Projects per year
Abstract
A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4 kcal·mol-1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity-pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.
Original language | English |
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Article number | gkad260 |
Pages (from-to) | 4508–4518 |
Number of pages | 11 |
Journal | Nucleic Acids Research |
Volume | 51 |
Issue number | 9 |
Early online date | 18 Apr 2023 |
DOIs | |
Publication status | Published - 22 May 2023 |
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Expanding the Chemical Range of RNA-mediated Catalysis: Structure and Mechanism
Lilley, D. (Investigator)
Engineering and Physical Sciences Research Council
1/04/23 → 31/03/26
Project: Research
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The Nucleic Acid Structure Research Group
Lilley, D. (Investigator)
1/01/16 → 31/12/22
Project: Research