Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.

ABSTRACT: Accurate modeling of the structural dynamics of ribonucleic acid (RNA) molecules, including common stem-loop motifs, remains challenging. This study presents de novo folding simulations of a diverse set of 26 RNA stem-loops, ranging from 10 to 36 residues, with and without bulges or internal loops, starting from their extended conformations. These simulations employed conventional molecular dynamics using an atomistic force field extensively refined by the Shaw group (TanD., Proc. Natl. Acad. Sci. U.S.A.2018, 115, E1346-E1355, 10.1073/pnas.1713027115) and an implicit solvent model developed by the Simmerling group (NguyenH., J. Chem. Theory Comput.2015, 11, 3714-3728, 10.1021/acs.jctc.5b00271). The 18 stem-loops without bulges or internal loops were folded into their respective stru

SUBMITTER: Ando T 

PROVIDER: S-EPMC12593105 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature