Molecular dynamics simulations of human tRNA _UUU ^Lys,3: The role of modified bases in mRNA recognition

Accuracy in translation of the genetic code into proteins depends upon correct tRNA-mRNA recognition in the context of the ribosome. In human tRNA _UUU^Lys,3 three modified bases are present in the anticodon stem-loop - 2-methylthio- N 6-threonylcarbamoyladenosine at position 37 (ms²t₆ A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm⁵ s² U34) and pseudouridine (ψ) at position 39-two of which, ms²t⁶ A37 and mcm⁵s² U34, are required to achieve wild-type binding activity of wild-type human tRNA _UUU^Lys,3 [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390-13395]. Molecular dynamics simulations of nine tRNA anticodon stem-loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms² t⁶ modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms² t⁶ A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to ψ39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.