A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis
| Authors | |
|---|---|
| Year of publication | 2011 |
| Type | Article in Periodical |
| Magazine / Source | JOURNAL OF PHYSICAL CHEMISTRY B |
| MU Faculty or unit | |
| Citation | |
| Doi | http://dx.doi.org/10.1021/jp2065584 |
| Field | Physical chemistry and theoretical chemistry |
| Keywords | EDGE BASE-PAIRS; BOX C/D RNA; NUCLEIC-ACIDS; INTERACTION POTENTIALS; ISOSTERICITY MATRICES; STRUCTURAL DYNAMICS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASIS-SETS; SIMULATIONS |
| Description | The RNA kink-turn is an important recurrent RNA motif; an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A center dot G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G=C receptor base pair during evolution while the inverted pair (C=G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G=C and C=G base pairs in sequences. We carried out an extended set (similar to 5 mu s) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with similar to 0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G=C and A-I/C=G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns. |
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