Abstract
Modified and unmodified yeast tRNA(Phe) in solution was simulated to understand the effect of nucleotide modifications on the dynamics of tRNA. High performance computing techniques were employed to obtain a “dynamic picture” at spacial and time resolutions hardly accessible experimentally for these systems. Local flexibility, secondary and tertiary structure, global rearrangements and movements of the whole tRNA were probed by a microsecond of all atom explicit solvent molecular dynamics simulations.The results of our simulations give new insight on experimentally observed biological impact of nucleotide modifications. Amongst other results we find that tRNA modification leads to a decrease in secondary structure and tertiary interactions in the anticodon stem loop. Nucleotides U16 and U17 show different orientations when modified to dihydrouridine. Modification of A58 to 1-methyladenosine causes local rearrangements in the elbow region. Implications of our results on external factor binding are discussed.
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