Molecular dynamics simulations of human tRNA Lys,3 UUU: 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(Lys,3)UUU three modified bases are present in the anticodon stem-loop--2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34) and pseudouridine (psi) at position 39--two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of wild-type human tRNA(Lys,3)UUU [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 ms2t6 modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms2t6A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to psi39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.

Figure 1

Secondary structure of human tRNA^Lys,3 ASL. Chemical structures of modified bases found in ASL^Lys,3.

Figure 2

Plots of r.m.s.d. from the average structures. For each simulation, the average structure was calculated solely for the production run. The r.m.s.d. values have an arbitrary zero.

Figure 3

Stair-stepped conformation. (A) Stair-stepped conformation of the anticodon bases from the side (left) and from above (right) with dx, dy and dz parameters shown. (B) Snapshot of the wild-type simulation showing ms²t⁶A37 hydrogen bonding across the loop (left) and a snapshot of the ASL^Lys,3 ψ39 simulation when U36 is rotated into solution (right).

Figure 4

Conformations of ms²t⁶A. (A) with an ureido ring (B) without an ureido ring as calculated at the MPW1K/6-31+G (d,p) level of theory.