Document Type

Book Chapter

Department/Unit

Department of Physics

Title

Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis

Language

English

Abstract

Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg2 + ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns that involve either a bridging Mg2 + ion or multiple Na+ ions, one of which is also in a bridging coordination pattern. In the case of a single Mg2 + ion bound in the active site, the Mg2 + ion undergoes a migration that is coupled with deprotonation of the nucleophile (C17:O2'). As the reaction proceeds, the Mg2 + ion stabilizes the accumulating charge of the leaving group and significantly increases the general acid ability of G8:O2'. Further computational mutagenesis simulations suggest that the disruptions due to mutations may severely impact HHR catalysis at different stages of the reaction. Catalytic mechanisms supported by the simulation results are consistent with available structural and biochemical experiments, and together they advance our understanding of HHR catalysis. © 2013 Elsevier Inc.

Keywords

catalysis, combined QM/MM, enzyme, free energy, hammerhead ribozyme, mechanism, RNA, simulation

Publication Date

2013

Source Publication Title

Catalytic RNA

Editors

Soukup, Garrett A.

Volume

120

Start Page

25

End Page

91

Series Title

Progress in molecular biology and translational science

Publisher

Elsevier Science

DOI

10.1016/B978-0-12-381286-5.00002-0

ISBN (print)

9780123812865

ISBN (electronic)

9780123812872

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