Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.
To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) 'seed' region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 'hinge' and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs.
Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Zhen
Z
Xia
Peter
P
Clark
Tien
T
Huynh
Phillipe
P
Loher
Yue
Y
Zhao
Huang-Wen
HW
Chen
Pengyu
P
Ren
Isidore
I
Rigoutsos
Ruhong
R
Zhou
D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009154:Mutation; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D055550:Protein Stability; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics; D034743:RNA-Induced Silencing Complex / Q000737:chemistry*
D035683:MicroRNAs; D012333:RNA, Messenger; D034743:RNA-Induced Silencing Complex