Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.

ABSTRACT: The growing recognition of the functional and therapeutic roles played by RNA and the difficulties in gaining atomic-level insights by experiments are paving the way for all-atom simulations of RNA. One of the main impediments to the use of all-atom simulations is the imbalance between the energy terms of the RNA force fields. Through exhaustive sampling of an RNA helix-junction-helix (HJH) model using enhanced sampling, we critically assessed the select Amber force fields against small-angle X-ray scattering (SAXS) experiments. The tested AMBER99SB, DES-AMBER, and CUFIX force fields show deviations from measured profiles. First, we identified parameters leading to inconsistencies. Then, as a way to balance the forces governing RNA folding, we adopted strategies to refine hydrogen bonding,

SUBMITTER: He W 

PROVIDER: S-EPMC9036580 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature