Ivana Beššeová

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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(More)
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90-92 (H90-H92) of 23S rRNA; the 3WJ formed by H42-H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the(More)
We present an extensive molecular dynamics study (0.6 micros in total) on three A-RNA duplexes. The dependence of the A-RNA geometry on force fields (Parm99 and Parmbsc0) and salt strength conditions (approximately 0.18 M net-neutralizing Na(+) and approximately 0.3 M KCl) was investigated. The Parmbsc0 force field makes the A-RNA duplex more compact in(More)
To address fundamental questions in bioinorganic chemistry, such as metal ion selectivity, accurate computational protocols for both the gas-phase association of metal-ligand complexes and solvation/desolvation energies of the species involved are needed. In this work, we attempt to critically evaluate the performance of the ab initio and DFT electronic(More)
C-loop is an internal loop motif found in the ribosome and used in artificial nanostructures. While its geometry has been partially characterized, its mechanical properties remain elusive. Here we propose a method to evaluate global shape and stiffness of an internal loop. The loop is flanked by short A-RNA helices modeled as rigid bodies. Their relative(More)
Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair(More)
We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 μs of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0χ(OL3), while several other RNA force fields have been tested. The(More)
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