Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA

<p>The interactions in the tertiary structure of a ribosomal RNA fragment in the GTPase Associating Center (<i>GAC</i>) have been experimentally studied, but the roles of the bound and diffuse cations in its folding pathway have not yet been fully elucidated. Melting experiments have shown that the temperature of the first of the two distinguishable transitions in the unfolding pathway of the <i>GAC</i> RNA can be regulated by altering the magnesium concentration, yet the physical interpretation of such ion-dependent effects on folding have not been clearly understood in spite of the availability of crystal structures that depict many <i>GAC</i> RNA–ion interactions. Here, we use umbrella sampling and molecular dynamics (MD) simulations to provide a physical description for the first transition in this unfolding pathway, with a focus on the role of a chelated magnesium ion. Our results indicate that the presence of cations mediating the local interaction of two loops stabilizes the folded state relative to the unfolded or partially folded states. Also, our findings suggest that a bridging magnesium ion between the two loops improves the stabilizing effect. This is consistent with the multistep unfolding pathway proposed for the <i>GAC</i> RNA and highlights the importance of ions in the first unfolding step. The results suggest how MD simulations can provide insight into RNA unfolding pathways as a complementary approach to experiments.</p

Structural and Energetic Analysis of 2‑Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations

Despite the many biological functions of RNA, very few drugs have been designed or found to target RNA. Here we report the results of molecular dynamics (MD) simulations and binding energy analyses on hepatitis C virus internal ribosome entry site (IRES) RNA in complex with highly charged 2-aminobenzimidazole inhibitors. Initial coordinates were taken from NMR and crystallography studies that had yielded different binding modes. During MD simulations, the RNA–inhibitor complex is stable in the crystal conformation but not in the NMR conformation. Additionally, we found that existing and standard MD trajectory postprocessing free energy methods, such as the MM-GBSA and MM-PBSA approaches available in AMBER, seem unsuitable to properly rank the binding energies of complexes between highly charged molecules. A better correlation with the experimental data was found using a rather simple binding enthalpy calculation based on the explicitly solvated potential energies. In anticipation of further growth in the use of small molecules to target RNA, we include results addressing the impact of charge assignment on docking, the structural role of magnesium in the IRES–inhibitor complex, the entropic contribution to binding energy, and simulations of a plausible scaffold design for new inhibitors

Structural and Energetic Analysis of 2‑Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations

Despite the many biological functions of RNA, very few drugs have been designed or found to target RNA. Here we report the results of molecular dynamics (MD) simulations and binding energy analyses on hepatitis C virus internal ribosome entry site (IRES) RNA in complex with highly charged 2-aminobenzimidazole inhibitors. Initial coordinates were taken from NMR and crystallography studies that had yielded different binding modes. During MD simulations, the RNA–inhibitor complex is stable in the crystal conformation but not in the NMR conformation. Additionally, we found that existing and standard MD trajectory postprocessing free energy methods, such as the MM-GBSA and MM-PBSA approaches available in AMBER, seem unsuitable to properly rank the binding energies of complexes between highly charged molecules. A better correlation with the experimental data was found using a rather simple binding enthalpy calculation based on the explicitly solvated potential energies. In anticipation of further growth in the use of small molecules to target RNA, we include results addressing the impact of charge assignment on docking, the structural role of magnesium in the IRES–inhibitor complex, the entropic contribution to binding energy, and simulations of a plausible scaffold design for new inhibitors