title: Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.
abstract: The family of adenosine deaminases acting on RNA (ADARs) targets adenosines in RNA that is mainly double stranded. Some substrates are promiscuously deaminated whereas others, such as the mammalian glutamate receptor B (gluR-B) pre-mRNA, are more selectively deaminated. Many DNA/RNA-base modification enzymes use a base flipping mechanism to be able to reach their target base and it is believed that ADARs function in a similar way. In this study we used molecular dynamics (MD) simulations to describe two sites on the gluR-B pre-mRNA, the selectively targeted R/G site and the nontargeted 46 site, in an attempt to explain the substrate specificity. We used regular MD and also a forced base flipping method with umbrella sampling to calculate the free energy of base opening. Spontaneous opening of the mismatched adenosine was observed for the R/G site but not for the 46 site.
authors.affiliation: Department of Biosciences at NOVUM, Center for Structural Biochemistry, Karolinska Institutet, SE-141 57 Huddinge, Sweden.
authors.forename: Katarina
authors.initials: K
authors.lastname: Hart
authors.forename: Boel
authors.initials: B
authors.lastname: Nyström
authors.forename: Marie
authors.initials: M
authors.lastname: Ohman
authors.forename: Lennart
authors.initials: L
authors.lastname: Nilsson
mesh_terms: D000241:Adenosine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000243:Adenosine Deaminase / Q000378:metabolism; D020137:Base Pair Mismatch / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D021122:Protein Subunits / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017470:Receptors, Glutamate / Q000235:genetics; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D021122:Protein Subunits; D012322:RNA Precursors; D012330:RNA, Double-Stranded; D017470:Receptors, Glutamate; D000243:Adenosine Deaminase; D000241:Adenosine