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Nucleic Acids Research 2006 34(2):697-708; doi:10.1093/nar/gkj470
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Published online 2 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Molecular dynamics simulations of sarcin–ricin rRNA motif

Nad'a Spacková1,* and Jirí Sponer1,2

1Institute of Biophysics, Academy of Sciences of the Czech Republic Královopolská 135, 612 65 Brno, Czech Republic 2Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic Flemingovo námestí 2, 166 10 Prague 6, Czech Republic

*To whom correspondence should be addressed. Tel: +420 541 517 109; Fax: +420 541 212 179; Email: spackova{at}ncbr.chemi.muni.cz

Received August 24, 2005. Revised January 10, 2006. Accepted January 10, 2006.

Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin–ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 1–1.4 Å. Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair. The deformed flexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson–Crick base pairs are rigid and mediated by long-residency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.


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