in a consensus view. Basic residues on the protein contribute favorably to binding despite the desolvation expense. The electrostatics arising from the acidic and neutral residues proves unfavorable to binding. An enveloping mode of binding to short stretches of DNA makes for a strong unfavorable net electrostatics but a highly favorable van der Waals and cavitation contribution. Thus, noncovalent protein-DNA association is a system-specific fine balancing act of these diverse competing forces. With the advances in computational methods as applied to macromolecular recognition, the challenge now seems to be to correlate the differential (initial vs. final) energetics to substituent effects in drug design and to move from affinity to specificity.

Algorithms↗

PubMed2003

Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations.

A method of statistical estimation is applied to the problem of one-dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitting an appropriate statistical-mechanical distribution to the random variable of internal rotation angle. The function of reduced moment of inertia of an internal rotation is averaged over the thermodynamic ensemble of atomic configurations of the molecule obtained in stochastic simulations. When quantum effects are not important, an accurate estimate of the absolute internal rotation entropy of a molecule with a single rotatable bond is obtained. When there is more than one rotatable bond, the "marginal" statistical-mechanical properties corresponding to a given internal rotational degree of freedom are reduced. The method is illustrated using Monte Carlo simulations of two public health relevant halocarbon molecules, each having a single internal-rotation degree of freedom, and a molecular dynamics simulation of an immunologically relevant polypeptide, in which several dihedral angles are analyzed.

Algorithms↗

PubMed2005

Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters.

The thermodynamic and kinetic aspects of hydration reactions of cis-/transplatin were explored. The polarizable continuum model was used for estimation of solvent effects. Using the B3LYP/6-31+G(d) method, the structures were optimized and vibrational frequencies estimated. Interaction energies and activation barriers were determined at the CCSD(T)/6-31++G(d,p) level within the COSMO approach. An associative mechanism was assumed with a trigonal-bipyramidal structure of the transition state. Within the applied model, all the hydration reactions are slightly endothermic. The Gibbs energies of cisplatin hydration amount to 7.0 and 14.2 kcal/mol for the chloride and ammonium replacement, respectively. Analogous values for the transplatin reactions are 6.8 and 11.9 kcal/mol. The determined rate constants are by several (three to four) orders of magnitude larger for the dechlorination process than for deammination. The cisplatin dechlorination rate constant was established as 1.3 x 10(-4) s(-1) in excellent accord with the experiment.

Antineoplastic Agents↗

PubMed2006

Modified calculations of hydrocarbon thermodynamic properties.

A test set of 65 hydrocarbons was examined to elucidate theoretically their thermodynamic properties by performing the density-functional theory (DFT) and ab initio calculations. All the calculated data were modified using a three-parameter calibration equation and the least-squares approach, to determine accurately enthalpies of formation (DeltaH(f)), entropies (S), and heat capacities (C(p)). Calculation results demonstrated that the atomization energies of all compounds exhibited an average absolute relative error ranging between 0.11- 0.13%, and an DeltaH(f) of formation with a mean absolute absolute error (M.|A.E.|) ranging from only 5.7-6.8 kJ/mol (1.3-1.6 kcal/mol) (i.e., those results correlated with those of Dr. Herndon's 1.1 kcal/mol). Additionally, the entropy ranged from 3.5-4.2 J/mol K (0.8-1.0 cal/mol K) M.|A.E.|; a heat capacity between 2.3-2.9 J/mol K (0.5-0.7 cal/mol K) M.|A.E.| was obtained as well.

Hydrocarbons↗

PubMed2006

Thermodynamic properties of Ag2O--B2O3 glasses by a modified scale-transformed energy space sampling Monte Carlo method.

