Structural Dynamics of Human Argonaute2 and Its Interaction with siRNAs Designed to Target Mutant tdp43

Abstract

The human Argonaute2 protein (Ago2) is a key player in RNA interference pathway and small RNA recognition by Ago2 is the crucial step in siRNA mediated gene silencing mechanism. The present study highlights the structural and functional dynamics of human Ago2 and the interaction mechanism of Ago2 with a set of seven siRNAs for the first time. The human Ago2 protein adopts two conformations such as “open” and “close” during the simulation of 25 ns. One of the domains named as PAZ, which is responsible for anchoring the 3′-end of siRNA guide strand, is observed as a highly flexible region. The interaction between Ago2 and siRNA, analyzed using a set of siRNAs (targeting at positions 128, 251, 341, 383, 537, 1113, and 1115 of mRNA) designed to target tdp43 mutants causing Amyotrophic Lateral Sclerosis (ALS) disease, revealed the stable and strong recognition of siRNA by the Ago2 protein during dynamics. Among the studied siRNAs, the siRNA341 is identified as a potent siRNA to recognize Ago2 and hence could be used further as a possible siRNA candidate to target the mutant tdp43 protein for the treatment of ALS patients.

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

“…Computer simulation of the structural and functional dynamics of human Ago2 and the interaction mechanism with siRNAs confirmed that Ago2 adopts two conformations such as "open" and "close" and the PAZ is a highly flexible region. (Bhandare and Ramaswamy, 2016). Models of miRNA-loaded Argonautes imply that Argonautes adopt variable conformations at distinct target sites that generate distorted, imperfect miRNA-target duplexes where structural distortions are better tolerated in solvent-exposed seed and 3'-end regions than in the central duplex region (Gan and Gunsalus, 2015).…”

A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2

“…TYR529, LYS533 residues of MID domain interacted with first U/A of the siRNA which is also reported by others [ 68 ]. Some residues that interacted with all Cluster 1 siRNAs such ARG277, ARG315, THR526, TYR529, LYS533, LYS566, THR759, ARG812 are previously reported to form interactions with other siRNA as well [ 68 , 69 ]. (See Fig.…”

“…Previously reported interactive residues of Ago2 such as ARG635, ARG710, ARG792 interact with all eight siRNAs [ 68 , 69 ]. Other reported residues do not encapsulate any particular cluster e.g.…”

“…ARG635, ARG710, ARG792 interacts with n7, g15, g21, g22, g44, g46, g59, g70 whereas ARG761, TYR804 interacts with the aforementioned siRNAs except g21. Table 4 contains previously reported [ 68 , 69 ] protein residues involved in siRNA-Ago2 interactions that also participated in the interaction with siRNAs of the current study.…”

Plasma and Liver Protein Binding ofN-Acetylgalactosamine–Conjugated Small Interfering RNA

“…siRNA-X is highly efficacious, eliciting greater than 80% target mRNA and protein knockdown over at least three months after a single 3-mg/kg dose in nonhuman primates (manuscript in preparation). Numerous chemical modifications and ligands used in the current generation of oligonucleotide therapeuticsnamely, ASO therapeutics-have been demonstrated to alter the extent of protein binding (Wilce et al, 2012;Geary et al, 2015;Bhandare and Ramaswamy, 2016;Juliano, 2016;Schirle et al, 2016;Bailey et al, 2017;Gaus et al, 2018). To understand how RNA modifications and ligand conjugation affect siRNA PPB specifically, we investigated the effects of PS, 29-OMe, 29-F, GalNAc, and biotin on f u,plasma .…”