Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water

In the present study we examine the enthalpy of binding of 2-methoxy-3-isobutylpyrazine (IBMP) to the mouse major urinary protein (MUP), using a combination of isothermal titration calorimetry (ITC), NMR, X-ray crystallography, all-atom molecular dynamics simulations, and site-directed mutagenesis. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than a classical entropy-driven signature that might be expected given that the binding pocket of MUP-1 is very hydrophobic. The only ligand-protein hydrogen bond is formed between the side-chain hydroxyl of Tyr120 and the ring nitrogen of the ligand in the wild-type protein. ITC measurements on the binding of IBMP to the Y120F mutant demonstrate a reduced enthalpy of binding, but nonetheless binding is still enthalpy dominated. A combination of solvent isotopic substitution ITC measurements and all-atom molecular dynamics simulations with explicit inclusion of solvent water suggests that solvation is not a major contributor to the overall binding enthalpy. Moreover, hydrogen/deuterium exchange measurements suggest that there is no significant contribution to the enthalpy of binding derived from "tightening" of the protein structure. Data are consistent with binding thermodynamics dominated by favorable dispersion interactions, arising from the inequality of solvent-solute dispersion interactions before complexation versus solute-solute dispersion interactions after complexation, by virtue of poor solvation of the binding pocket.     

Thermodynamics of binding of D-galactose and deoxy derivatives thereof to the L-arabinose-binding protein

We report the thermodynamics of binding of d-galactose and deoxy derivatives thereof to the arabinose binding protein (ABP). The "intrinsic" (solute-solute) free energy of binding DeltaG degrees (int) at 308 K for the 1-, 2-, 3-, and 6-hydroxyl groups of galactose is remarkably constant (approximately -30 kJ/mol), despite the fact that each hydroxyl group subtends different numbers of hydrogen bonds in the complex. The substantially unfavorable enthalpy of binding (approximately 30 kJ/mol) of 1-deoxygalactose, 2-deoxygalactose, and 3-deoxygalactose in comparison with galactose, cannot be readily accounted for by differences in solvation, suggesting that solute-solute hydrogen bonds are enthalpically significantly more favorable than solute-solvent hydrogen bonds. In contrast, the substantially higher affinity for 2-deoxygalactose in comparison with either 1-deoxygalactose or 3-deoxygalactose derives from differences in the solvation free energies of the free ligands.     

Additivity and the physical basis of multivalency effects: a thermodynamic investigation of the calcium EDTA interaction

To better understand the origin of multivalency effects in ligand binding, the binding of a series of mono-, bi-, tri- and tetravalent carboxylate ligands to Ca(II) was examined by isothermal titration calorimetry (ITC). The data are inconsistent with an entropic origin of enhanced affinity, but rather show that at least in this instance the multivalency effect is enthalpic in origin. Analysis of binding data using the Jencks model shows the addition of incremental carboxylate "ligands" produces an unfavorable interaction entropy that is more than offset by a strongly favorable interaction enthalpy. The most likely source of this interaction enthalpy is the relief of repulsive Coulombic interactions in the unbound state. The conformational entropy penalty arising from the restriction of flexible dihedrals is negligible, within experimental error. On the other hand, an enthalpic contribution from linker restriction contributes strongly to the overall thermodynamics of ligand binding. Together, these data suggest that enthalpic effects dominate ligand binding, and design strategies should seek to optimize these interactions. The incorporation of unfavorable interactions in the unbound ligand that are relieved during binding provides an important mechanism by which to enhance ligand affinities.     

