Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data
Figure 6
RMSD graph for three types of tRNA simulations presented in this study. This graph represents the root mean square deviation between the simulation of tRNAPhe with that of the crystal structure for tRNAPhe (1EHZ) [33]. As time progresses the initial tRNAPhe relaxes under the force field and the biased and unbiased states of tRNA progress toward the crystal form. (a) “Line a” represents the constrained anticodon MD simulation of the A/T state kinked model, which converges to the A-site ensemble after 4 ns. (b) “Line b” represents the free MD simulation of the A/T state kinked model that converges much quicker to the A-site ensemble of structures (2 ns). (c) “Line c” represents the free molecular dynamics simulation for the A-site crystal structure model, which moves from the starting structure to an average ensemble around 4 Å RMSD from the original as it relaxes under MD.
