title: Effect of mutations on internal dynamics of an RNA hairpin from hepatitis B virus.
abstract: Conformational dynamics plays a key role in mediating specific interactions between RNAs and proteins. Flexible parts, such as the loop regions, are often involved in protein binding. Characterization of the factors that influence the flexibility of loop regions will improve our understanding of RNA-protein binding. Here we use molecular dynamics simulations to study the dynamical features of the apical stem-loop of hepatitis B virus and a mutant, with two consensus-based secondary structure mutations (A-U→C-G) in the stem region. The mutations reduce the dynamics of the system and influence the hairpin conformations. The simulations show that inducing rigidity in the stem affects the loop conformational flexibility: the loop residues become less mobile and less accessible to the solvent, and thus less accessible to a possible targeting protein.
authors: Department of Biosciences and Nutrition, Karolinska Institute, SE-141 83 Huddinge, Sweden.
authors: Alok
authors: A
authors: Juneja
authors: Department of Biosciences and Nutrition, Karolinska Institute, SE-141 83 Huddinge, Sweden.
authors: Lennart
authors: L
authors: Nilsson
authors: Department of Biosciences and Nutrition, Karolinska Institute, SE-141 83 Huddinge, Sweden. Electronic address: alessandra.villa@ki.se.
authors: Alessandra
authors: A
authors: Villa
mesh_terms: D006515:Hepatitis B virus / Q000235:genetics*; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism
chemical_list: D012367:RNA, Viral; D016601:RNA-Binding Proteins
keywords: Apical stem loop; Hepatitis B virus; Loop flexibility; Molecular dynamics simulation; Order parameter; RNA