title: Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA.
abstract: The interactions in the tertiary structure of a ribosomal RNA fragment in the GTPase Associating Center (GAC) 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 GAC 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 GAC 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 GAC 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.
authors.affiliation: a Department of Medicinal Chemistry , College of Pharmacy, The University of Utah , 2000 East 30 South Skaggs 307, Salt Lake City , Utah 84112-5820 , USA.
authors.forename: Hamed S
authors.initials: HS
authors.lastname: Hayatshahi
authors.affiliation: a Department of Medicinal Chemistry , College of Pharmacy, The University of Utah , 2000 East 30 South Skaggs 307, Salt Lake City , Utah 84112-5820 , USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Bergonzo
authors.affiliation: a Department of Medicinal Chemistry , College of Pharmacy, The University of Utah , 2000 East 30 South Skaggs 307, Salt Lake City , Utah 84112-5820 , USA.
authors.forename: Thomas E
authors.identifier: 0000-0003-0298-3904
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D002412:Cations / Q000737:chemistry* / Q000378:metabolism; D020558:GTP Phosphohydrolases / Q000737:chemistry* / Q000378:metabolism; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000378:metabolism
chemical_list: D002412:Cations; D012335:RNA, Ribosomal; D020558:GTP Phosphohydrolases; D008274:Magnesium
keywords: AmberZ; GTPase-Associating Center; chelated magnesium; molecular dynamics; umbrella sampling; unfolding pathway