Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment

• DOI: 10.1021/acs.jcim.4c00756
• Publication Date: 2024-07-13T17:52:03Z
• Authors: Jason T. Linzer; Ethan Aminov; Aalim S. Abdullah; Colleen E. Kirkup; Rebeca I. Diaz Ve...; Vinay R. Bijoor; Jiyun Jung; Sophie Huang; Chi Gee Tse; Emily Álvarez Toucet; Hugo P. Onghai; Arghya P. Ghosh; Alex C. Grodzki; Emilee R. Haines; Aditya S. Iyer; Mark K. Khalil; Alexander P. Leong; Michael A. Neuhaus; Joseph Park; Asir Shahid; Matthew Xie; Jan M. Ziembicki; Carlos Simmerling; Maria C. Nagan
• Keywords: 0301 basic medicine; 0303 health sciences; Solvents; RNA; Nucleic Acid Conformation; Molecular Dynamics Simulation

Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one the more common motifs. Here, we present systematic analysis 15 RNA stem-loop sequences simulated molecular dynamics simulations an implicit solvent environment. Analysis cluster ensembles showed that generally A-form stem region. Loop are sensitive, experimental could only be reproduced modification CH···O interactions force field, combined nonpolar correction to better model base stacking interactions. Accurately modeling current atomistic physics-based models remains challenging, but systems studied herein may provide useful benchmark set for testing other methods future.