TDeltaS Degrees Research Articles

The Roles of Three Serratia marcescens Chitinases in Chitin Conversion Are Reflected in Different Thermodynamic Signatures of Allosamidin Binding

Binding of allosamidin to the three family 18 chitinases of Serratia marcescens has been studied using isothermal titration calorimetry (ITC). Interestingly, the thermodynamic signatures of allosamidin binding were different for all three chitinases. At pH 6.0, chitinase A (ChiA) binds allosamidin with a K(d) value of 0.17 +/- 0.06 microM where the main part of the driving force is due to enthalpic change (DeltaH(r) degrees = -6.2 +/- 0.2 kcal/mol) and less to entropic change (-TDeltaS(r) degrees = -3.2 kcal/mol). A large part of DeltaH is due to allosamidin stacking with Trp(167) in the -3 subsite. Binding of allosamidin to both chitinase B (ChiB) (K(d) = 0.16 +/- 0.04 microM) and chitinase C (ChiC) (K(d) = 2.0 +/- 0.2 microM) is driven by entropy (DeltaH(r) degrees = 3.8 +/- 0.2 kcal/mol and -TDeltaS(r) degrees = -13.2 kcal/mol for ChiB and DeltaH(r) degrees = -0.6 +/- 0.1 and -TDeltaS(r) degrees = -7.3 kcal/mol for ChiC). For ChiC, the entropic term is dominated by changes in solvation entropy (DeltaS(conf) = 1 cal/K.mol and DeltaS(solv) = 31 cal/K.mol), while, for ChiB, changes in conformational entropy dominate (DeltaS(conf) = 37 cal/K x mol and DeltaS(solv) = 15 cal/K x mol). Corresponding values for ChiA are DeltaS(conf) = 4 cal/K x mol and DeltaS(solv) = 15 cal/K x mol. These remarkable differences in binding parameters reflect the different architectures of the catalytic centers in these enzymes that are adapted to different types of actions: ChiA and ChiB are processive enzymes that move in opposite directions, meaning that allosamidin binds in to "product" subsites in ChiB, while it binds to polymer-binding subsites in ChiA. The values for ChiC are compatible with this enzyme being a nonprocessive endochitinase with a much more open and solvated substrate-binding-site cleft.

Interaction of Isoquinoline Alkaloids with an RNA Triplex: Structural and Thermodynamic Studies of Berberine, Palmatine, and Coralyne Binding to Poly(U).Poly(A)*Poly(U)

The interaction of two natural protoberberine alkaloids berberine and palmatine and the synthetic derivative coralyne with the RNA triplex poly(U).poly(A)(*)poly(U) was studied using various biophysical and calorimetric techniques. All the three alkaloids bind noncooperatively to the triplex. The affinity of berberine and palmatine was in the order of 10(5) M(-1), while that of coralyne was one order higher as inferred from spectroscopic studies. The alkaloids stabilized the Hoogsteen base-paired third strand of the triplex without affecting the stability of the duplex. Fluorescence quenching and viscosity studies gave convincing evidence for the partial intercalation of berberine and palmatine and a true intercalative binding of coralyne to the triplex. This was further supported from the significant polarization of the emission spectra of the complex and the energy transfer from the base triplets to the alkaloids. Circular dichroic studies suggested that the conformation of the triplex was perturbed significantly by the binding of the alkaloids, being more by coralyne compared to berberine and palmatine and also evidenced by the generation of strong induced optical activity in the bound coralyne molecules. Isothermal titration calorimetric studies revealed that the binding to the triplex was favored by a predominantly large negative enthalpy change (DeltaH degrees = -5.42 kcal/mol) with small favorable entropy contribution (TDeltaS degrees = 2.02 kcal/mol) in berberine, favored by almost equal negative enthalpy (DeltaH degrees = -3.93 kcal/mol) and entropy changes (TDeltaS degrees = 3.89 kcal/mol) in palmatine and driven by predominant entropy contributions (DeltaH degrees = -1.84 and TDeltaS degrees = 7.44 kcal/mol) in coralyne. These results advance our knowledge on the binding of small molecule isoquinoline alkaloids that are specific binders of RNA structures, particularly triplexes.

Anion Binding by Protonated Forms of the Tripodal Ligand Tren

The interaction of the protonated forms of tris(2-aminoethyl)amine (tren) with NO(3)(-), SO(4)(2-), TsO(-), PO(4)(3-), P(2)O(7)(4-), and P(3)O(10)(5-) was studied by means of potentiometric and microcalorimetric measurements in a 0.10 M NMe(4)Cl aqueous solution at 298.1 +/- 0.1 K, affording stability constants and the relevant energetic terms DeltaH degrees and TDeltaS degrees of complexation. Thermodynamic data show that these anion complexation processes are mainly controlled by electrostatic forces, although hydrogen-bond interactions and solvation effects also contribute to complex stability, leading, in some cases, to special DeltaH degrees and TDeltaS degrees contributions. The crystal structures of [H(3)L][NO(3)](3) and [H(3)L][TsO](3) evidence a preferred tridentate coordination mode of the triprotonated ligands in the solid state. Accordingly, the H(3)L(3+) receptor binds a single oxygen atom of both NO(3)(-) and TsO(-) by means of its three protonated fingers, although in the crystal structure of [H(3)L][TsO](3), one conformer displaying bidentate coordination was also found. Modeling studies performed on the [H(3)L(NO(3))](2+) complex suggested that the tridentate binding mode is the preferred one in aqueous solution, while in the gas phase, a different complex conformation in which the receptor interacts with all three oxygen atoms of NO(3)(-) is more stable.

Delineation of Alternative Conformational States in Escherichia coli Peptide Deformylase via Thermodynamic Studies for the Binding of Actinonin

We investigated the binding of a naturally occurring antibiotic, actinonin, to the Ni(2+)-reconstituted recombinant form of Escherichia coli peptide deformylase (PDF(Ec)) via isothermal titration microcalorimetry. The binding data conformed to both exothermic and endothermic phases with magnitudes of DeltaG degrees , DeltaH degrees , and TDeltaS degrees being equal to -12, -2.7, and 9.3 kcal/mol and -8.7, 3.9, and 12.6 kcal/mol, respectively. Evidently, although both phases are dominated by favorable entropic changes, the exothermic phase has about 6.7 kcal/mol enthalpic advantage over the endothermic phase. We observed that the removal of bound Ni(2+) from PDF(Ec) abolished the exothermic phase without affecting the endothermic phase, but it was regained upon addition of Zn(2+). In conjunction with metal analysis data, we propose that the recombinant form of PDF(Ec) is expressed in two stable conformational states that yield markedly distinct ITC profiles (i.e., exothermic versus endothermic) upon interaction with actinonin. The existence of two conformational states of PDF(Ec) is further supported by the observation of two distinct and independent transitions during the thermal unfolding of the enzyme. In addition, the thermodynamic data reveal that the formation of the PDF(Ec)-actinonin complex results in the transfer of one H(+) from the enzyme phase to the bulk solvent at pH 6.3. Both exothermic and endothermic phases produce highly negative DeltaC(p) degrees values, but there is no apparent enthalpy-entropy compensation effect upon formation of the PDF(Ec)-actinonin complex. In view of the known structural features of the enzyme, arguments are presented that the alternative conformational states of PDF(Ec) are modulated by the metal ligation at the enzyme site.

Characterization of pokeweed antiviral protein binding to mRNA cap analogs: Competition with nucleotides and enhancement by translation initiation factor iso4G

Pokeweed antiviral protein (PAP) is a type I ribosomal inactivating protein (RIP). PAP binds to and depurinates the sarcin/ricin loop (SRL) of ribosomal RNA resulting in the cessation of protein synthesis. PAP has also been shown to bind to mRNA cap analogs and depurinate mRNA downstream of the cap structure. The biological role of cap binding and its possible role in PAP activity are not known. Here we show the first direct quantitative evidence for PAP binding to the cap analog m(7)GTP. We report a binding affinity of 43.3+/-0.1 nM at 25 degrees C as determined by fluorescence quenching experiments. This is similar to the values reported for wheat cap-binding proteins eIFiso4E and eIFiso4F. van't Hoff analysis of m(7)GTP-PAP equilibrium reveals a binding reaction that is enthalpy driven and entropy favored with TDeltaS degrees contributing 15% to the overall value of DeltaG degrees . This is in contrast to the wheat cap-binding proteins which are enthalpically driven in the DeltaG degrees for binding. Competition experiments indicate that ATP and GTP compete for the cap-binding site on PAP with slightly different affinities. Fluorescence studies of PAP-eIFiso4G binding reveal a protein-protein interaction with a K(d) of 108.4+/-0.3 nM. eIFiso4G was shown to enhance the interaction of PAP with m(7)GTP cap analog by 2.4-fold. These results suggest the involvement of PAP-translation initiation factor complexes in RNA selection and depurination.

Effect of β-Cyclodextrin Charge Type on the Molecular Recognition Thermodynamics of Reactions with (Ferrocenylmethyl)dimethylaminium Derivatives

Complex stability constants (KS), standard molar enthalpic changes (DeltaH degrees ), and entropic changes (TDeltaS degrees ) for the inclusion complexations of native beta-cyclodextrin (1) and two oppositely charged beta-cyclodextrins, i.e., mono(6-amino-6-deoxy)- beta-cyclodextrin (2) and mono[6-O-6-(4-carboxylphenyl)]- beta-cyclodextrin (3), with two (ferrocenylmethyl)dimethylaminium derivatives, i.e., FC4+Br(-) and FC8+Br(-), were determined at 25 degrees C in aqueous phosphate buffer solution (pH 7.20) by means of isothermal titration microcalorimetry (ITC). Cyclic voltammetry studies showed that the ferrocene groups of the guests were included in the beta-cyclodextrin cavity to form host-guest complexes. As compared with neutral beta-cyclodextrin, the positively charged host 2 showed decreased binding toward (ferrocenylmethyl)dimethylaminium guests. This was attributed to electrostatic repulsion, while the negatively charged host 3 displayed increased binding due to electrostatic attractions. Thermodynamically, the ionization of host CDs affects both enthalpic and entropic changes of host-guest complexations presumably by changing the hydrophobicity and the desolvation effect of hosts upon inclusion complexation. Moreover, the solvent effect was also discussed from the viewpoint of thermodynamics.

On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes

BackgroundIn this study we investigated the predictability of three thermodynamic quantities related to complex formation. As a model system we chose the host-guest complexes of β-cyclodextrin (β-CD) with different guest molecules. A training dataset comprised of 176 β-CD guest molecules with experimentally determined thermodynamic quantities was taken from the literature. We compared the performance of three different statistical regression methods – principal component regression (PCR), partial least squares regression (PLSR), and support vector machine regression combined with forward feature selection (SVMR/FSS) – with respect to their ability to generate predictive quantitative structure property relationship (QSPR) models for ΔG°, ΔH° and ΔS° on the basis of computed molecular descriptors.ResultsWe found that SVMR/FFS marginally outperforms PLSR and PCR in the prediction of ΔG°, with PLSR performing slightly better than PCR. PLSR and PCR proved to be more stable in a nested cross-validation protocol. Whereas ΔG° can be predicted in good agreement with experimental values, none of the methods led to comparably good predictive models for ΔH°. In using the methods outlined in this study, we found that ΔS° appears almost unpredictable. In order to understand the differences in the ease of predicting the quantities, we performed a detailed analysis. As a result we can show that free energies are less sensitive (than enthalpy or entropy) to the small structural variations of guest molecules. This property, as well as the lower sensitivity of ΔG° to experimental conditions, are possible explanations for its greater predictability.ConclusionThis study shows that the ease of predicting ΔG° cannot be explained by the predictability of either ΔH° or ΔS°. Our analysis suggests that the poor predictability of TΔS° and, to a lesser extent, ΔH° has to do with a stronger dependence of these quantities on the structural details of the complex and only to a lesser extent on experimental error.

Large ground-state entropy changes for hydrogen atom transfer reactions of iron complexes.

Reported herein are the hydrogen atom transfer (HAT) reactions of two closely related dicationic iron tris(alpha-diimine) complexes. FeII(H2bip) (iron(II) tris[2,2'-bi-1,4,5,6-tetrahydropyrimidine]diperchlorate) and FeII(H2bim) (iron(II) tris[2,2'-bi-2-imidazoline]diperchlorate) both transfer H* to TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) to yield the hydroxylamine, TEMPO-H, and the respective deprotonated iron(III) species, FeIII(Hbip) or FeIII(Hbim). The ground-state thermodynamic parameters in MeCN were determined for both systems using both static and kinetic measurements. For FeII(H2bip) + TEMPO, DeltaG degrees = -0.3 +/- 0.2 kcal mol-1, DeltaH degrees = -9.4 +/- 0.6 kcal mol-1, and DeltaS degrees = -30 +/- 2 cal mol-1 K-1. For FeII(H2bim) + TEMPO, DeltaG degrees = 5.0 +/- 0.2 kcal mol-1, DeltaH degrees = -4.1 +/- 0.9 kcal mol-1, and DeltaS degrees = -30 +/- 3 cal mol-1 K-1. The large entropy changes for these reactions, |TDeltaS degrees | = 9 kcal mol-1 at 298 K, are exceptions to the traditional assumption that DeltaS degrees approximately 0 for simple HAT reactions. Various studies indicate that hydrogen bonding, solvent effects, ion pairing, and iron spin equilibria do not make major contributions to the observed DeltaS degrees HAT. Instead, this effect arises primarily from changes in vibrational entropy upon oxidation of the iron center. Measurement of the electron-transfer half-reaction entropy, |DeltaS degrees Fe(H2bim)/ET| = 29 +/- 3 cal mol-1 K-1, is consistent with a vibrational origin. This conclusion is supported by UHF/6-31G* calculations on the simplified reaction [FeII(H2N=CHCH=NH2)2(H2bim)]2+...ONH2 left arrow over right arrow [FeII(H2N=CHCH=NH2)2(Hbim)]2+...HONH2. The discovery that DeltaS degrees HAT can deviate significantly from zero has important implications on the study of HAT and proton-coupled electron-transfer (PCET) reactions. For instance, these results indicate that free energies, rather than enthalpies, should be used to estimate the driving force for HAT when transition-metal centers are involved.

Oligoribonucleotide Analogues Containing a Mixed Backbone of Phosphodiester and Formacetal Internucleoside Linkages, Together with Vicinal 2′‐O‐Methyl Groups

Oligoribonucleotides containing formacetal internucleoside linkages have been prepared and studied by UV melting experiments. In RNA duplexes, the formacetal substitution is stabilizing (Deltat(m)=0 to +0.9 degrees C per modification) at physiological salt concentrations (0.1 M) but destabilizing (Deltat(m)=-0.4 to -0.8 degrees C per modification) at high salt concentrations (1 M); this suggests that reduction of electrostatic repulsion contributes substantially to the stabilization. The presence of 2'-O-Me substituents increases the stabilities of the duplexes (Deltat(m)=+0.5 to +1.1 degrees C per modification). The positive effects of formacetals and 2'-O-Me groups were independent and additive. (1)H NMR studies on monomeric model compounds containing 3'-(ethyl phosphate) or 3'-O-ethoxymethyl groups showed that the formacetal and 2'-O-Me substitutions shift the conformational equilibria of the ribose residues towards the North conformers by 5 to 12 %. Although the preference for the North conformers qualitatively correlates with increased duplex stabilities, changes in thermodynamic parameters (DeltaH degrees and TDeltaS degrees ) for formation of oligonucleotide duplexes and differences in dependence on concentrations of sodium acetate, sodium chloride and sodium perchlorate suggest that solvation effects are also important for the duplex stabilities. Overall the formacetal linkages fit well in A-type RNA duplexes, making them potentially interesting modifications for RNA-based gene-control strategies (e.g., antisense and RNA interference).

Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics

The inhibition of glycoside hydrolases, through transition-state mimicry, is important both as a probe of enzyme mechanism and in the continuing quest for new drugs, notably in the treatment of cancer, HIV, influenza, and diabetes. The high affinity with which these enzymes are known to bind the transition state provides a framework upon which to design potent inhibitors. Recent work [for example, Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568; Zechel, D. L. et al. J. Am. Chem. Soc. 2003, 125, 14313-14323] has revealed quite confusing and counter-intuitive patterns of inhibition for a number of glycosidase inhibitors. Here we describe a synergistic approach for analysis of inhibitors with a single enzyme 'model system', the Thermotoga maritima family 1 beta-glucosidase, TmGH1. The pH dependence of enzyme activity and inhibition has been determined, structures of inhibitor complexes have been solved by X-ray crystallography, with data up to 1.65 A resolution, and isothermal titration calorimetry was used to establish the thermodynamic signature. This has allowed the characterization of 18 compounds, all putative transition-state mimics, in order to build an 'inhibition profile' that provides an insight into what governs binding. In contrast to our preconceptions, there is little correlation of inhibitor chemistry with the calorimetric dissection of thermodynamics. The ensemble of inhibitors shows strong enthalpy-entropy compensation, and the random distribution of similar inhibitors across the plot of DeltaH degrees a vs TDeltaS degrees a likely reflects the enormous contribution of solvation and desolvation effects on ligand binding.

Molecular Recognition Thermodynamics of Pyridine Derivatives by Sulfonatocalixarenes at Different pH Values

The complex stability constants (Ka) and thermodynamic parameters (DeltaG degrees, DeltaH degrees, and TDeltaS degrees) for 1:1 complexation of water-soluble calix[4]arene, thiacalix[4]arene, and calix[5]arene sulfonates with pyridine and their methylated derivatives have been determined by means of isothermal titration calorimetry at pH 2.0 and 7.2 at 298.15 K, and their binding modes have been investigated by NMR spectroscopy. The results obtained show that sulfonatocalixarenes afford stronger binding ability toward pyridine guests at pH 2.0, attributable to the positive electrostatic interactions and the more extensive desolvation effects, but present higher molecular selectivity at pH 7.2 owing to the strengthened C-H...pi interactions. The pH-responsible binding ability and molecular selectivity are discussed from the viewpoint of electrostatic, pi-stacking, van der Waals interactions and size-fit relationship between host and guest. A close comparison further demonstrates that the C-H...pi interactions and van der Waals interactions play a more important role than pi...pi interactions in the present inclusion complexation.

Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall.

Glycopeptide antibiotics, including vancomycin, form complexes via a set of five hydrogen bonds with the acyl-l-Lys-d-Ala-d-Ala portion of the peptidyl stems of the bacterial cell wall peptidoglycan. This complexation deprives the organism from the ability to cross-link peptidyl stems of the peptidoglycan, leading to bacterial cell death. Four synthetic fragments as surrogates of the components of the bacterial cell wall have been prepared in our lab in multistep syntheses. These synthetic samples were used in investigations of the thermodynamics properties (DeltaG degrees , DeltaH degrees , and TDeltaS degrees ) for the complexation with vancomycin by isothermal titration calorimetry (ITC). Complexation with the glycopeptide analogues is largely enthalpy-driven (formation of five hydrogen bonds), and in the analogues with a single peptidyl stem, the complexation is 1:1. The complexation is more complicated with an approximately 2 kDa cell wall surrogate (compound 4), which possesses two peptidyl stems. The data were suggestive of interactions between the two vancomycin molecules, with an entropic penalty attributable to restriction of molecular movements within the complex due to restriction of motion of the highly mobile acyl-d-Ala-d-Ala moiety of the peptidyl stems. These data were reconciled with the recently determined NMR solution structure for the peptidoglycan fragment 4 and its implications for the larger cell wall.

The Structure and Thermodynamics of Calix[n]arene Complexes with Dipyridines and Phenanthroline in Aqueous Solution Studied by Microcalorimetry and NMR Spectroscopy

The complex stability constants (K(S)) and thermodynamic parameters (DeltaH degrees and TDeltaS degrees) for 1:1 intermolecular complexation of three water-soluble calixarenes, that is, p-sulfonato calix[4]arene (C4AS), p-sulfonato thiacalix[4]arene (TCAS), and p-sulfonato calix[5]arene (C5AS), with dipyridines (4-DPD and 2-DPD) and 1,10-phenanthroline (Phen) have been determined by means of titration microcalorimetry in an acidic buffer solution (pH = 2.0) at 298.15 K, and their binding modes have been investigated by (1)H NMR and 2D ROESY NMR spectroscopy. The results obtained indicate that 4-DPD, 2-DPD, and Phen are included in the cavity of C5AS with the different patterns, this is, accumbent for 4-DPD, acclivitous for 2-DPD and Phen, while Phen is included upright in the cavity of C4AS. The K(S) values decrease with increasing cavity size of host molecules but enhance with extending conjugation degree of guest molecules, and thus C4AS exhibits an exceptionally high Phen/4-DPD selectivity of 22.5. Thermodynamically, the complexation of DPDs/Phen with the water-soluble calixarenes is obviously enthalpy-driven, but the molecular selectivity is mainly governed by the entropy term.

