Aromatic and basic residues play a key role at the NCL
RBD3-4-miRNA interface
RNA-NCL docking scenarios of both RBD3-4 and RBD1-4 with miRNA models
highlight the role of some of the positively charged arginine residues
in β-2 (R291, R293) as well as the linker between β-2 and β-3 on RBD4
(R298) as these residues are consistently predicted to be involved in
nearly all of the docking scenarios analyzed. These basic residues form
salt bridges with the phosphate backbone of the various miRNAs.
Similarly, our results indicate that aromatic residues on β-1 (F269 in
RBD4) and β-3 (Y219 and F221 in RBD3 & F306 and F308 in RBD4) interact
with miRNA molecules through π- π stacking and π-anion interactions with
the nucleobases and the phosphate backbone, respectively. Importantly,
the docking analysis of RBD1-4 models align with those of RBD3-4 models
(Supporting Figure S3 ). Our results also show that residues on
RNP motifs from RBD1-2 are largely not involved in NCL RBD-miRNA
interactions, despite the similar functional profile of the RNP motifs.
A control docking analysis using only RBD1-2 yields noisy scenarios with
no clear trend (Supporting Figure S4 ), again reinforcing the
idea that NCL RBD3-4 preferentially interact with the miRNA under study.
Based on the docking results, we show that NCL-RBDs interact with
pri-miRNA nucleotides almost exclusively within the region that
corressponds to the mature miRNA molecule. In our results, NCL is
predicted to interact frequently with G-U pairs and kink turns
(Supporting Figure S5 ). Interactions were observed
predominantly at the major groove regions of the double stranded miRNA
molecules as these regions were more accessible when compared to the
minor groove regions.