Confusing cause and effect: energy-entropy compensation in the preferential solvation of a nonpolar solute in dimethyl sulfoxide/water mixtures

We performed molecular simulations to analyze the thermodynamics of methane solvation in dimethyl sulfoxide (DMSO)/water mixtures (298 K, 1 atm). Two contributions to the interaction thermodynamics are studied separately: (i) the introduction of solute-solvent interactions (primary contribution) and (ii) the solute-induced disruption of cohesive solvent-solvent interactions (secondary contribution). The energy and entropy changes of the secondary contribution always exactly cancel in the free energy (energy-entropy compensation), hence only the primary contribution is important for understanding changes of the free energy. We analyze the physical significance of the solute-solvent energy and solute-solvent entropy associated with the primary contribution and discuss how to obtain these quantities from experiments combining solvation thermodynamic and solvent equation of state data. We show that the secondary contribution dominates changes in the methane solvation entropy and enthalpy: below 30 mol % DMSO in the mixture, methane, because of more favorable dispersion interactions with DMSO molecules, preferentially attracts DMSO molecules, which, in response, release water molecules into the bulk, causing an increase in the entropy. This large energy-entropy compensating process easily causes a confusion in the cause for and the effect of preferred methane-DMSO interactions. Methane-DMSO dispersion interactions are the cause, and the entropy change is the effect. Procedures that infer thermodynamic driving forces from analyses of the solvation entropies and enthalpies should therefore be used with caution.     

Excess free energies and entropies of aqueous solutions of methyl-D-pyranosides at 25°C

The excess Gibbs free energies of four -methyl-D-aldopyranosides in water were determined at 25°C from isopiestic measurements. The excess entropies were obtained by subtracting the free energy values from the enthalpy data. The results show a remarkable enthalpy-entropy compensation. The positive sign of the excess free energies is interpreted as due to the favorable solute-solvent interactions that prevent the favorable solute-solute interaction. The signs and magnitudes of the pair interaction coefficients are attributed to the release of water from the hydration cospheres during the concentration process. The excess properties seem to depend, however, on the stereochemistry of the solutes. This effect is discussed and attributed to the different specific stabilities of the hydration shells.     

Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes

Entropic and enthalpic contributions to the hydrophobic interaction between nanoscopic hydrophobic solutes, modeled as graphene plates in water, have been calculated using molecular dynamics simulations in the isothermal-isobaric (NPT) ensemble with free energy perturbation methodology. We find the stabilizing contribution to the free energy of association (contact pair formation) to be the favorable entropic part, the enthalpic contribution being highly unfavorable. The desolvation barrier is dominated by the unfavorable enthalpic contribution, despite a fairly large favorable entropic compensation. The enthalpic contributions, incorporating the Lennard-Jones solute-solvent terms, largely determine the stability of the solvent separated configuration. We decompose the enthalpy into a direct solute-solute term, the solute-solvent interactions, and the remainder that contains pressure-volume work as well as contributions due to solvent reorganization. The enthalpic contribution due to changes in water-water interactions arising from solvent reorganization around the solute molecules is shown to have major contribution in the solvent induced enthalpy change.     

水溶液中氯化铯与糖(D-葡萄糖、D-果糖和蔗糖)相互作用的热力学参数研究(298.15K)

用钾离子选择性电极为测量电极,氯离子选择性电极为参比电极,设计组成无液接电池,用于氯化铯-糖(葡萄糖、果糖及蔗糖)-水三元体系中组分之间弱相互作用的热力学性质研究.通过测量电池的电动势获得氯化铯在糖水溶液中的活度系数,根据Scatchard理论推测出糖在氯化铯水溶液中的活度系数.通过Mcmillan-Mayer理论将体系的过量热力学函数与溶液中溶质的相互作用参数相关联,获得氯化铯与糖在水溶液中相互作用的吉布斯自由能参数及盐效应常数.运用结构相互作用模型、糖的羟基水化效应及色散能理论,探讨体系中溶质-溶质、溶质-溶剂间的相互作用及糖的立体结构和金属离子体积对热力学参数的影响.     

Monte Carlo simulation of the influence of solvent on nucleic acid base associations

The results of Monte Carlo calculations of the association between nucleic acid bases in a nonpolar solvent (CCl4) are described. The influence of the solvent on planar and stacked associations of bases was examined by analyzing the total energy of the system, including solute-solute, solute-solvent, and solvent-solvent contributions. Good quantitative agreement with the available experimental data was obtained. Solute-solvent interactions are primarily determined by dispersion forces; consequently, solute-solvent interactions vertical to the solute plane that maximize dispersion interactions are most favored, and a rough proportionally between solute-solvent energy and the surface of the solute was observed. Analysis of solvent-solvent energy is not necessarily reduced when surface area decreases, contrary to the simple cavity concept. "Single molecule probe" calculations were performed to explain the differences in base associations in H2O and CCl4. In CCl4 dispersion forces dominate and planar complexes are stabilized by maximum exposure of molecular planes to the solvent. In H2O electrostatic forces dominate so that the most stable structures are stacked association that allow the maximum number of hydrophilic centers to be exposed to the solvent.     

