Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain elusive. In this talk, I will present a two-step mechanism for miRNA loading into human Ago-2 protein: selective binding followed by structural re-arrangement. To achieve this, we adopted computational approaches combining Markov State Models (MSMs), large-scale protein-RNA docking, and MD simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are featured by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations via a conformational selection model. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure.  Furthermore, we compared the molecular recognition mechanisms between human Ago-2 and a bacterium Ago system (TtAgo). We show that an induced-fit dominant mechanism for guide-strand loading in TtAgo, drastically different from the two-step mechanism for human Ago-2. Such a difference between TtAgo and human Ago-2 is found to mainly originate from the distinct rigidity of their L1-PAZ hinge.  Our results provide novel insights in Ago-miRNA recognition mechanisms and facilitate the rational design of the Ago systems as promising gene editing tools.<br/>

Elucidating molecular recognition mechanisms of miRNA loading into the Argonaute protein by Markov state models

254th National Meeting (2017)

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