1National Center for Biomolecular Research, Kotlářská 2, 611 37 Brno, Czech Republic.
2Institute of Biophysics, Academy of Sciences of the Czech Republic and National Center for Biomolecular Research, Královopolská 135, 612 65, Brno, Czech Republic.
3Chemistry Department and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, OH 43403
Ribosomal 5S RNA (5S rRNA) is an integral component of the large ribosomal subunit in all known organisms with the exception of the small ribosomes of fungal and animal mitochondria. The 5S rRNA of Escherichia coli (E. coli) interacts with ribosomal proteins L5, L18 and L25 and enhances protein synthesis by stabilization of the ribosome structure but its exact role in protein synthesis is still not known. 5S rRNA contains internal loop - Loop E. The Loop E is a salient example of a uniquely structured non-Watson-Crick motif, as it contains seven consecutive non-Watson-Crick base pairs, including wobble G.U base pair and substantial cross-strand purine stacking. This unique duplex architecture together with adjacent sequence helix IV form binding site for ribosomal protein L25.
To understand the structure and function of internal Loop E and interaction between 5S rRNA Loop E and ribosomal protein L25, we have carried out set of molecular dynamics simulations.
Initial structures were directly taken from x-ray crystallography - crystal structure of 5S rRNA Loop E (E. coli)  and crystal structure of ribosomal protein L25 complexed with the 5S rRNA fragment . Another studied structure was chloroplast Loop E for which there is no atomic resolution structure yet available and which is sufficiently different from bacterial Loop E motifs in sequence, but evolutionarily related to it. Model of chloroplast Loop E was proposed based on homology modeling , initial structure for this model was bacterial Loop E, mutation of three base pairs was performed based on the isosteric mutation.
Main focus of our investigation was to study of the structure, dynamics, hydration and cation binding of non-Watson-Crick base pairs and interaction between ribosomal protein L25 and 5S rRNA Loop E. Another aim of this study was to test the usefulness of the MD technique in evaluating the dynamics and energetics of molecular models of RNA motifs constructed by phylogenetic analysis and isostericity principles.
 C. C. Correll, B. Freeborn & P. B. Moore T. A. Steitz. Cell, 91 (1997) 705-712.
 M. Lu & T. A. Steitz. Proc. Natl. Acad. Sci. U S A, 97 (2000) 2023-2028.
 N. B. Leontis & E. Westhof. RNA, 4 (1998) 1134-1153.