Download Catalytic RNA, Volume 120 by Garrett A. Soukup PDF

By Garrett A. Soukup

This specified quantity of Progress in Molecular Biology and Translational Science makes a speciality of catalytic RNA. Written through specialists within the box, the studies conceal a number themes, from hammerhead ribozymes to spliceosome catalysis to Varkud satellite tv for pc and hairpin ribozymes.

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Example text

The RT-B-Mg (Mg2þ at the B-site) simulation, on the other hand, is dramatically different. 00). Cluster A, containing a high degree of in-line near attack conformations, represents the vast majority of the sampled data (over 99%), whereas cluster B is observed less than 1% of the time. This suggests that a bridging Mg2þ ion contributes to stabilization of catalytically active conformations in the reactant simulations. This feature is even more pronounced in the dRT-Mg simulations (activated precursor state with Mg2þ).

5B depicts the 2D free-energy profile for the Mg2þ-binding mode during the phosphoryl transfer step. Comparing to the free-energy barrier in another 2D PMF profile for the general acid catalysis (Fig. 5C), we conclude that this phosphoryl step is rate controlling. To further refine the samplings in MD simulations, we generated a 1D PMF profile following the minimum free-energy reaction path (Fig. 5B). 4 kcal/mol. The minimum free-energy reaction path indicates that the position of the Mg2þ ion follows the negative charge along the phosphoryl transfer reaction coordinate, in order to provide electrostatic stabilization.

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. 1 Solvent/ion equilibration The following equilibration procedures (total 1 ns) were applied to the system prior to the production simulations in order to insure reasonable relaxation of the solvent and ion environment.

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