Dynamics of water molecules and sodium ions in solid hydrates of nucleotides

Abstract

Nuclear magnetic resonance experiments, together with molecular dynamics simulations and NMR calculations, are used to investigate mobility of water molecules and sodium ions in solid hydrates of two nucleotides. The structure of guanosine monophosphate system (GMP) is relatively rigid, with a well-ordered solvation shell of the nucleotide, while the water molecules in the uridine monophosphate system (UMP) are shown to be remarkably mobile, even at −80 °C. The disorder of water molecules is observed in the ¹³C, ³¹P, and ²³Na solid-state NMR experiments as multiple signals for equivalent sites of the nucleotide corresponding to different local arrangements of the solvation shell. Deuterium NMR spectra of the samples recrystallized from D₂O also confirm differences in water mobility between the two systems. The experiments were complemented with NMR calculations on an ensemble of structures obtained from DFT molecular dynamics (MD) simulations. The MD simulations confirmed higher water mobility in the UMP system and the calculated chemical shifts and quadrupolar couplings were consistent with the experimental data. The disordered solvation shell in UMP is likely to be a good model for solvated nucleotides in general, with fast reorientation of water molecules and fluctuations in the hydrogen-bond network.