We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500？ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16. 1. Introduction tRNA is a key component for protein synthesis in the cell. tRNA delivers amino acids to the ribosome, where they are incorporated to the growing nascent polypeptide chains. The characteristic L-shaped tertiary structure of tRNA is intimately related to its function, and it has intrigued investigators for decades [1, 2]. With the first high-resolution crystal structure for tRNA [1, 2], it was suggested that the molecule may possess a flexible hinge between the D-stem and the anticodon stem (Figure 1). Figure S6 (see Figure in Supplementary Material available online at doi: 10.1155/2011/219515) shows a diagrammed version of tRNA for illustration. The interarm consists of the hinge formed between the acceptor stem and the anticodon stem (Supplementary Figure S6). Figure 1(a) schematic shows a two-dimensional layout for the RNA nucleotides that account for the acceptor stem, anticodon stem, D-stem, and T-stem. Early light scattering experiments were interpreted in terms of bending motions between the two arms of the L-shaped tRNA that were thought to facilitate functional flexibility [3]. tRNA binds to aminoacyl tRNA synthetases, elongation factors, as well as different sites on the ribosome. Figure 1: tRNA
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