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Full-Text Articles in Chemistry
Molecular Dynamics Simulations Suggest That Rna Three-Way Junctions Can Act As Flexible Rna Structural Elements In The Ribosome, Neocles B. Leontis, Ivana Beššová, Kamila Réblová, Jiří Šponer
Molecular Dynamics Simulations Suggest That Rna Three-Way Junctions Can Act As Flexible Rna Structural Elements In The Ribosome, Neocles B. Leontis, Ivana Beššová, Kamila Réblová, Jiří Šponer
Chemistry Faculty Publications
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90-92 (H90-H92) of 23S rRNA; the 3WJ formed by H42-H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3'-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess …