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

Abstract

Accuracy in translation of the genetic code into proteins depends upon correct tRNA-mRNA recognition in the context of the ribosome. In human tRNA UUULys,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 UUULys,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. © 2006 Oxford University Press.