Theoretical studies of the interaction of water with DNA oligomers and proteins

The effects of hydration on the structure and dynamics of DNA oligomers and small proteins have been studied. The hydration of small biomolecules was studied by means of molecular dynamics and Monte Carlo simulations that explicitly include the water-electrolyte solvent. From these simulations and from simulations of pure water and simple solutes in water, a potential of mean force (PMF) was constructed. This PMF approach was used to describe equilibrium hydration patterns around any biomolecule without the need to do extensive simulations. The effect of water on the dynamics of biological macromolecules is understood by combined theoretical and experimental studies. Methodologies that involve the use of molecular dynamics simulations and theoretical approaches to interpret multi-dimensional nuclear magnetic resonance (NMR) and x-ray diffraction data have been developed