The application of Kirkwood-Buff theory to study hydration properties of $α$-amino acids

Abstract

Protein conformational stability and function depend on non-covalent interactions that are strongly influenced by the surrounding environment. To explore protein properties, amino acids are often utilized as model systems. In this study, we determined the densities of seven $α$-amino acids in aqueous solutions between 278.15 K and 308.15 K and calculated the apparent molar volumes. Linear extrapolation yielded standard molar volumes, which were analyzed to characterize amino-acid hydration. The contributions of side chains to the standard molar volume were determined relative to glycine. The standard molar volume increased with temperature, indicating reduced electrostriction of water around the amino acids, consistent with lower hydration numbers at higher temperatures. We employed the Ornstein-Zernike integral equation with hypernetted-chain closure and a coarse-grained Lennard-Jones bead model to calculate pair correlation functions and Kirkwood-Buff integrals, from which standard molar volumes were obtained. The model reproduced the experimental standard molar volumes very well.

Figures (4)

• Figure 1: The apparent molar volumes ($V_{\phi}$) of L-glycine at 298.15 K across various molar concentrations (the size of the symbol correspond to the estimated measurement error). The dotted line represents the extrapolation to apparent molar volumes at infinite dilution ($V^{\circ}_{\phi}$). Note that the discrepancies from linearity at low amino acid concentrations are due to a low density measurement accuracy of the densimeter at low concentration range.
• Figure 2: The partial molar volumes at infinite dilution ($V^{\circ}_{\phi}$) of L-glycine at four different temperatures: 278.15 K, 288.15 K, 298.15 K, and 308.15 K (the size of the symbol correspond to the estimated measurement error).
• Figure 3: (Colour online) Experimental ($x$-axis) vs. theoretically derived ($y$-axis) standard apparent molar volumes $V_{\phi}^{\circ}$ for seven $\alpha$-amino acids in water at 298.15 K. Filled circles correspond to the single-bead van der Waals parametrisation; the dotted line indicates perfect agreement ($y = x$). Triangles show results using bead diameters based on hydration radii $2R_h$ for Gly (down triangle) and Trp (up triangle).
• Figure 4: (Colour online) Correlation between the hydration number $n_{\text{H}}$ and the structural hydration number $N_{\mathrm{shell}}$ for the studied amino acids at $T=298.15\ \mathrm{K}$. The dashed line represents the linear fit.