By Garrett A. Soukup

This targeted quantity of Progress in Molecular Biology and Translational Science specializes in catalytic RNA. Written via specialists within the box, the experiences disguise more than a few issues, from hammerhead ribozymes to spliceosome catalysis to Varkud satellite tv for pc and hairpin ribozymes.

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Extra info for Catalytic RNA, Volume 120

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With hydrogen atoms built and the Mg2þ cation position established, the ribozyme was immersed in a rhombic dodecahedral cell of 10,062 preequilibrated TIP3P water molecules centered about the active site, and pruned ˚ from the solute was removed. 14 M. 7 A˚ away from any solute atoms. The resulting system (the reactant state) contained 9053 water molecules, 82 Naþ and 23 ClÀ ions, and 2021 RNA atoms. 0 kcal/mol-ps2, respectively. 35 A B-spline interpolation order of six. Nonbonded interactions were treated using an atom-based cutoff of 10 A˚ with shifted van der Waals potential.

And ETS-C) and in the reactant state simulation where the nucleophilic O20 has been deprotonated (dRT-C). However, in the parent reactant state system (RT-C), where C17:O20 is protonated, the divalent metal ion stays in the C-site in the course of the 12 ns MD simulation. 5 A (data not shown). 1 and A9 phosphate oxygens fluctuates between axial–axial and axial–equatorial modes, resulting in a shorter 40 Tai-Sung Lee et al. 2). 5 A˚. 3). In the deprotonated reactant state simulation (dRT-C), Mg2þ migrates from the C-site to the bridging B-site position after about 2 ns while maintaining coordination in the axial–equatorial mode.

05 (26) ˚ and degrees, respectively. Standard deviations (SDs) are listed in Analysis was performed over the last 250 ns (10 ps sampling frequency). 01). 1:O2P; all others are distance between the Mg2þ and the indicated ligand site. Hammerhead Ribozyme Catalysis 57 coordination pattern is not highly conducive to formation of an in-line attack conformation. On the other hand, the RT-B-Mg simulation shows a more rigid Mg2þ coordination with both the A9 and scissile phosphate oxygens and sustains a considerable population of in-line attack conformations.

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