Hydration of C—H groups in tRNA

Abstract

Molecular dynamic (MD) simulations of the anticodon hairpin of tRNA^Asp and of the full tRNA, both in a solvent bath with neutralizing NH₄⁺ counter-ions, have been produced with the particle mesh ewald (PME) method and the multiple molecular dynamics (MMD) strategy. The latter consists of generating uncorrelated trajectories starting from the same initial configuration but with a slightly perturbed initial velocity distribution. The 3 ns (six uncorrelated 500 ps MD trajectories) MMD set of the 17 nucleotide anticodon fragment and the single 500 ps trajectory of the 75 nucleotide tRNA were analysed with the aim of characterizing long lived C—H⋯O_w interactions for the two main nucleic acid base and ribose C—H bond types. Some C—H sites present very long residence lifetimes for water molecules, especially those around the ribose H(3′) and the pyrimidine H(5) atoms. The C(3′)—H(3′)⋯O_w contacts occur concurrently with the strong hydration of the anionic phosphate oxygen atoms and especially with the water bridges linking successive phosphate groups along the polynucleotide chain. Therefore, these contacts are of opportunistic character and result from the geometries of the covalent structure and adjacent interactions. On the other hand, the pyrimidine H(5) atoms display a hydrophilic character with interaction geometries indicating that water contacts in which they are involved should be considered as bona fide hydrogen bonds.