Novel Insights into Guide RNA 5′-Nucleoside/Tide Binding by Human Argonaute 2

International Journal of Molecular Sciences

Munishikha Kalia²  Sarah Willkomm²  Jens Christian Claussen¹  Tobias Restle²  Alexandre M. J. J. Bonvin³ 

[1] Institute for Neuro- and Bioinformatics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany;Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany;;Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science—Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

关键词: RNAi;    MD;    enzyme kinetics;    pre-steady-state kinetics;    fluorescence spectroscopy;   

DOI  :  10.3390/ijms17010022

来源: mdpi

【 摘 要 】

The human Argonaute 2 (hAgo2) protein is a key player of RNA interference (RNAi). Upon complex formation with small non-coding RNAs, the protein initially interacts with the 5′-end of a given guide RNA through multiple interactions within the MID domain. This interaction has been reported to show a strong bias for U and A over C and G at the 5′-position. Performing molecular dynamics simulations of binary hAgo2/OH–guide–RNA complexes, we show that hAgo2 is a highly flexible protein capable of binding to guide strands with all four possible 5′-bases. Especially, in the case of C and G this is associated with rather large individual conformational rearrangements affecting the MID, PAZ and even the N-terminal domains to different degrees. Moreover, a 5′-G induces domain motions in the protein, which trigger a previously unreported interaction between the 5′-base and the L2 linker domain. Combining our in silico analyses with biochemical studies of recombinant hAgo2, we find that, contrary to previous observations, hAgo2 is capable of functionally accommodating guide strands regardless of the 5′-base.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland.