Solvent isotope effect on thermodynamics of hydration

Partial molar heat capacities of five linear alcohols (methanol, ethanol, n-propanol, n-butanol, n-pentanol) and five N-substituted amides (n-propionamide, N-methylformamide, N-methylacetamide, N-methylpropionamide, N-ethylacetamide) in aqueous D(2)O solution have been measured at 25 degrees C. The heat capacities of transfer of these compounds from H(2)O to D(2)O were calculated using previously reported (Makhatadze et al., Biophys. Chem. 64 (1997) 93) values of partial heat capacities of alcohols and amides in aqueous H(2)O solutions. It is shown that the sign and magnitude of the heat capacity change upon transfer from H(2)O to D(2)O depends on the relative amount of polar and non-polar solvent accessible surface areas of solute. Analysis shows that transfer of non-polar surface from H(2)O to D(2)O is accompanied by a positive heat capacity change. In contrast, transfer of polar surface from H(2)O to D(2)O occurs with negative heat capacity change. Estimates show that the solvent isotope effect on the heat capacity changes upon protein unfolding can be predicted using the changes of the polar and non-polar surface area changes upon protein unfolding and the transfer data of model compounds. Analysis of the thermodynamic functions of transfer of non-polar compounds from H(2)O to D(2)O shows puzzling behavior which contradicts current definitions of the hydrophobic effect.     

Solvation thermodynamics of biopolymers. II. Correlations between functional groups

The extent of correlations between functional groups that can form hydrogen bonds with solvent molecules has been estimated. From the observed distance distribution of functional groups on the surfaces of several proteins, and from the extent of correlation between pairs of such functional groups, we conclude that the assumption of independence of functional groups made in part I is probably a good approximation. The reason is that even when correlations exist there is, on average, cancellation of the positive and negative correlations. The relevance of hydrogen bonding with the solvent to the relative stability of different conformers of biopolymers is also indicated.     

The effect of pyridyl substituents on the thermodynamics of porphyrin binding to G-quadruplex DNA

Most of the G-quadruplex interactive molecules reported to date contain extended aromatic flat ring systems and are believed to bind principally by π–π stacking on the end G-tetrads of the quadruplex structure. One such molecule, TMPyP4, (5,10,15,20-tetra(N-methyl-4-pyridyl)porphyrin), exhibits high affinity and some selectivity for G-quadruplex DNA over duplex DNA. Although not a realistic drug candidate, TMPyP4 is used in many nucleic acid research laboratories as a model ligand for the study of small molecule G-quadruplex interactions. Here we report on the synthesis and G-quadruplex interactions of four new cationic porphyrin ligands having only 1, 2, or 3 (N-methyl-4-pyridyl) substituents. The four new ligands are: P(5) (5-(N-methyl-4-pyridyl)porphyrin), P(5,10) (5,10-di(N-methyl-4-pyridyl)porphyrin), P(5,15) (5,15-di(N-methyl-4-pyridyl)porphyrin), and P(5,10,15) (5,10,15-tri(N-methyl-4-pyridyl)porphyrin). Even though these compounds have been previously synthesized, we report alternative synthetic routes that are more efficient and that result in higher yields. We have used ITC, CD, and ESI-MS to explore the effects of the number of N-methyl-4-pyridyl substituents and the substituent position on the porphyrin on the G-quadruplex binding energetics. The relative affinities for binding these ligands to the WT Bcl-2 promoter sequence G-quadruplex are: K_TMPyP4 ≈ K_P(5,15) > K_P(5,10,15) >>> K_P(5,10), K_P(5). The saturation stoichiometry is 2:1 for both P(5,15) and P(5,10,15), while neither P(5) nor P(5,10) exhibit significant complex formation with the WT Bcl-2 promoter sequence G-quadruplex. Additionally, binding of P(5,15) appears to interact by an ‘intercalation mode’ while P(5,10,15) appears to interact by an ‘end-stacking mode’.     

The 'dynamics' in the thermodynamics of binding

Assumptions of restricted flexibility upon binding conflict with emerging data showing that motion can increase, decrease or stay the same within molecular complexes. Now, calculations of entropic contributions from dynamics at specific positions in a complex suggest that increases in motion can dominate the free energy of association in certain cases.     

Fundamental equation of thermodynamics for protein-ligand binding

For the internal energy and every thermodynamic potential that can be defined by a Legendre transform, there is a fundamental equation that contains all the thermodynamic information about a system. For a system involving the binding of molecular oxygen and hydrogen ions by a protein, fundamental equations are given for the Gibbs energy G, the transformed Gibbs energy G' at specified pH, and the further transformed Gibbs energy G" at specified pH and specified concentration of molecular oxygen. The Maxwell equations for these various Gibbs energies are important because they provide the connection with experimentally determined properties and increase our understanding of these properties. Measurements of the average number of oxygen molecules bound as a function of T, pH and concentration of molecular oxygen make it possible to calculate Delta(f)G"(o) of the reactant. Maxwell equations make it possible to calculate the average number of hydrogen ions bound, Delta(f)S"(o), Delta(f)H"(o) and their partial derivatives. These relations are illustrated with numerical calculations on a simple reaction system.     

The thermodynamics of calcium binding to thermolysin

Calcium binding isotherms were determined for thermolysin in the range pH 5.6-10.5, and from 5 to 45 degrees C. An extensive statistical analysis of the binding data suggests that at least two of the four binding sites bind Ca2+ with complete positive cooperativity and independently of the other two. Nonlinear regression analysis of the binding data was used to calculate cooperative (K1) and independent (K2) binding constants for the four calcium sites. Thermodynamic parameters obtained from a van't Hoff analysis indicate that calcium binding to both cooperative and independent sites is an entropy-driven process. At pH 7.0, delta H1 = 90.4 kJ/mol; delta H2 = 97.5 kJ/mol; delta S1 = 456 J K-1 mol-1; delta S2 = 262 J K-1 mol-1. These results are compared to those obtained for other calcium-binding proteins. An analysis of the pH dependence of the calcium binding constants indicates that the binding of four protons at the cooperative site and one to two protons at the independent sites, modulates the calcium affinity. This confirms an earlier structural assignment of the double-site as the locus of the two cooperatively binding Ca2+. Calcium binding to thermolysin is enhanced in the presence of an active site directed inhibitor, suggesting that there may be positive cooperativity between substrate and calcium binding.     

Activation of ionotropic receptors and thermodynamics of binding

The structure, thermodynamics and activation mechanism of Cys-loop ionotropic receptors such as glycine, nicotinic acetylcholine, 5-HT3-type serotonin and A-type gamma-aminobutyric acid receptors are discussed. Based on the interrelationship of receptor binding and ionophore function, a ternary displacement mechanism of binding including the activation of ionophores is outlined. This displacement model can explain the enigmatic thermodynamic discrimination of agonists versus antagonists of Cys-loop ionotropic receptors. Binding of both agonists and antagonists is exothermic while activation is endothermic driven by large increases in entropy. Closure of the binding cavities around agonists in concert with subunit rotations and/or removal of water-filled crevices between transmembrane (TM) regions can account for entropy increases. Recombinant glycine and gamma-aminobutyric acidA receptors and their point mutations support the predominant role of entropy in receptor activation.     

The thermodynamics of lanthanide ion binding to adriamycin

We have examined the thermodynamics of lanthanide ion binding to adriamycin by monitoring the effects of variations in temperature on the dissociation constants of various lanthanide ion complexes of the drug. These constants were obtained by analyzing the extent of quenching of the fluorecence of adriamycin in the presence of lanthanide ions in terms of an equilibrium binding process. Our binding model included the following features, all of which are supported by evidence derived from previous published reports, vide infra. The lanthanides form 1:1 complexes with adriamycin. The binding is dependent on the pH of the solution, indicating that only the nonprotonated amine form of the drug participates in lanthanide ion binding. And finally the drug self-associates in solution to for a dimeric species. Our present results indicate that the binding process is almost completely independent of temperature, indicating that the enthalpy of complex formation is extremely small. The entropy terms are consistent with the formation of a complex in which the adriamycin acts as a bidentate ligand. Our results suggest that the lanthanide complexes are isostructural, at least as far as the adriamycin is concerned, throughout the lanthanide series.     

Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules.

The experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute-solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute molecules in their respective neat solvents using the equilibrium vapor pressure and the heat of vaporization data for the pure liquid. The enthalpy and the free energy changes upon cavity formation were also estimated using the temperature dependence of the solute-solvent interaction energy. Both the enthalpy and T delta S for cavity formation rapidly increase with temperature in both solvent types, and the free energy of cavity formation can be reproduced accurately by the scaled particle theory over the entire temperature range in all cases. These results indicate that the characteristic structure formation around an inert solute molecule in water produces compensating changes in enthalpy and entropy, and that the hydrophobicity arises mainly from the difference in the excluded volume effect.     

Solvent effect on hemin-catalyzed polymerization of phenols

Phenol and 4-substituted phenols were polymerized by H₂O₂ as an oxidant and hemin as a catalyst in organic/buffer mixed solvents. The chemical structures of the polymers were similar to those synthesized by the catalysis with horseradish peroxidase. Among the organic solvents used, pyridine gave the highest yield of polymer. Also, the manner of addition of H₂O₂ solution affected the polymer yield.     

ESR investigation of the binding of acidic biopolymers to synthetic apatite.

The interaction between synthetic crystalline calcium phosphate (apatite) and acidic macromolecules (sodium polyacrylate, sodium poly(L -glutamate), chondroitin sulfate, phosvitin) was investigated by electron spin resonance spectroscopy of mineral-macromolecule complexes doped with vanadyl ion (VO⁺⁺) as a paramagnetic probe. Changes in magnetic parameters were interpreted in terms of bonding between mineral and macromolecule. The VO⁺⁺ probe data indicated that polymer acidic functional groups were bound to mineral surfaces in all cases.     

Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA

The polypyrimidine tract binding protein (PTB) is involved in many physiological processes, including alternative splicing, internal ribosomal entry side (IRES)-mediated initiation of translation, and polyadenylation, as well as in ensuring mRNA stability. However, the role of PTB in these processes is not fully understood, and this has motivated us to undertake a computational study of the protein. PTB RNA binding domains (RBDs) 3 and 4 and their complexes with oligopyrimidine RNAs were simulated using the GROMOS simulation software using the GROMOS 45A4 force field. First, the stability and fluctuations of the tertiary fold and of the secondary structural elements in individual domains, the combined RBD34 domain, and their complexes with RNA were studied. Second, the simulation results were validated against the experimental NMR NOE data. The analysis of hydrogen bonding patterns, salt bridge networks, and stacking interactions of the RNA to the binding pockets of the protein domains showed that binding is not sequence-specific and that many RNA fragments can bind to them successfully. Further calculations of the relative free energy of binding for different polypyrimidine sequences were carried out using the thermodynamic integration (TI) and single-step perturbation (SSP) methods. It is was not possible to calculate the relative free energies with high accuracy, but the obtained results do give qualitative insights into PTB's affinity for different RNA sequences. Furthermore, the low-energy conformations of the complexes that were found provided additional information about the mechanism of binding.     

Solvation thermodynamics of biopolymers. I. Separation of the volume and surface interactions with estimates for proteins

The present paper is a systematic first approach to the problem of solvation thermodynamics of biomolecules. Most previous approaches have been only crude estimates of solvent contributions, and have simply assessed solvation free energy as proportional to surface areas. Here we estimate the various contributions and divide them into (a) hard-core interactions dependent upon the entire volume of solute and (b) the remainder of interactions manifested through surfaces, such as van der Waals, charge-charge, or hydrogen bonds. We have estimated the work to create a cavity with scaled-particle theory (SPT), the van der Waals interactions on the surface, and hydrogen bonds between the surface and the solvent. The conclusion here is that this latter term is the largest component of the solvation free energy of proteins. From estimates on nine diverse proteins, it is clear that the larger the protein, the more dominant is the hydrogen-bond term. In the next paper, we indicate that correlations between hydrogen-bonding groups on the surfaces could increase the magnitude of the hydrogen-bond contribution.     

Solvent effect on the stability of mannobiose conformers

The conformational equilibria of seven methyl β-D -mannobioside conformers have been studied theoretically in five solvents. The structure of each individual conformer has been refined by the PCILO quantum-chemical method from the seven distinct low-energy regions determined from (Φ, Ψ) maps calculated by a potential function method. The stability of the conformers in dilute solution has been evaluated by using a method that consists of electrostatic, dispersion, and cavity terms. The calculated abundance of conformers depends on the solvent and results indicate that the preponderant conformer in the solution may not be the one adopted by mannobiose in the crystalline form. Based on the determined abundance of conformers, thermodynamically averaged nmr parameters, dipole moment, and linkage rotation have been calculated. The solvation behavior of methyl β-D -mannobioside is compared to those previously estimated for cellobiose and maltose.     

Lysozyme binding with sulfa group of antibiotics: Comparative binding thermodynamics and computational study

Protein–drug binding study addresses a broad domain of biological problems associating molecular functions to physiological processes composing and modifying safe and coherent drug therapeutics. Comparison of the binding and thermodynamic aspect of sulfa drugs, sulfamethazine (SMZ) and sulfadiazine (SDZ) with the protein, lysozyme (Lyz) was carried out using spectroscopic, molecular docking, and dynamic simulation studies. The fluorescence quenching and apparent binding constant for the binding reaction were calculated to be in the order of 10⁴ M⁻¹, slightly higher for SMZ as compared to that of SDZ and the binding stoichiometry values show 1:1 drug binding with each protein molecule. The binding was an enthalpy-driven spontaneous exothermic reaction favored by a negative enthalpy and a positive entropy contribution for both the complexes. The binding from the fluorescence quenching data suggests a static quenching mechanism dominated by non-polyelectrolytic components. Synchronous fluorescence denoted a conformational change in the tryptophan moiety of the protein. Molecular docking and dynamic simulation study provided a clearer view of the interaction pattern, where the drug resides on the binding pocket of the protein structure. Overall the protein, Lyz binding of SMZ was slightly more favored over SDZ.     

Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion

Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop–loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug–RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (K_d ~ 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (K_d ~ 1.6 µM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop–loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA.