Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets

Abstract

Explicit solvent molecular dynamics (MD) simulations were carried out for three RNA kissing-loop complexes. The theoretical structure of two base pairs (2 bp) complex of H3 stem-loop of Moloney murine leukemia virus agrees with the NMR structure with modest violations of few NMR restraints comparable to violations present in the NMR structure. In contrast to the NMR structure, however, MD shows relaxed intermolecular G-C base pairs. The core region of the kissing complex forms a cation-binding pocket with highly negative electrostatic potential. The pocket shows nanosecond-scale breathing motions coupled with oscillations of the whole molecule. Additional simulations were carried out for 6 bp kissing complexes of the DIS HIV-1 subtypes A and B. The simulated structures agree well with the X-ray data. The subtype B forms a novel four-base stack of bulged-out adenines. Both 6 bp kissing complexes have extended cation-binding pockets in their central parts. While the pocket of subtype A interacts with two hexacoordinated Mg2+ ions and one sodium ion, pocket of subtype B is filled with a string of three delocalized Na+ ions with residency times of individual cations 1-2 ns. The 6 bp complexes show breathing motions of the cation-binding pockets and loop major grooves.

The effect of topology on the structure and free energy landscape of DNA kissing complexes

“…13 and 14, the original parameterization appears to be physically reasonable. Moreover, that the detailed pattern of base pairing is consistent with known structures for RNA kissing complexes [22][23][24] further corroborates this conclusion.…”

“…21 They have, therefore, been much better characterized for RNA, both in terms of their structure [22][23][24] and mechanical properties, 25,26 than for DNA. This structural knowledge has even been exploited in structural RNA nanotechnology, where kissing loop interactions have also been used as a means to join RNA components with a well-defined geometry.…”

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

“…The stabilizing role of magnesium ions in natural or artificial kissing complexes has been characterized (Eguchi and Tomizawa 1991;Gregorian and Crothers 1995;Ducongé et al 2000). One magnesium ion would bind at the center of a pocket made by the two phosphate clusters at the stem-loop junctions (Chang and Tinoco 1997;Lee and Crothers 1998;Jossinet et al 1999;Reblova et al 2003). In theory, the high concentration of RNA used for the NMR experiments (1.2-1.4 mM) should have compensated for the absence of magnesium, since the stability of bimolecular nucleic acid-nucleic acid complexes depends on the total concentration (Puglisi and Tinoco 1989).…”

Trapped water molecules are essential to structural dynamics and function of a ribozyme

“…The initial structures were solvated in a rectangular periodic box of TIP3P waters extending Ն10 Å from the RNA. The Sander module of AMBER 6.0 was used for the equilibration and production simulations based on standard protocols (5,8,10,(23)(24)(25). The particle mesh Ewald method (44) was applied with a heuristic pair list update, using a 2.0-Å non-bonded pair list buffer and a 9.0-Å cutoff.…”

“…(Table 1; with and without six crystallographically placed Mg 2ϩ ions) on a truncated form of the 2.4-Å resolution precatalytic hairpin ribozyme crystal structure (Fig. 1a), using our well established protocols (5,8,(23)(24)(25). We separately introduced two singlefunctional group modifications, 2Ј-deoxy-A38 (dA38) and 2Ј-deoxy-G11 (dG11), and two single-nucleotide mutations, Gϩ1A and U42C, to closely mimic the variants used in our smFRET experiments that show the most significant acceleration of undocking (16,17) (Fig.…”