Vitamin A and vitamin E interaction behavior on chitosan microspheres

Chitosan is a biodegradable natural polymer with great potential for pharmaceutical applications due to its biocompatibility, high charge density, and non-toxicity. In this study, chitosan microspheres were successfully prepared by an adapted method of coagulation/dispersion. The degree of deacetylation of chitosan powder was obtained by NMR ¹H and FTIR techniques. Chitosan powder and chitosan microspheres were characterized by BET surface area and scanning electron microscopy (SEM). The interactions among the chitosan microspheres and the vitamins A and E were characterized by FTIR. In order to evaluate the ability of interaction of vitamin A and vitamin E with the chitosan microspheres, the thermodynamic parameters were followed by calorimetric titration. Different experimental approaches were applied, such as adsorption isotherms, kinetics and thermodynamics studies. The obtained results showed that the interactions of chitosan microspheres with the vitamins were spontaneous, enthalpically and entropically favorable, indicating that the chitosan microspheres can be used with success in the controlled release of these vitamins.     

Thermodynamics of porphyrin binding to human serum albumin using affinity capillary electrophoresis

Summary The interaction thermodynamics of heptacarboxylporphyrin (HCP) and protoporhyrin (PP) with human serum albumin (HSA) was studied by affinity capillary electrophoresis (ACE) over the temperature range of 25–50°C, where HCP and PP bound to HSAvia 1:1 molecular association. The binding equilibrium constants (pH 7.4, phosphate buffer) for the binding of HCP with HSA were found to decrease with an increase in temperature, whereas the binding constants of the PP/HSA system appeared to be independent of temperature changes over the range studied. The van’t Hoff relationship (25–50°C) was found to be linear for the interaction of either HCP or PP with HSA. However, the interaction thermodynamics for both of these porphyrins with HSA were found to be quite different. In particular, the interaction of HCP (a hydrophilic porphyrin) with HSA appeared to be based on an enthalpy-driven process, whereas the binding between PP (a hydrophobic porphyrin) and HSA driven by a favorable change in entropy. The ability of using ACE to evaluate the interaction thermodynamics of serum proteins (e.g., HSA) with ligands (e.g., porphyrins and related compounds) should aid in the development of new and more effective photosensitizers in the photodynamic therapy of cancer.     

Concentration Polarization of Interacting Solute Particles in Cross-Flow Membrane Filtration

A theoretical approach for predicting the influence of interparticle interactions on concentration polarization and the ensuing permeate flux decline during cross-flow membrane filtration of charged solute particles is presented. The Ornstein-Zernike integral equation is solved using appropriate closures corresponding to hard-spherical and long-range solute-solute interactions to predict the radial distribution function of the solute particles in a concentrated solution (dispersion). Two properties of the solution, namely the osmotic pressure and the diffusion coefficient, are determined on the basis of the radial distribution function at different solute concentrations. Incorporation of the concentration dependence of these two properties in the concentration polarization model comprising the convective-diffusion equation and the osmotic-pressure governed permeate flux equation leads to the coupled prediction of the solute concentration profile and the local permeate flux. The approach leads to a direct quantitative incorporation of solute-solute interactions in the framework of a standard theory of concentration polarization. The developed model is used to study the effects of ionic strength and electrostatic potential on the variations of solute diffusivity and osmotic pressure. Finally, the combined influence of these two properties on the permeate flux decline behavior during cross-flow membrane filtration of charged solute particles is predicted. Copyright 1999 Academic Press.     

