Book of Abstracts: Albany 2011
June 14-18 2011
©Adenine Press (2010)
Intrinsically Flexible Ribosomal RNA Segments. Family C 3-Way Junctions and their Possible Role in the Translation
We carried out extensive explicit solvent molecular dynamics analysis (1.4 µs) of several RNA three-way junctions (3WJs) from the large ribosomal subunit. The aim was to analyze the intrinsic flexibility of the 3WJs and to consider them in the ribosomal context in available ribosomal crystal structures. The flexibility of the RNA is inferred from stochastic thermal fluctuations sampled in unrestrained simulations. The simulations identify the intrinsic low-energy deformation modes of the molecules that can co-operate with the surrounding ribosomal elements to achieve the functional dynamics.
All studied 3WJs possess significant anisotropic hinge-like flexibility between their stacked stems and dynamics within the compact regions of their adjacent stems. The most interesting is the GAC (GTPase associated center) 3WJ which may support large-scale dynamics of the L7/L12-stalk rRNA, i.e. rRNA Helices (H) 42-44 (1). Projection of the observed anisotropic movement into the ribosome shows that H43/H44 rRNA is flexible in direction towards and away (closing-opening geometry path of the GAC 3WJ) of the large ribosomal subunit, see the Figure. When the H42-H44 domain is in the overall "closed” conformation, the tip of the hairpin loop of H89 can fit into the groove defined by the docking of the hairpin loops of H43/44. However, such contact is only seen in the 2AW4 crystal structure of vacant E.coli ribosome (2). In other crystal structures the distance between the H89 and GAC RNA varies widely (it even exceeds in some cases 10 Å) (3, 4). The experimental structures show a wide range of positions sampling a set of more inward and more outward structures with respect to the A-site of the large subunit and H89. The range of observed positions agrees with the anisotropic flexibility direction predicted by MD. We conclude that the X-ray observed flexibility of the GAC RNA originates from the 3WJ and includes also the H42 stem region below the 3WJ and above the conserved H42-H97 tertiary interaction. The GAC rRNA could undergo large-scale rapid thermal fluctuations or structural adaptations to facilitate gliding of the tRNA to H89, which leads it into its functional destinations (A/A state) (5), see the Figure. The H42-44 rRNA region is not fully relaxed in the ribosome. It is deformed towards the body of the large subunit by some of the surrounding elements. The simulations suggest that the L10 protein can regulate or contribute to this deformation. The intrinsic flexibility of the GAC 3WJ will be briefly compared with intrinsic flexibility of RNA from other flexible parts of the large subunit, namely the elbow region at the base of the A-site finger and the bottom part of the L1 stalk.
1Institute of Biophysics
Figure: Left - Large ribosomal subunit (RNA in tan, proteins in cyan, pdb code 2WRO2) from Thermus termophilus including tRNA in the A/T state (in red, 2WRN2). The GAC 3WJ in the X-ray data is in purple, open and closed geometries of the junction occurring in the MD simulations are shown in green and blue, respectively. Right - Detailed view on coordinated hypothetical movement of the tRNA and GAC 3WJ. The closed MD geometry of the GAC 3WJ forms contact with H89 (marked by ellipse), which might be important for guiding the tRNA to H89 (in yellow).