NMR RELAXATION-TIMES, DYNAMICS, AND HYDRATION OF A NUCLEIC-ACID FRAGMENT FROM MOLECULAR-DYNAMICS SIMULATIONS

Molecular dynamics simulations were performed on the nucleic acid fragment guanylyl-3',5'-uridine in aqueous solution using the CHARMM program. The nucleic acid fragment was simulated using united-atom parameters in three different water models, SPC, SPC/E, and TIP3P, in the microcanonical ensemble (NVE) with periodic boundary conditions. One NVE simulation was performed using the all-atom parameters of the nucleic acid fragment solvated in TIP3P water with periodic boundary conditions. Simulations were also performed on the nucleic acid fragment using the united-atom parameters in the canonical and isothermal-isobaric ensembles in TIP3P water with periodic boundary conditions. The last NVE simulation was carried out on the nucleic acid fragment using the united-atom parameters with stochastic boundary conditions. The electrostatic energy term was observed to be more important at short distances for the base-base, interactions in the all-atom parameter set than in the united-atom parameter set, but for both parameter sets the bases were observed to be parallel to each other. The rotational and translational motions were examined, and the hydration of the polar atoms of the bases, sugar moieties, and phosphate oxygens, was analyzed in terms of the distribution of water molecules around the solute-and hydrogen bonding to the solute. The strongest interaction with water was observed for the phosphate oxygens. Although some differences in dynamic behavior and hydration of the solute were observed, the various ensembles, water models, potential energy functions, and boundary conditions used gave strikingly similar results. The degree of correlation between all the backbone, glycosidic, and endocyclic ribose torsion angles was;determined. The proton spin-spin and spin-lattice relaxation times were determined taking into account the correlation time of each proton-proton pair, and good agreement with experiment was found. Influences from different protons on the proton relaxation rates were investigated.