title: Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.
abstract: Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Vlad
authors.initials: V
authors.lastname: Cojocaru
authors.forename: Reinhard
authors.initials: R
authors.lastname: Klement
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Jovin
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020029:Base Pairing; D003198:Computer Simulation; D006147:Guanine / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012342:RNA, Small Nuclear / Q000737:chemistry* / Q000378:metabolism; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry / Q000378:metabolism
chemical_list: D012342:RNA, Small Nuclear; D017411:Ribonucleoproteins, Small Nuclear; C405482:U4 small nuclear RNA; D006147:Guanine; D000225:Adenine