Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models

Ionizable residues play important roles in protein structure and activity, and proton binding is a valuable reporter of electrostatic interactions in these systems. We use molecular dynamics free energy simulations (MDFE) to compute proton pKa shifts, relative to a model compound in solution, for three aspartate side chains in two proteins. Simulations with explicit solvent and with an implicit, dielectric continuum solvent are reported. The implicit solvent simulations use the generalized Born (GB) model, which provides an approximate, analytical solution to Poisson's equation. With explicit solvent, the direction of the pKa shifts is correct in all three cases with one force field (AMBER) and in two out of three cases with another (CHARMM). For two aspartates, the dielectric response to ionization is found to be linear, even though the separate protein and solvent responses can be nonlinear. For thioredoxin Asp26, nonlinearity arises from the presence of two substates that correspond to the two possible orientations of the protonated carboxylate. For this side chain, which is partly buried and has a large pKa upshift, very long simulations are needed to correctly sample several slow degrees of freedom that reorganize in response to the ionization. Thus, nearby Lys57 rotates to form a salt bridge and becomes buried, while three waters intercalate along the opposite edge of Asp26. Such strong and anisotropic reorganization is very difficult to predict with Poisson-Boltzmann methods that only consider electrostatic interactions and employ a single protein structure. In contrast, MDFE with a GB dielectric continuum solvent, used for the first time for pKa calculations, can describe protein reorganization accurately and gives encouraging agreement with experiment and with the explicit solvent simulations.     

Apparent molar volumes of aqueous calcium chloride to 250°C, 400 bars,and from molalities of 0.242 to 6.150

Relative densities of CaCl ₂ (aq) with 0.22ml(mol-kg^–1)6.150 were measured with vibrating- tube densimeters between 25 and 250°C and near 70 and 400 bars. Apparent molar volumes V calculated from the measured density differences were represented with the Pitzer ioninteraction treatment, with appropriate expressions chosen for the temperature and pressure dependence of the virial coefficients of the model. It was found that the partial molar volume at infinite dilution V ^o , and the second and third virial coefficients B ^V and C ^V , were necessary to represent V near the estimated experimental uncertainty. The ionic-strength dependent ^(1)v term in the B ^V coefficient was included in the fit. The representation for V has been integrated with respect to pressure to establish the pressure dependence of excess free energies over the temperature range studied. The volumetric data indicate that the logarithm of the mean ionic activity coefficient, ln ±(CaCl ₂ ), increases by a maximum of 0.3 at 400 bars, 250°C, and 6 mol-kg^–1 as compared with its value at saturation pressure.     

A Titration Microcalorimetric Study of the Effects of Halide Counterions on Vesicle-Forming Aggregation in Aqueous Solution of Branched-Chain Alkylpyridinium Surfactants

Titration microcalorimetry is used to study the influences of iodide, bromide, and chloride counterions on the aggregation of vesicle-forming 1-methyl-4-(2-pentylheptyl)pyridinium halide surfactants. Formation of vesicles by these surfactants was characterised using transmission electron microscopy. When the counterion is changed at 303 K through the series iodide, bromide, to chloride, the critical vesicular concentration (cvc) increases and the enthalpy of vesicle formation changes from exo- to endothermic. With increase in temperature to 333 K, vesicle formation becomes strongly exothermic. Increasing the temperature leads to a decrease in enthalpy and entropy of vesicle formation for all three surfactants. However the standard Gibbs energy for vesicle formation is, perhaps surprisingly, largely unaffected by an increase in temperature, as a consequence of a compensating change in both standard entropy and standard enthalpy of vesicle formation. Interestingly, standard isobaric heat capacities of vesicle formation are negative, large in magnitude but not strikingly dependent on the counterion. We conclude that the driving force for vesicle formation can be understood in terms of overlap of the thermally labile hydrophobic hydration shells of the alkyl chains. Copyright 2000 Academic Press.