Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex

Lizhe Zhu,Xuhui Huang,Xin Gao,Siqin Cao,Hanlun Jiang,Ilona Christy Unarta

doi:10.1038/s42003-021-02822-7

Abstract

Despite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo2). Interestingly, we found that the slowest mode of motion therein is not the gRNA-target base-pairing, but the coordination of the target phosphate groups with a set of positively charged residues of hAgo2. Moreover, the ability of Helix-7 to approach the PIWI and MID domains was found to reduce the effective volume accessible to the target mRNA and therefore facilitate both the backbone coordination and base-pair formation. Further mutant simulations revealed that alanine mutation of the D358 residue on Helix-7 enhanced a trap state to slow down the loading of target mRNA. Similar trap state was also observed when wobble pairs were introduced in g6 and g7, indicating the role of Helix-7 in suppressing non-canonical base-paring. Our study pointed to a general mechanism for mRNA recognition by eukaryotic Agos and demonstrated the promise of qMSM in investigating complex conformational changes of biomolecular systems.

Highlights

IntroductionThe molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive
Despite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive
We recently developed the quasi-Markov state model (MSM) method based on the generalized master equation formalism, which encodes non-Markovian dynamics into memory kernel functions63. quasi-Markov State Model (qMSM) has been applied to the study of bacterial RNA-polymerase[64] and provides a promising approach to study the conformational changes during the RNA-induced silencing complex (RISC)-mRNA recognition

Summary

Introduction

The molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo[2]). Since the lag-time (Δt) in an MSM must be long enough to allow Markovian interstate transitions, the estimation of transition probabilities in MSMs of the slow RISCmRNA recognition could still be limited by the upper bound in the affordable length of the MD simulations To address this issue, we recently developed the quasi-MSM (qMSM) method based on the generalized master equation formalism, which encodes non-Markovian dynamics into memory kernel functions.

Methods

Results

Conclusion