title: A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus.
abstract: Argonaute proteins (Ago) are core components of the RNA Induced Silencing Complex (RISC) that load and utilize small guide nucleic acids to silence mRNAs or cleave foreign DNAs. Despite the essential role of Ago in gene regulation and defense against virus, the molecular mechanism of guide-strand loading into Ago remains unclear. We explore such a mechanism in the bacterium Thermus thermophilus Ago (TtAgo), via a computational approach combining molecular dynamics, bias-exchange metadynamics, and protein-DNA docking. We show that apo TtAgo adopts multiple closed states that are unable to accommodate guide-DNA. Conformations able to accommodate the guide are beyond the reach of thermal fluctuations from the closed states. These results suggest an induced-fit dominant mechanism for guide-strand loading in TtAgo, drastically different from the two-step mechanism for human Ago 2 (hAgo2) identified in our previous study. Such a difference between TtAgo and hAgo2 is found to mainly originate from the distinct rigidity of their L1-PAZ hinge. Further comparison among known Ago structures from various species indicates that the L1-PAZ hinge may be flexible in general for prokaryotic Ago's but rigid for eukaryotic Ago's.
authors.forename: Lizhe
authors.initials: L
authors.lastname: Zhu
authors.forename: Hanlun
authors.initials: H
authors.lastname: Jiang
authors.forename: Fu Kit
authors.initials: FK
authors.lastname: Sheong
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955-6900, Saudi Arabia.
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Cui
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal 23955-6900, Saudi Arabia.
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
authors.affiliation: Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, China.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Wang
authors.forename: Xuhui
authors.initials: X
authors.lastname: Huang
mesh_terms: D060565:Argonaute Proteins / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D016963:Thermus thermophilus / Q000737:chemistry*
chemical_list: D060565:Argonaute Proteins; D004247:DNA