Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data
Figure 3
Jittergram of kinked A/T-tRNA from molecular dynamics simulations. (a) Using multiple unbiased molecular dynamics for kinked A/T-tRNA, we generated a set of structures. These are superposed based on all P-atoms found in the backbone of the stem regions. This orientation optimally shows the alignment of the stems and the variation at the acceptor stem loop and anticodon stem loop. The different tRNA colors help distinguish the different conformations. (b) Illustrated in cyan as a series of snapshots is a simulation for kinked A/T-tRNA using free molecular dynamics with tethering constraints at the anticodon atoms (H-bond atoms of nucleotides 34, 35, 36), which was run for >10 ns. We used tethering (harmonic constraints) at the anticodon atoms to mimic base pairing at the codon. This data was used for the contact map (Figure 5). This orientation best shows the wide range of motion that the tRNA covers (over 70 Å from beginning to end for the 3′CCA end).