Conformation of Solvent N,N-Dimethylpropionamide in the Coordination Sphere of the Zinc(II) Ion Studied by Raman Spectroscopy and DFT Calculations

Solvation structure of the zinc(II) ion in N,N-dimethylpropionamide (DMPA) was studied by Raman spectroscopy at varying temperature and by quantum mechanical calculations. No significant ion-pair formation was found for the Zn(ClO4)2 solution in the molality range m(Zn) < 1.5 mol kg(-1), and the solvation number of the zinc(II) ion was determined to be 4, indicating that 6-coordination of DMPA is sterically hindered. Interestingly, DMPA molecules are under equilibrium between planar cis and nonplanar staggered conformers, and the latter is more preferred in the coordination sphere, while the reverse is the case in the bulk. The DeltaG degrees , DeltaH degrees , and TDeltaS degrees values of conformational change from planar cis to nonplanar staggered in the coordination sphere were obtained to be -0.9, -8.5, and -7.5 kJ mol(-1), respectively. Density functional theory (DFT) calculations show that the planar cis conformer is more favorable than the nonplanar staggered one in the 1:2 cluster, as is the case for a single DMPA molecule and H(DMPA)+, indicating that there hardly occurs solvent-solvent interaction through the metal ion in the Zn2+-DMPA 1:2 cluster. On the other hand, the SCF energy of [Zn(planar cis-DMPA)4-n(nonplanar staggered DMPA)n]2+ (n = 0-4) decreases with increasing n, implying that the nonplanar staggered conformer is preferred in the solvate ion. It is thus concluded that solvent-solvent interaction through space, or solvation steric effect, plays a crucial role in the conformational equilibrium in the coordination sphere of the four-solvate metal ion.

Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin.

Accurate and precise determinations of thermodynamic parameters of binding are important steps toward understanding many biological mechanisms. Here, a multi-method approach to binding analysis is applied and a detailed error analysis is introduced. Using this approach, the binding thermodynamics and kinetics of the reconstitution of the protein monellin have been quantitatively determined in detail by simultaneous analysis of data collected with fluorescence spectroscopy, surface plasmon resonance and isothermal titration calorimetry at 25 degrees C, pH 7.0 and 150 mM NaCl. Monellin is an intensely sweet protein composed of two peptide chains that form a single globular domain. The kinetics of the reconstitution reaction are slow, with an association rate constant, k(on) of 8.8 x 10(3) M(-1) s(-1) and a dissociation rate constant, k(off) of 3.1 x 10(-4) s(-1). The equilibrium constant K(A) is 2.8 x 10(7) M(-1) corresponding to a standard free energy of association, DeltaG degrees , of -42.5 kJ/mol. The enthalpic component, DeltaH degrees , is -18.7 kJ/mol and the entropic contribution, DeltaS degrees , is 79.8 J mol(-1) K(-1) (-TDeltaS degrees = -23.8 kJ/mol). The association of monellin is therefore a bimolecular intra-protein association whose energetics are slightly dominated by entropic factors.

Thermodynamic stability of hydrogen-bonded nanostructures: a calorimetric study.

The self-assembly of hydrogen-bonded aggregates (rosettes) in solvent mixtures of different polarity has been studied by calorimetry. The C(50) parameter, the concentration when 50 % of the components are incorporated in the assembly, is used to compare assemblies with different stoichiometry. C(50) for the single rosette 1(3).(BuCYA)(3) (1=N,N-di(4-tert-butylphenyl)melamine; BuCYA=n-butylcyanuric acid) in 1,2-dichloroethane is 25 microM, whereas for double rosettes 2 a(3).(BuCYA)(6) and 2 b(3).(BuCYA) (2=calix[4]arene-dimelamine) it is 0.7 and 7.1 microM, respectively. DeltaG degrees, DeltaH degrees, and TDeltaS degrees values indicate that the thermodynamics of double rosettes reflect the independent assembly of two individual single rosette structures or two rosettes reinforced by additional stabilizing interactions. In more polar solvents the stability of double rosettes decreases. From the correlation of DeltaG degrees with solvent polarity it is predicted that it should be possible to assemble double rosettes in methanol or water. The assembly of 2 b(3).(BuCYA)(6) in 100 % MeOH was proven by (1)H NMR and CD spectroscopy.

Receptor binding thermodynamics at the neuronal nicotinic receptor.

Simple determination of K(A) or K(D) values makes it possible to calculate the standard free energy DeltaG degrees = -RTlnK(A) = RT lnK(D)(T= 298.15 K) of the binding equilibrium but not that of its two components as defined by the Gibbs equation DeltaG degrees = DeltaH degrees - TDeltaS degrees where DeltaH degrees and DeltaS degrees are the equilibrium standard enthalpy and entropy, respectively. Recently, it has been shown that the relative DeltaH degrees and DeltaS degrees magnitudes can often give a simple "in vitro" way for discriminating "the effect", that is the manner in which the drug interferes with the signal transduction pathways. This particular effect, called "thermodynamic discrimination", results from the fact that binding of antagonists may be enthalpy-driven and that of agonists entropy-driven, or vice-versa. In the past, the thermodynamic discrimination was reported for the beta-adrenergic G-protein-coupled receptor (GPCR) and confirmed later for adenosine A(1), A(2A) and A(3) receptors. Moreover, it has been found that the binding of all ligand-gated ion-channel receptors (LGICR) investigated was thermodynamically discriminated. In particular, affinity constants for typical neuronal nicotinic receptor ligands were obtained by both saturation and inhibition experiments with the radioligand [(3)H]-cytisine, a ganglionic nicotinic agonist. Thermodynamic parameters indicated that agonistic binding was both enthalpy- and entropy-driven, while antagonistic binding was totally entropy-driven. These results have shown that neuronal nicotinic receptor agonists and antagonists were thermodynamically discriminated. On these grounds, the thermodynamic behaviour makes it possible to discriminate drug pharmacological profiles in vivo through binding experiments in vitro.

Interactions of the peripheral subunit-binding domain of the dihydrolipoyl acetyltransferase component in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.

The enzymes pyruvate decarboxylase (E1) and dihydrolipoyl dehydrogenase (E3) bind tightly but in a mutually exclusive manner to the peripheral subunit-binding domain (PSBD) of dihydrolipoyl acetyltransferase in the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. The use of directed mutagenesis, surface plasmon resonance detection and isothermal titration microcalorimetry revealed that several positively charged residues of the PSBD, most notably Arg135, play an important part in the interaction with both E1 and E3, whereas Met131 makes a significant contribution to the binding of E1 only. This indicates that the binding sites for E1 and E3 on the PSBD are overlapping but probably significantly different, and that additional hydrophobic interactions may be involved in binding E1 compared with E3. Arg135 of the PSBD was also replaced with cysteine (R135C), which was then modified chemically by alkylation with increasingly large aliphatic groups (R135C -methyl, -ethyl, -propyl and -butyl). The pattern of changes in the values of DeltaG degrees, DeltaH degrees and TDeltaS degrees that were found to accompany the interaction with the variant PSBDs differed between E1 and E3 despite the similarities in the free energies of their binding to the wild-type. The importance of a positive charge on the side-chain at position 135 for the interaction of the PSBD with E3 and E1 was apparent, although lysine was found to be an imperfect substitute for arginine. The results offer further evidence of entropy-enthalpy compensation ('thermodynamic homeostasis') - a feature of systems involving a multiplicity of weak interactions.

A new strategy for the design of water-soluble synthetic receptors: specific recognition of DNA intercalators and diamines.

