Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

Abstract

Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segment (Hinge1) is the highly anharmonic kink of Kt-42. The second one (Hinge2) is localized at the junction between helix 42 and helices 43/44. The rigid segments are the two arms of helix 42 flanking the kink. The whole molecule ends up with compact helices 43/44 (Head) which appear to be modestly compressed towards the subunit in the Haloarcula marismortui X-ray structure. Overall, the helix 42-44 rRNA is constructed as a sophisticated intrinsically flexible anisotropic molecular limb. The leading flexibility modes include bending at the hinges and twisting. The Head shows visible internal conformational plasticity, stemming from an intricate set of base pairing patterns including dynamical triads and tetrads. In summary, we demonstrate how rRNA building blocks with contrasting intrinsic flexibilities can form larger architectures with highly specific patterns of preferred low-energy motions and geometries.

Figure 1.

Kt-42+rGAC rRNA system. (A) Base pairing in the simulated Kt-42+rGAC system (helices 42–44 from the 23S rRNA of H. marismortui) using standard nomenclature (54). The two flexible regions are marked as rectangles and the individual helices are marked as H42, H43 and H44. Strand connectivity is not highlighted to keep the figure readable. (B) Secondary structure of the Kt-42+rGAC. (C) Schematic representation of the Kt-42+rGAC showing its modularity with five consecutive segments (C-stem, Hinge1, NC-stem, Hinge2 and Head) with very distinct intrinsic mechanical properties and dynamics (see the text). Two flexible Hinges (circles) link three rigid segments (C-stem, NC-stem and Head). Arrows indicate the direction of preferred motions at both Hinges.

Figure 2.

Essential dynamics of Kt-42+rGAC rRNA system. Schematic (left) and surface (right) representations of the leading essential dynamics motions, double arrows indicate oscillations. (A) The initial displacement of the Head stemming from the rearrangement of Hinge2 (purple) observed during the first 5 ns of simulation and causing the permanent increase of the inter-helical angle by ca 25° (initial geometry in black, final in red). (B) Anisotropic anharmonic oscillation of rGAC pivoting at Kt-42 (Hinge1) (purple, EDA mode 1). (C) Internal breathing of rGAC (EDA mode 2) not contributing to the overall motion of rGAC and involving mainly the dynamics of non-canonical base pairs (see Supplementary Data). (D) Fluctuations of rGAC around Hinge2 (purple, EDA mode 3) characterized as anisotropic oscillatory bending of the duplex containing the upper part of helix 42 and helix 43. (E) Twisting of rGAC (EDA mode 4) stemming from twisting inherent to Kt-42 (35) and twisting in the Hinge2 region.

Figure 3.

Base tetrad A1207/G1160 … G1190/C1186 at the helix 42/rGAC junction. The overall X-ray geometry (A), the trans H/SE A1207/G1160 base pair with dynamical water insertion (B left), the trans WC/WC G1190/C1186 base pair assisted either by water or ion (B right) and the unusual G1190/G1160 base pair (X-ray structure, C left). A similar A1192/C1182 contact is shown (C right). Extended analysis of base pairing dynamics is given in Supplementary Data.