An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.
ABSTRACT Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. 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 (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na(+) vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational transition towards the solution 2D structure. Free energy calculations confirm that the X-ray arrangement is less stable than the solution structure. LES, TMD and NEB provide a rather consistent pathway for interconversion between the X-ray and NMR structures. In simulations, the incomplete cWS A/U base pair of the NMR structure is water mediated and alternates with the canonical A-U base pair, which is not indicated by the NMR data. Completion of full cWS A/U base pair is prevented by the overall internal loop arrangement. In summary, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.
Article: Full-thickness macular hole in a patient with diabetic cystoid macular oedema treated by intravitreal triamcinolone injections.[show abstract] [hide abstract]
ABSTRACT: Full-thickness macular hole associated with diabetic macular oedema is a rare feature and its pathogenesis remains incompletely elucidated. We report the occurrence of a full-thickness macular hole, documented with optical coherence tomography (OCT), in a patient with diabetic cystoid macular oedema treated by intravitreal triamcinolone injections. A 48-year-old woman with refractory diabetic cystoid macular oedema underwent successive intravitreal triamcinolone injections, which were followed by a progressive thinning of the neurosensory retina at the fovea, and then by a full-thickness macular hole, associated with a perifoveal posterior hyaloid detachment, visible on OCT. During pars plana vitrectomy, a thin epiretinal macular membrane was diagnosed and removed. Pathogenesis of the present full-thickness macular hole associated with diabetic macular oedema is different from that of idiopathic macular holes because anteroposterior vitreous tractions were not involved in its formation. Recurrent intravitreal triamcinolone injections may have had an indirect role in the development of the macular hole, by favouring the rupture of distended Muller cells and intraretinal pseudocysts.Acta Ophthalmologica Scandinavica 12/2007; 85(7):795-8. · 1.85 Impact Factor