The density of states of Ag(2)O--B(2)O(3) glasses has been calculated by using a modified scale-transformed energy space sampling algorithm. This algorithm combines the scale-transformed energy space sampling algorithm and the Wang-Landau method. It is shown how the two algorithms can be combined to improve the efficiency of calculation. The thermodynamic properties, in particular the specific heat C(V), of the above-mentioned glass system is studied. At temperatures above 80 K, the value of specific heat C(v) is close to 22 J/mol/K. At low temperatures, the deviations of C(v) from a T(3) behavior are discernible, that is, C(v)/T(3) exhibits a hump at T = 7 K, which is in good agreement with the reported experimental behavior.

Algorithms↗

PubMed1989

Molecular recognition between oligopeptides and nucleic acids. Sequence specific binding of (4S)-(+)- and (4R)-(-)-dihydrokikumycin B to DNA deduced from 1H NMR, footprinting studies and thermodynamic data.

The sequence specific binding of the antibiotic (4S)-(+)-dihydrokikumycin B and its (4R)-(-) enantiomer, [(S)-1 and (R)-1, respectively] to DNA were characterized by DNase I and MPE footprinting, calorimetry, UV spectroscopy, circular dichroism, and 1H NMR studies. Footprinting analyses showed that both enantiomers [(S)-1 and (R)-1] bind to AT-rich regions of DNA. 1H NMR studies (ligand induced chemical shift changes and NOE differences) of the dihydrkikumycins with d-[CGCAATTGCG]2 show unambiguously that the N to C termini of the ligands are bound to 5'-A5T6T7-3' reading from left to right. From quantitative 1D-NOE studies, the AH2(5)-ligand H7 distance of complex A [(S)-1 plus decamer (which is bound more strongly)] and complex B [(R)-1 and decamer] are estimated to be 3.8 +/- 0.3 A and 4.9 +/- 0.4 A, respectively. This difference in binding properties is reflected in the thermodynamic profiles of the two enantiomeric ligands determined by a combination of spectroscopic and calorimetric techniques. The binding free energies (delta G degrees) of (S)-1 and (R)-1 to poly d(AT).poly d(AT) at 25 degrees C are -31.8 and -29.3 kJ mol-1, respectively while the corresponding binding enthalpies (delta H degrees) are -11.3 and -0.8 kJ mol-1. These data permit the construction of models for the binding of the enantiomeric dihydrokikumycins to DNA and account for the more efficient binding of the natural (S) isomer to DNA.

Anti-Bacterial Agents↗

PubMed1989

Binding of basic pancreatic trypsin inhibitor and related isoinhibitors to leukocytic elastase. Determination of thermodynamic parameters.

The effect of temperature, ionic strength and solvation power of mono- and divalent cations on the interaction of BPTI-like inhibitors with human leukocytic elastase has been determined. The binding process is characterized by a non-linear dependence of the equilibrium association constant on 1/T indicating a thermal transition at temperature values ranging between 20 degrees C and 35 degrees C depending on the solvent. The marked dependence of the thermodynamic parameters (delta H degrees, delta S degrees, delta G degrees) and of the transition temperature on the concentration and nature of the cations present in solution seems to indicate that the transition, probably of conformational nature, is related to removal of water molecules upon enzyme/inhibitor complex formation.

Algorithms↗

PubMedDate not supplied

Binding of the recombinant proteinase inhibitor eglin c from leech Hirudo medicinalis to serine (pro)enzymes: a comparative thermodynamic study.

The binding of the recombinant proteinase inhibitor eglin c from the leech Hirudo medicinalis to serine (pro)enzymes belonging to the chymotrypsin and subtilisin families has been investigated from the thermodynamic viewpoint, between pH 4.5 and 9.5 and from 10 degrees C to 40 degrees C. The affinity of eglin c for the serine (pro)enzymes considered shows the following trend: Leu-proteinase [the leucine specific serine proteinase from spinach (Spinacia oleracea L.) leaves] greater than human leucocyte elastase congruent to human cathepsin G congruent to subtilisin Carlsberg congruent to bovine alpha-chymotrypsin greater than bovine alpha-chymotrypsinogen A congruent to porcine pancreatic elastase congruent to bovine beta-trypsin. The serine (pro)enzyme-inhibitor complex formation is an entropy-driven process. On increasing the pH from 4.5 to 9.5, the affinity of eglin c for the serine (pro)enzymes considered increases thus reflecting the acid pK shift of the invariant hystidyl catalytic residue from approximately to 6.9 in the free serine proteinases and bovine alpha-chymotrypsinogen A to congruent to 5.1 in the serine (pro)enzyme-inhibitor complexes. Considering the known molecular models, the observed binding behaviour of eglin c was related to the inferred stereochemistry of the serine (pro)enzyme-inhibitor contact regions.

