Effects of the PIWI/MID domain of Argonaute protein on the association of miRNAi's seed base with the target

Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins

The four human Argonaute (AGO) proteins, critical in RNA interference and gene regulation, exhibit high sequence and structural similarity but differ functionally. We investigated the underexplored structural relationships of these paralogs through microsecond-scale molecular dynamics simulations. Our findings reveal that AGO proteins adopt similar, yet unsynchronized, open-close states. We observed similar and unique local conformations, interdomain distances and intramolecular interactions. Conformational differences at GW182/ZSWIM8 interaction sites and in catalytic/pseudo-catalytic tetrads were minimal. Tetrads display conserved movements, interacting with distant miRNA binding residues. We pinpointed long common protein subsequences with consistent molecular movement but varying solvent accessibility per AGO. We observed diverse conformational patterns at the post-transcriptional sites of the AGOs, except for AGO4. By combining simulation data with large datasets of experimental structures and AlphaFold's predictions, we identified proteins with genomic and proteomic similarities. Some of the identified proteins operate in the mitosis pathway, sharing mitosis-related interactors and miRNA targets. Additionally, we suggest that AGOs interact with a mitosis initiator, zinc ion, by predicting potential binding sites and detecting structurally similar proteins with the same function. These findings further advance our understanding for the human AGO protein family and their role in central cellular processes.

Role of Argonaute proteins in RNAi pathway in Plutella xylostella: A review

Argonaute (Ago) proteins act as key elements in RNA interference (RNAi) pathway, orchestrating the intricate machinery of gene regulation within eukaryotic cells. Within the RNAi pathway, small RNA molecules, including microRNA (miRNA), small interfering RNA (siRNA), and PIWI-interacting RNA (piRNA), collaborate with Ago family member proteins such as Ago1, Ago2, and Ago3 to form the RNA-induced silencing complex (RISC). This RISC complex, in turn, either cleaves the target mRNA or inhibits the process of protein translation. The precise contributions of Ago proteins have been well-established in numerous animals and plants, although they still remain unclear in some insect species. This review aims to shed light on the specific roles played by Ago proteins within the RNAi mechanism in a destructive lepidopteran pest, the diamondback moth (Plutella xylostella). Furthermore, we explore the potential of double-stranded RNA (dsRNA)-mediated RNAi as a robust genetic tool in pest management strategies. Through an in-depth examination of Ago proteins and dsRNA-mediated RNAi, this review seeks to contribute to our understanding of innovative approaches for controlling this pest and potentially other insect species of agricultural significance.

Effect of Cas9 Protein on the Seed-Target Base Pair of the sgRNA/DNA Hybrid Duplex

CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated protein (Cas9) has been widely used for gene editing. Not all guide RNAs can cleave the DNA efficiently remains a major challenge to CRISPR/Cas9-mediated genome engineering. Therefore, understanding how the Cas9 complex successfully and efficiently identifies specific functional targets through base-pairing has great implications for such applications. The 10-nt seed sequence at the 3' end of the guide RNA is critical to target recognition and cleavage. Here, through stretching molecular dynamics simulation, we studied the thermodynamics and kinetics of the binding-dissociation process of the seed base and the target DNA base with the Cas9 protein. The results showed that in the presence of Cas9 protein, the enthalpy change and entropy change in binding-dissociation of the seed base with the target are smaller than those without the Cas9 protein. The reduction of entropy penalty upon association with the protein resulted from the pre-organization of the seed base in an A-form helix, and the reduction of enthalpy change was due to the electrostatic attraction of the positively charged channel with the negative target DNA. The binding barrier coming from the entropy loss and the dissociation barrier resulting from the destruction of the base pair in the presence of Cas9 protein were lower than those without protein, which indicates that the seed region is crucial for efficiently searching the correct target by accelerating the binding rate and dissociating fast from the wrong target.

Mechanistic Insights into the Protection Effect of Argonaute-RNA Complex on the HCV Genome

While host miRNA usually plays an antiviral role, the relentless tides of viral evolution have carved out a mechanism to recruit host miRNA as a viral protector. By complementing miR-122 at the 5' end of the genome, the hepatitis C virus (HCV) gene can form a complex with Argonaute 2 (Ago2) protein to protect the 5' end of HCV RNA from exonucleolytic attacks. Experiments showed that the disruption of the stem-loop 1(SL1) structure and the 9th nucleotide (T9) of HCV site 1 RNA could enhance the affinity of the Ago2 protein to the HCV site 1 RNA (target RNA). However, the underlying mechanism of how the conformation and dynamics of the Ago2: miRNA: target RNA complex is affected by the SL1 and T9 remains unclear. To address this, we performed large-scale molecular dynamics simulations on the AGO2-miRNA complex binding with the WT target, T9-abasic target and SL1-disruption target, respectively. The results revealed that the T9 and SL1 structures could induce the departing motion of the PAZ, PIWI and N domains, propping up the mouth of the central groove which accommodates the target RNA, causing the instability of the target RNA and disrupting the Ago2 binding. The coordinated motion among the PAZ, PIWI and N domains were also weakened by the T9 and SL1 structures. Moreover, we proposed a new model wherein the Ago2 protein could adopt a more constraint conformation with the proximity and more correlated motions of the PAZ, N and PIWI domains to protect the target RNA from dissociation. These findings reveal the mechanism of the Ago2-miRNA complex's protective effect on the HCV genome at the atomic level, which will offer guidance for the design of drugs to confront the protection effect and engineering of Ago2 as a gene-regulation tool.

Salt effect on thermodynamics and kinetics of a single RNA base pair

Due to the polyanionic nature of RNAs, the structural folding of RNAs are sensitive to solution salt conditions, while there is still lack of a deep understanding of the salt effect on the thermodynamics and kinetics of RNAs at a single base-pair level. In this work, the thermodynamic and the kinetic parameters for the base-pair AU closing/opening at different salt concentrations were calculated by 3-µsec all-atom molecular dynamics (MD) simulations at different temperatures. It was found that for the base-pair formation, the enthalpy change [Formula: see text] is nearly independent of salt concentration, while the entropy change [Formula: see text] exhibits a linear dependence on the logarithm of salt concentration, verifying the empirical assumption based on thermodynamic experiments. Our analyses revealed that such salt concentration dependence of the entropy change mainly results from the dependence of ion translational entropy change for the base pair closing/opening on salt concentration. Furthermore, the closing rate increases with the increasing of salt concentration, while the opening rate is nearly independent of salt concentration. Additionally, our analyses revealed that the free energy surface for describing the base-pair opening and closing dynamics becomes more rugged with the decrease of salt concentration.