Hydration Gibbs Energies of Nucleic Acid Bases Determined by Gibbs Energy Perturbation, Continuous and Hybrid Approaches

Binding of calcium and other metal ions to the EF-hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations

Calcium ion binding by the four EF-hand motifs of the protein calmodulin (CaM) is a central event in Ca2+-based cellular signaling. To understand molecular details of this complex process, isolated Ca2+-binding loops can be studied, by use of both experiments and calculations. In this work, we explore the metal specificity of the four Ca2+-binding loops of CaM using density functional theory (DFT) quantum chemical calculations and molecular dynamics simulations. We study CaM complexes with the physiologically important ions of calcium (Ca2+) and magnesium (Mg2+) and also with two other ions, strontium (Sr2+) and lanthanum (La3+). The former is of interest in the area of radioactive waste bioremediation, whereas the latter is often used as a probe of Ca2+-binding sites. We obtain intrinsic metal ion-loop binding energies as well as their components: vacuum, charge-transfer, solvation, entropy, and deformation terms. A detailed analysis of the results reveals that the total binding energy depends on a delicate balance among these energy components. They, in turn, are determined by the cation's charge and size as well as the amino acid composition and flexibility of the loops and the identity of the metal-chelating residues.

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.