Concentration fluctuations in fluid mixtures. II

The method developed in a previous paper [R. Mazo, J. Chem. Phys. 129, 154101 (2008)] for extracting information on the size of relative fluctuations in multicomponent systems is tested on ten binary systems and one ternary system. For the binary systems, it is found that the approximation works well for mole fractions in the range of 0.15-0.85 in most cases. For the ternary case, the method inherently yields less information and is valid only over a more restricted range for the case studied (chloroform-methanol-acetone). It is found that the predicted ratio of number fluctuations is approximately equal to the ratio of molar volumes of the components.

Direct observation of gold nanoparticle assemblies with the porin MspA on mica

The octameric porin MspA from Mycobacterium smegmatis is sufficiently stable to form a nonmembrane-supported stand-alone porin on mica surfaces. About 98% of all MspA octamers were found to stand upright on mica, with their periplasmic loop regions bound to the hydrophilic mica surface. Both, small (d = 3.7 nm) and large (d = 17 nm) gold nanoparticles bind to MspA, however, in different positions: small gold nanoparticles bind within the MspA pore, whereas the large gold nanoparticles bind to the upper region of MspA. These experiments demonstrate that gold nanoparticles can be positioned at different, well-defined distances from the underlying surface using the MspA pore as a template. These findings represent a significant step toward the use of electrically insulating stable proteins in combination with metal nanoparticles in nanodevices.

On the Kirkwood-Buff inversion procedure

A general approach is presented to express the Kirkwood-Buff integrals, the central component of the Kirkwood-Buff theory of solutions, in terms of thermodynamic properties of solution mixtures. A general expression valid for any number of components is provided in terms of matrix cofactors, while explicit expressions are given for three and four component mixtures. The corresponding symmetric ideal solution values are also presented for four and higher component mixtures.

Kirkwood-Buff theory of four and higher component mixtures

Explicit expressions are developed for the chemical potential derivatives, partial molar volumes, and isothermal compressibility of solution mixtures involving four components at finite concentrations using the Kirkwood-Buff theory of solutions. In addition, a general recursion relationship is provided which can be used to generate the chemical potential derivatives for higher component solutions.

Theory and computer simulation of solute effects on the surface tension of liquids

A complete description of the thermodynamics of planar mixed solute-solvent interfaces suitable for the analysis of computer simulation data is provided. The approach uses surface probability distributions to characterize the interface regions, coupled with radial distribution functions and the Kirkwood-Buff theory of solutions to characterize the bulk solution properties. The approach is then used to understand the relationship between changes in the surface tension, the degree of surface adsorption or depletion, and the bulk solution properties of two aqueous solute systems. The first, aqueous NaCl solutions, provides an example of a surface excluded solute. The second, aqueous methanol solutions, provides an example of a surface adsorbed solute. The numerical results support the theoretical relationships described here and provide a consistent picture of the thermodynamics of solution interfaces involving any number of components which can be applied to a wide variety of systems.

On the theory of solute solubility in mixed solvents

A series of equations are developed for the study of the effects of cosolvents on the solubility of a solute in mixed solutions where the solute displays a finite solubility. The equations differ depending on the scale used for the solute (and cosolvent) concentrations. The expressions use Kirkwood-Buff integrals to relate the changes in solubility to changes in the local solution composition around the solute and can be applied to study any type of ternary system including electrolyte cosolvents. The expressions provided here differ from previous approaches because of the use of a semi-open ensemble and the extension to finite solute solubilities.

MspA Porin-Gold Nanoparticle Assemblies: Enhanced Binding through a Controlled Cysteine Mutation

In this study, the interactions of two gold nanoparticles of different sizes (average diameters of 3.7 +/- 2.6 and 17 +/- 3 nm) with octameric mycobacterial porin A from Mycobacterium smegmatis (MspA) and a mutant of MspA featuring a cysteine mutation in position 126 (Q126C) are investigated. From the observation of enhanced photoluminescence quenching, it is inferred that the presence of eight cysteines in the MspA Q126C mutant significantly enhances the binding of selected small gold nanoparticles within the inner pore of MspA. The large gold nanoparticle/porin complex shows photoluminescence enhancement, which is expected since the larger nanoparticles cannot dock within the homopore of MspA due to size exclusion. In addition to the fluorescence experiments, observation of energy transfer from the small gold nanoparticles to the MspA shows the close proximity of the small gold nanoparticles with the porin. Interestingly, the energy transfer of the large nanoparticle/MspA complex is completely missing. From high-performance liquid chromatography data, the estimated binding constants for small Au@MspA, large Au@MspA, small Au@MspAcys, and large Au@MspAcys are 1.3 x 10 (9), 2.22 x 10 (10), > 10 (12) (irreversible), and 1.7 x 10 (10), respectively.

Recent applications of Kirkwood-Buff theory to biological systems

The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.

Equilibrium dialysis data and the relationships between preferential interaction parameters for biological systems in terms of Kirkwood-Buff integrals

Equilibrium dialysis data has provided valuable information concerning the preferential interaction of a cosolvent with a biomolecule in aqueous solutions. Here, we formulate the experimental data in terms of Kirkwood-Buff (KB) theory, resulting in equations that provide a simple physical picture of the dialysis experiment and thereby the interaction of a cosolvent with a biomolecule. These results are then used to establish exact relationships between preferential interaction coefficients, defined in different ensembles and/or using different concentration scales, in terms of KB integrals. It is then argued that the molality based equilibrium dialysis data represent the situation most relevant to computer simulations performed in either open or closed systems.

A Kirkwood-Buff derived force field for amides

A force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and Kirkwood-Buff integrals for N-methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N'-dimethylacetamide and acetamide with good success. Analysis of the simulations of low concentrations of NMA in water indicates a high degree of solvation with only 15% of the NMA molecules involved in solute-solute hydrogen bonding. There is only a weak angular dependence of the solute-solute hydrogen bonding interaction with a minimum at an angle of 65 degrees for the N-H and C=O dipole vectors. The models presented here provide a basis for an accurate force field for peptides and proteins.

Simulated surface tensions of common water models

Initial simulated values of the surface tension for the SPC/E water model have indicated excellent agreement with experiment. More recently, differing values have been obtained which are significantly lower than previous estimates. Here, we attempt to explain the differences between the previous studies and show that a variety of simulation conditions can affect the final surface tension values. Consistent values for the surface tensions of six common fixed charge water models (TIP3P, SPC, SPC/E, TIP4P, TIP5P, and TIP6P) are then determined for four temperatures between 275 and 350 K. The SPC/E and TIP6P models provide the best agreement with experiment.

A Kirkwood-Buff derived force field for the simulation of aqueous guanidinium chloride solutions

A force field for the simulation of aqueous guanidinium chloride solutions is presented. The force field was parametrized to reproduce the experimental density and Kirkwood-Buff integrals as a function of composition. Consequently, a reasonable description of the salt activity is obtained. The model also performs well for other properties such as the relative permittivity and enthalpy of mixing.

Chemical potential derivatives and preferential interaction parameters in biological systems from Kirkwood-Buff theory

New expressions for chemical potential derivatives and preferential interaction parameters for ternary mixtures are derived for open, semiopen, and closed ensembles in terms of Kirkwood-Buff integrals, where all three components are present at finite concentrations. This is achieved using a simple approach that avoids the use of the general matrix formulation of Kirkwood-Buff theory. The resulting expressions provide a rigorous foundation for the analysis of experimental and simulation data. Using the results, a simple model is developed and used to investigate the possible effects of finite protein concentrations on the corresponding cosolvent dependent chemical potential and denaturation thermodynamics.

NMR Structure and Dynamic Studies of an Anion-Binding, Channel-Forming Heptapeptide

The synthetic peptide (C(18)H(37))(2)NCOCH(2)OCH(2)CON-(Gly)(3)-Pro-(Gly)(3)-OCH(2)Ph forms chloride-selective channels in liposomes and exhibits voltage-gating properties in planar phospholipid bilayers. The peptide fragment of the channel is based on a conserved motif in naturally occurring chloride transporters. Membrane-anchoring residues at the N- and C-terminal ends augment the peptide. NMR spectra (1D and 2D) of the channel in CDCl(3) showed significant variation in the absence and presence of stoichiometric tetrabutylammonium chloride (Bu(4)NCl). One-dimensional solution-state NMR titration studies combined with computational molecular simulation studies indicate that the peptide interacts with the salt as an ion pair and H-bonds chloride. To our knowledge, this is the first structural analysis of any synthetic anion-channel salt complex.

A Kirkwood−Buff Derived Force Field for Methanol and Aqueous Methanol Solutions

A force field for the simulation of methanol and aqueous methanol mixtures is presented. The force field was specifically designed to reproduce the experimental Kirkwood-Buff integrals as a function of methanol mole fraction, thereby ensuring a reasonable description of the methanol cosolvent and water solvent activities. Other thermodynamic and physical properties of pure methanol and aqueous methanol solutions, including the density, enthalpy of mixing, translational diffusion constants, compressibility, thermal expansion, and dielectric properties, were also well reproduced.

Protein volume changes on cosolvent denaturation

A thermodynamic relationship is obtained which links the effect of a cosolvent on the denaturation equilibrium of a protein to the effect of the cosolvent on the change in partial molar volume (pmv) of a protein on denaturation. The relationship uses the concept of preferential interactions and is exact for an infinitely dilute protein. Analysis of the literature data on protein volume changes suggests that many of the observed volume changes are thermodynamically inconsistent with the corresponding free energy changes, especially at low cosolvent concentrations. It is argued that the most reasonable explanation for this involves cosolvent induced changes in the degree of protein-protein association.

The role of the unfolded state in hairpin stability

The effects of a T3S mutation on the stability of a 3:5 beta-hairpin forming peptide (YITNSNGTWT) are investigated. Molecular dynamics simulations in explicit water indicate that the wild-type peptide forms a stable hairpin whereas the T3S mutant does not, in agreement with the experimental data. Thermodynamic integration calculations for the mutation of Thr to Ser suggest that the free-energy changes in the folded state are small, but the corresponding changes in the unfolded state are large and favorable. One of the main reasons for the difference appears to be the formation of a stable cluster involving the Tyr1 and Ser3 hydroxyl groups and their interaction with the C-terminal carboxylate group, which was observed after unfolding of the T3S mutant. Further analysis of the side-chain preferences of Thr and Ser indicate that the corresponding cluster in the wild-type peptide is unstable due to the high preference of the Thr chi1 dihedral for g+ states, which appeared to be incompatible with formation of a stable cluster. The results suggest that one should consider the nature of the unfolded state when attempting to fully explain the effects of mutations on hairpin stability.

Modeling and simulation of the human delta opioid receptor

A model for the human delta opioid receptor has been generated via sequence alignment, structure building using the crystal structure of bovine rhodopsin as a template, and refinement by molecular dynamics simulation. The model building suggested that, in addition to the previously postulated interaction between D128 and Y308, an internal salt bridge also exists between residues D128 and R192, both of which are conserved in all the opioid receptors. The model and salt bridge were then shown to be stable during a 20-nsec simulation in a lipid bilayer. It is therefore proposed that both of these interactions play a role in stabilizing the inactive state of the receptor. The model is also used in an effort to rationalize many of the mutational studies performed on delta opioid receptors, and to suggest a plausible explanation for the differences between known delta opioid agonists and antagonists.