Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

ABSTRACT: The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exch

SUBMITTER: Kuhrova P 

PROVIDER: S-EPMC6169534 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature