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. 2007 Jun 6;35(12):4007–4017. doi: 10.1093/nar/gkm245

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© 2007 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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.