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Nucleic Acids Research Advance Access originally published online on June 6, 2007
Nucleic Acids Research 2007 35(12):4007-4017; doi:10.1093/nar/gkm245
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Nucleic Acids Research, 2007, Vol. 35, No. 12 4007-4017
© 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.

RNA

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

Filip Rázga1, Jaroslav Koca2, Ali Mokdad3 and Jirí Sponer1,*

1Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, 2National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic and 3Department of Biochemistry and Biophysics, School of Medicine, University of California at San Francisco, San Francisco, CA 94158, USA

*To whom correspondence should be addressed. Tel: (420) 5415 17133; Fax: (420) 5412 12179; Email: sponer{at}ncbr.chemi.muni.cz

Received November 27, 2006. Revised February 28, 2007. Accepted April 3, 2007.

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.


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