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How do metal ions direct ribozyme folding?

Natalia A. Denesyuk, D. Thirumalai
doi: https://doi.org/10.1101/037895
Natalia A. Denesyuk
1Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742
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D. Thirumalai
1Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, 20742
2Department of Chemistry and Biochemistry and Biophysics Program, University of Maryland, College Park, Maryland 20742
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  • For correspondence: thirum@umd.edu
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Abstract

Ribozymes, which carry out phosphoryl transfer reactions, often require Mg2+ ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner which is not fully understood. Here, we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg2+ concentrations, and are transiently stabilized by coordination of Mg2+ ions to specific nucleotides. However, competition for scarce Mg2+ and topological constraints arising from chain connectivity prevent complete folding of the ribozyme. A much higher Mg2+ concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg2+ is replaced by Ca2+ the ribozyme folds but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.

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Posted January 26, 2016.
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How do metal ions direct ribozyme folding?
Natalia A. Denesyuk, D. Thirumalai
bioRxiv 037895; doi: https://doi.org/10.1101/037895
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How do metal ions direct ribozyme folding?
Natalia A. Denesyuk, D. Thirumalai
bioRxiv 037895; doi: https://doi.org/10.1101/037895

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