Computational analysis of binding affinity and neural response at the l-alanine receptor

Summary A model of analogue-receptor binding is developed for the l-alanine receptor in the channel catfish using the AM1-SM2 and ab initio SCRF computational methods. Besides interactions involving the zwitterionic moiety of the amino acid analogue and complementary subsites on the receptor, the model suggests the presence of a hydrophobic pocket with dispersion interactions between the receptor and the residue on the amino acid analogue. Conformational analysis suggests not only a small compact active site on the receptor, but also that the analogues with the highest affinity occupy nearly identical regions of space. Although the binding interaction is dominated by the ionic terms, AM1-SM2 calculations indicate that free energy terms associated with cavity formation, solvent reorganization, and dispersion interactions can be correlated to activation and neural response. From a consideration of this model, molecular features of the analogues that are important for binding and neural response were deduced and other analogues or ligands were developed and tested.     

Water‐Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase

This study uses mutants of human carbonic anhydrase (HCAII) to examine how changes in the organization of water within a binding pocket can alter the thermodynamics of protein–ligand association. Results from calorimetric, crystallographic, and theoretical analyses suggest that most mutations strengthen networks of water‐mediated hydrogen bonds and reduce binding affinity by increasing the enthalpic cost and, to a lesser extent, the entropic benefit of rearranging those networks during binding. The organization of water within a binding pocket can thus determine whether the hydrophobic interactions in which it engages are enthalpy‐driven or entropy‐driven. Our findings highlight a possible asymmetry in protein–ligand association by suggesting that, within the confines of the binding pocket of HCAII, binding events associated with enthalpically favorable rearrangements of water are stronger than those associated with entropically favorable ones.     

Enhanced Aerogen–π Interaction by a Cation–π Force

The interaction between a noble gas atom and an aromatic π‐electron system, which mainly originates from the London dispersion force, is very weak and has not attracted enough attention yet. Herein, we reported a type of notably enhanced aerogen–π interaction between cation–π systems and noble gas atoms. The binding strength of a divalent cation–π system with a xenon atom is comparable to a moderate hydrogen bond (up to ca. 7 kcal mol^?1), whereas krypton and argon atoms produce slightly weaker interactions. Energy‐decomposition analysis reveals that the induction interaction is responsible for the stabilization of divalent cation–π?Xe species besides the dispersion interaction. Our results might be helpful to increase the understanding of some unsolved mysteries of aerogens.     

Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement

The oxy-Cope rearrangement reaction in the antibody AZ28 is investigated using ab initio molecular orbital calculations and molecular mechanical molecular dynamics simulations. This antibody, AZ28, is known as one of the few systems where the mature catalytic antibody shows a negative correlation between the transition state analogue (TSA) binding affinity and the catalytic rate of the oxy-Cope rearrangement compared to the germ line catalytic antibody. The ab initio optimized structure shows that the transition state structure has a more planar configuration than the TSA. The favorable electrostatic interactions between AZ28 and the transition state analogue overcome the unfavorable van der Waals interactions; thus, AZ28 shows higher binding affinity for the TSA than the germ line. However, the AZ28 is not flexible enough to accept the relatively planar transition state structure. Because the lower flexibility causes poorer antibody-hapten interaction energies, the activation free energy of the oxy-Cope rearrangement becomes larger in the mature antibody than the germ line. We show that the differences in flexibility between the germ line and the mature form and the differences in structure between TSA and the transition state are the origin of the negative correlation in AZ28-catalyzed oxy-Cope rearrangement. The mutation of residue 34 of the light chain, 34(L), affects the binding free energies through the interresidue interaction because it is the closest to the hapten among the six mutatable residues. However, it does not affect the negative correlation.     