Animals↗

PubMedDate not supplied

A potential role for isothermal calorimetry in studies of the effects of thermodynamic non-ideality in enzyme-catalyzed reactions.

Attention is drawn to the feasibility of using isothermal calorimetry for the characterization of enzyme reactions under conditions bearing greater relevance to the crowded biological environment, where kinetic parameters are likely to differ significantly from those obtained by classical enzyme kinetic studies in dilute solution. An outline of the application of isothermal calorimetry to the determination of enzyme kinetic parameters is followed by considerations of the nature and consequences of crowding effects in enzyme catalysis. Some of those effects of thermodynamic non-ideality are then illustrated by means of experimental results from calorimetric studies of the effect of molecular crowding on the kinetics of catalysis by rabbit muscle pyruvate kinase. This review concludes with a discussion of the potential of isothermal calorimetry for the experimental determination of kinetic parameters for enzymes either in biological environments or at least in media that should provide reasonable approximations of the crowded conditions encountered in vivo.

Calorimetry↗

PubMed2001

Standard state and thermodynamic self-consistency.

It is pointed out that even though the standard state for solutions is a fictitious state, it nonetheless should be thermodynamically self-consistent. Using a volumetric constraint, it is shown that the biochemical standard state concentration of 1M is too high for macromolecules like proteins and nucleic acids that it violates volumetric self-consistency. Also, at 1 M standard state, the mole fraction of these macromolecular solutes is not the commonly held value of 1/55.5, but rather a meaningless negative number. Thus, the ideal mixing entropy (also called cratic entropy) cannot be meaningfully calculated for macromolecules at such a standard state. The relevance of this conclusion to the interpretation of standard bimolecular binding entropy is discussed.

Chemistry, Pharmaceutical↗

PubMed2005

Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration.

The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.

Biopharmaceutics↗

PubMed2007

Impact of cremophor-EL and polysorbate-80 on digoxin permeability across rat jejunum: delineation of thermodynamic and transporter related events using the reciprocal permeability approach.

The effect of Cremophor-EL (Cr-EL) and polysorbate-80 (PS-80) on the transepithelial permeability of digoxin (DIG) has been evaluated using the reciprocal permeability approach to delineate thermodynamic and transporter related events. Permeability data were corrected for solubilization using the micellar association constant (Ka) obtained from Papp data generated in the presence of the nonspecific ATPase inhibitor sodium orthovanadate. In the presence of mucosal Cr-EL, a concentration dependent decrease in serosal-mucosal (S-M) and increase in M-S transport was observed. Whilst serosal Cr-EL resulted in a reduction in S-M DIG transport, no impact on M-S transport was apparent. For PS-80, the presence of either serosal or mucosal surfactant led to a decrease in secretory (S-M) DIG transport, however no effect on absorptive transport was evident. The data confirm the potential P-gp inhibitory effects of Cr-EL, but suggest that in contrast to Cr-EL, PS-80 is not a potent inhibitor of P-gp and is incapable of increasing absorptive drug transport, at least in excised rat intestinal tissue and at the concentrations tested. The data are also consistent with the involvement of additional transporters (both apical and basolateral) in the intestinal permeability of DIG, although more definitive data is required to confirm this possibility.

ATP Binding Cassette Transporter, Subfamily B, Mem↗