Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.

ABSTRACT: The determination of the three-dimensional structure of large RNA macromolecules in solution is a challenging task that often requires the use of several experimental and computational techniques. Small-angle X-ray scattering can provide insight into some geometrical properties of the probed molecule, but this data must be properly interpreted in order to generate a three-dimensional model. Here, we propose a multiscale pipeline which introduces SAXS data into modelling the global shape of RNA in solution, which can be hierarchically refined until reaching atomistic precision in explicit solvent. The low-resolution helix model (Ernwin) deals with the exploration of the huge conformational space making use of the SAXS data, while a nucleotide-level model (SPQR) removes clashes and disentang

SUBMITTER: Thiel BC 

PROVIDER: S-EPMC11381333 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature