Informace o publikaci

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective

Autoři

SZABLA Rafal HAVRILA Marek KRUSE Holger ŠPONER Jiří

Rok publikování 2016
Druh Článek v odborném periodiku
Časopis / Zdroj Journal of Physical Chemistry B
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b07551
Doi http://dx.doi.org/10.1021/acs.jpcb.6b07551
Obor Fyzikální chemie a teoretická chemie
Klíčová slova MOLECULAR-DYNAMICS SIMULATIONS; QUANTUM-CHEMICAL COMPUTATIONS; AUXILIARY BASIS-SETS; PARTICLE MESH EWALD; DIRECT-COSMO-RS; B-DNA STRUCTURE; PHOSPHATE BACKBONE; EXPLICIT-SOLVENT; NUCLEIC-ACIDS; FREE-ENERGIES
Popis 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+X-OL3) 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.
Související projekty:

Používáte starou verzi internetového prohlížeče. Doporučujeme aktualizovat Váš prohlížeč na nejnovější verzi.

Další info