Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective.
Classical force field (FF) molecular dynamics (MD) simulations of RNA tetranucleotides have substantial problems in reproducing conformer populations indicated by NMR experiments. To provide more information about the possible sources of errors, we performed quantum mechanical (QM, TPSS-D3/def2-TZVP) and molecular mechanics (MM, AMBER parm99bsc0+χOL3) calculations of different r(CCCC), r(GACC), and r(UUUU) conformers obtained from explicit solvent MD simulations. Solvent effects in the static QM and MM calculations were mimicked using implicit solvent models (COSMO and Poisson-Boltzmann, respectively). The comparison of QM and MM geometries and energies revealed that the two methodologies provide qualitatively consistent results in most of the cases. Even though we found some differences, these were insufficient to indicate any systematic corrections of the RNA FF terms that could improve the performance of classical MD in simulating tetranucleotides. On the basis of these findings, we inferred that the overpopulation of intercalated conformers in the MD simulations of RNA tetramers, which were not observed experimentally, might be predominantly caused by imbalanced water-solvent and water-water interactions. Apart from the large-scale QM calculations performed to assess the performance of the AMBER FF, a representative spectrum of faster QM methods was tested.
Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, CZ-61265 Brno, Czech Republic.
Rafał
R
Szabla
Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, CZ-61265 Brno, Czech Republic.|CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic.
Marek
M
Havrila
Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, CZ-61265 Brno, Czech Republic.
Holger
H
Kruse
Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, CZ-61265 Brno, Czech Republic.|CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic.
Jiří
J
Šponer