The small interfering RNAs (siRNA) or microRNAs (miRNA) incorporated into the RNA-induced silencing complex with the Argonaute (Ago) protein associates with target mRNAs through base-pairing, which leads to the cleavage or knockdown of the target mRNA. The seed region of the s(m)iRNA is crucial for target recognition. In this work, a molecular dynamic simulation was utilized to study the thermodynamics and kinetic properties of the third seed base binding to the target in the presence of the PIWI/MID domain of Ago. The results showed that in the presence of the PIWI/MID domain, the entropy and enthalpy changes for the association of the seed base with the target were smaller than those in the absence of protein. The binding affinity was increased due to the reduced entropy penalty, which resulted from the preorganization of the seed base into the A-helix form. In the presence of the protein, the association barrier resulting from the unfavorable entropy loss and the dissociation barrier coming from the destruction of hydrogen bonding and base-stacking interactions were lower than those in the absence of the protein. These results indicate that the seed region is crucial for fast recognition and association with the correct target.
Keywords: Argonaute protein; RNA interference; molecular dynamic simulation; seed.
© 2019 Wang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.