. . "Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt a distinctive structure inconsistent with secondary structure predictions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (dWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 mu s of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis." . "An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods" . . . "RIV/00216224:14310/10:00043541!RIV11-MSM-14310___" . "R\u00E9blov\u00E1, Kamila" . "Van Nostrand, Keith" . . . . . "P(1QS500040581), P(IAA400040802), P(KJB400040901), P(LC06030), Z(AV0Z50040507), Z(AV0Z50040702), Z(MSM0021622413)" . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . . . "Turner, Douglas H." . . . . "An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods"@en . . "RIV/00216224:14310/10:00043541" . . . "9"^^ . "\u0160poner, Ji\u0159\u00ED" . "19"^^ . . "Yildirim, Ilyas" . . "14310" . "1549-9618" . "An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods"@en . "246279" . . "5"^^ . "St\u0159elcov\u00E1, Zora" . "6" . "An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods" . . . . "Journal of Chemical Theory and Computation" . "Be\u0161\u0161eov\u00E1, Ivana" . "Mathews, David H." . . "2010" . . "Kulh\u00E1nek, Petr" . . "molecular dynamics; free energy; RNA"@en . "[7DA6AF8879D8]" . . "Functional RNA molecules such as ribosomal RNAs (rRNAs) frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt a distinctive structure inconsistent with secondary structure predictions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (dWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 mu s of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by molecular mechanics, Poisson-Boltzmann, and surface area free energy calculations; locally enhanced sampling (LES) runs; targeted MD (TMD); and nudged elastic band (NEB) analysis."@en .