Water-soluble zinc bisporphyrin receptors 1 and 2 having two Lewis acidic sites (zinc) in the hydrophobic environment consisting of alkyl chains and a bisporphyrin framework, and covered with hydrophilic exterior (twelve or eighteen carboxyl groups) were prepared. The receptors show high affinity for diamines and DNA intercalators in water where the binding constants K(a) are of the order of 10(7) and 10(8) M(-1), respectively. Diamines and DNA intercalators are bound to the receptor through different mechanisms. Diamines are bound through hydrophobic interactions and zinc-nitrogen interactions, while DNA intercalators are bound through hydrophobic interactions and charge-transfer interactions. Flexible alkyl chains can make van der Waals contact with guests and create a hydrophobic environment around the bound guest by an induced-fit-type mechanism. For the binding of DNA intercalators, the following features are noteworthy: 1). Binding constants are similar between the zinc porphyrins and zinc-free porphyrins; 2). the binding constant is larger for the guest having the lower LUMO; this indicates the important contribution of charge-transfer interactions to binding; 3). the hydrophobic and cationic nature of DNA intercalators is substantially important, and 4). higher ionic strength reduced the binding affinities; this shows a moderate contribution of electrostatic interactions. The conformational instability of the receptors also contributes to the tight binding: hydrophobic and electrostatic interactions cannot both be favorable at the same time in the guest-free receptor. Enthalpy-entropy compensation observed for the binding of diamines and DNA intercalators is characterized by a relatively small slope (alpha=0.74) and a large intercept (beta=7.75 kcal mol(-1)) in the DeltaH degrees versus TDeltaS degrees plot; this shows that a conformational change of receptors and a significant desolvation occur upon binding. The receptor can competitively bind to propidium iodide to deprive DNA of the intercalated propidium iodide. These features of water-soluble receptors consisting of a rigid framework and flexible side chains with a large solvent-accessible area are in contrast to highly preorganized rigid receptors, and they can provide useful guidelines for rational design of induced-fit artificial receptors in water.

Synthesis of Novel Bis(β-Cyclodextrin)s and Metallobridged Bis(β-Cyclodextrin)s with 2,2‘-Diselenobis(benzoyl) Tethers and Their Molecular Multiple Recognition with Model Substrates

To investigate quantitatively the cooperative binding ability of beta-cyclodextrin dimers, a series of bridged bis(beta-cyclodextrin)s with 2,2'-diselenobis(benzoyl) spacer connected by different lengths of oligo(ethylenediamine)s (2-5) and their platinum(IV) complexes (6-9) have been synthesized and their inclusion complexation behavior with selected substrates, such as Acridine Red, Neutral Red, Brilliant Green, Rhodamine B, ammonium 8-anilino-1-naphthalenesulfonate, and 6-p-toluidino-2-naphthalenesulfonic acid, were investigated by means of ultraviolet, fluorescence, fluorescence lifetime, circular dichroism, and 2D-NMR spectroscopy. The spectral titrations have been performed in aqueous phosphate buffer solution (pH 7.20) at 25 degrees C to give the complex stability constants (K(S)) and Gibbs free energy changes (-DeltaG degrees ) for the inclusion complexation of hosts 2-9 with organic dyes and other thermodynamic parameters (DeltaH degrees and TDeltaS degrees ) for the inclusion complexation of 2-5with fluorescent dyes ANS and TNS. The results obtained indicate that beta-cyclodextrin dimers 2-5 can coordinate with one or two platinum(IV) ions to form 1:1 or 1:2 stoichiometry metallobridged bis(beta-cyclodextrin)s. As compared with parent beta-cyclodextrin (1) and bis(beta-cyclodextrin)s 2-5, metallobridged bis(beta-cyclodextrin)s 6-9 can further switch the original molecular binding ability through the coordinating metal to orientate two beta-cyclodextrin cavities and an additional binding site upon the inclusion complexation with model substrates, giving the enhanced binding constants K(S) for both ANS and TNS. The tether length between two cyclodextrin units plays a crucial role in the molecular recognition with guest dyes. The binding constants for TNS decrease linearly with an increase in the tether length of dimeric beta-cyclodextrins. The Gibbs free energy change (-DeltaG degrees ) for the unit increment per ethylene is 0.32 kJ.mol(-)(1) for TNS. Thermodynamically, the higher complex stabilities of both ANS and TNS upon the inclusion complexation with 2-5 are mainly contributed to the favorable enthalpic gain (-DeltaH degrees ) by the cooperative binding of one guest molecule in the closely located two beta-cyclodextrin cavities as compared with parent beta-cyclodextrin. The molecular binding ability and selectivity of organic dyes by hosts 1-9 are discussed from the viewpoints of the multiple recognition mechanism and the size/shape-fitting relationship between host and guest.