Influence of the water molecule on cation-pi interaction: ab initio second order Møller-Plesset perturbation theory (MP2) calculations

The influence of introducing water molecules into a cation-pi complex on the interaction between the cation and the pi system was investigated using the MP2/6-311++G method to explore how a cation-pi complex changes in terms of both its geometry and its binding strength during the hydration. The calculation on the methylammonium-benzene complex showed that the cation-pi interaction is weakened by introducing H(2)O molecules into the system. For example, the optimized interaction distance between the cation and the benzene becomes longer and longer, the transferred charge between them becomes less and less, and the cation-pi binding strength becomes weaker and weaker as the water molecule is introduced one by one. Furthermore, the introduction of the third water molecule leads to a dramatic change in both the complex geometry and the binding energy, resulting in the destruction of the cation-pi interaction. The decomposition on the binding energy shows that the influence is mostly brought out through the electrostatic and induction interactions. This study also demonstrated that the basis set superposition error, thermal energy, and zero-point vibrational energy are significant and needed to be corrected for accurately predicting the binding strength in a hydrated cation-pi complex at the MP2/6-311++G level. Therefore, the results are helpful to better understand the role of water molecules in some biological processes involving cation-pi interactions.     

Noncovalent keystone interactions controlling biomembrane structure

There is a biomedical need to develop molecular recognition systems that selectively target the interfaces of protein and lipid aggregates in biomembranes. This is an extremely challenging problem in supramolecular chemistry because the biological membrane is a complex dynamic assembly of multifarious molecular components with local inhomogeneity. Two simplifying concepts are presented as a framework for basing molecular design strategies. The first generalization is that association of two binding partners in a biomembrane will be dominated by one type of non-covalent interaction which is referred to as the keystone interaction. Structural mutations in membrane proteins that alter the strength of this keystone interaction will likely have a major effect on biological activity and often will be associated with disease. The second generalization is to view the structure of a cell membrane as three spatial regions, that is, the polar membrane surface, the midpolar interfacial region and the non-polar membrane interior. Each region has a distinct dielectric, and the dominating keystone interaction between binding partners will be different. At the highly polar membrane surface, the keystone interactions between charged binding partners are ion-ion and ion-dipole interactions; whereas, ion-dipole and ionic hydrogen bonding are very influential at the mid-polar interfacial region. In the non-polar membrane interior, van der Waals forces and neutral hydrogen bonding are the keystone interactions that often drive molecular association. Selected examples of lipid and transmembrane protein association systems are described to illustrate how the association thermodynamics and kinetics are dominated by these keystone noncovalent interactions.     

1H NMR study on the self-association of quinacridone derivatives in solution

The pi-stacking structures and self-association thermodynamics of N, N'-di(n-alkyl) quinacridone derivatives (n-alkyl QAs) with various substituents on the side aromatic rings and different length of n-alkyl chains are investigated in organic solvents by (1)H NMR spectroscopy. The stacking geometries are built based on both the magnitudes and directions of peak shifts with concentration and solvent polarity. The intermolecular interaction between nitrogen atoms and oxygen atoms dominates the general geometrical preferences of the stacking in which the molecules are face-to-face arranged in a parallel and an antiparallel fashion, respectively. The stacking structures are little affected by the length of the n-alkyl chains but are regulated in an allowed range by the size and properties of the substituents. The association processes of all the n-alkyl QAs are enthalpically favorable at 298 K, while the relative stability of these n-alkyl QAs assemblies is governed mainly by the entropy of the association processes. The introduction of larger substituents and longer n-alkyl chains disfavors the association of the n-alkyl QAs, while the binding of the halogen atoms on the side aromatic rings is favorable to the association. The relative strength of the stacking interaction for the substituted n-alkyl QAs has not obvious correlation with the electron-donating or electron-withdrawing nature of the substituents, while it is well associated to the dispersion energy and repulsive exchange energy. The different entropy-enthalpy compensation of the halogen-substituted n-alkyl QAs from others may suggest different association mechanism for the two types of n-alkyl QAs.     

Diffusion of polyols in aqueous solution

The diffusion coefficients of aqueous solutions of the polyols CH₂OH-(CHOH)₄-CH₂OH (dulcitol, sorbitol, and myo-inositol) have been determinated using the Gouy interferometric method. Viscosity and density measurements have been carried out at the same temperature and concentration range for these and for mannitol. The concentration dependence of the diffusion coefficients are discussed in terms of solute-solute interactions with the help of thermodynamic literature data. Among the studied polyols, only dulcitol and myo-inositol exhibit a strong evidence for solute-solute interaction, whereas the other shows a preferential interaction with the solvent.