Catalytic RNA, Volume 120 by Garrett A. Soukup

By Garrett A. Soukup

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

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88. 66). 5 for clusters A and B, respectively. Cluster B (not in-line conformation) is the dominate population occurring 76% of the time. Cluster A (in-line conformation) occurs 24% of the time. A striking feature that distinguishes cluster A from B is that it exhibits a very high degree of bridging ion character in addition to higher Naþ occupancy. 36 for cluster B. These results suggest that the bridging coordination patterns are highly correlated with formation of in-line conformations for both cases with and without Mg2þ ions.

133 The results indicate that the HHR has an electronegative cation-recruiting pocket in the active site that, upon threshold occupancy, stabilizes catalytically active in-line attack conformations via specific cation-binding patterns. These results provide a first glimpse into a possibly common feature that might be exploited by other ribozymes: the engineering of electrostatically pre-organized active sites that are able to recruit solvent components to facilitate catalysis. 1. Results MD simulations were set up to explore the metal ion-binding modes in eHHR and their relationship to structure and catalysis.

1:N7 and A9:O2p. 1:O2p of the scissile phosphate. Right: Coordination sites for Naþ in the HHR active site found in the RT-Na and dRT-Na simulations. Red numbers next to the coordination sites are the scores used to calculate the coordination index (see text). 1:N7 through a water molecule. 1:O2p. M3 involves direct binding to C17:O20 and is positioned toward the outside of the active site. 52 Tai-Sung Lee et al. coordination site, and NB is the number of ions which coordinate to at least two of the four coordination sites.

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