Book of Abstracts: Albany 2007
June 19-23 2007
Ribosomal RNA Motifs and Segments have Salient Fexibilities
MD simulation technique captures qualitative differences in intrinsic flexibilities of rRNA building blocks possessing contrasting intrinsic flexibility signatures. The basic intrinsic physico-chemical properties of the RNA motifs can in many cases be maintained in the RNA assemblies and contribute to function and sequence constraints. Kink-turns show profound elbow-like intrinsic flexibility, without disruption of any single structural feature characteristic of a folded K-turn. The K-turn oscillatory dynamics is typically pivoting at the A-minor interaction mediating the contact between the C- and NC-stems, is associated with a dynamical water insertion and the motion is anharmonic. Such structural elements are well suited to passively mediate large-scale motions. The Sarcin-Ricin loop is very stiff in simulations and also the Loop E is rigid. Helix 44 from the small subunit is an isotropic flexible element with modest sequence-dependence of elasticity along the helix and a possible structural switch at its base. Consecutive RNA building blocks can further create architectures with complex patterns of preferred low-energy motions, as in 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 Kt-42. The second one (Hinge2) is localized at the junction between Helix 42 and Helices 43/44, which is a family C type three way junction. The rigid segments are the two arms of Helix 42 flanking the Kink. The whole molecule ends up with compact Helices 43/44 (Head) subtly compressed towards the subunit in the H.m. x-ray structure. Overall, the He42-44 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. The dynamics is not captured by the Elastic Network Mode NMA method. Variation of the length of stems of He42 would considerably change the direction of Kt-42+rGAC anisotropic flexibility. He42 length is entirely conserved and when mitochondria and chloroplasts are considered, He42 is among the ~30% of the entirely length-conserved ribosomal helices.
References and Footnotes
1Institute of Biophysics