RNP motifs are conserved on all 4 NCL RBDs but RBD-miRNA
interactions are driven primarily by RBD 3 and 4
An alignment of NCL RBDs with the hnRNP A1 shows the conservation of the
RNP motifs as well as the key residues that are involved in hnRNP
A1-RNA/DNA interactions in all 4 NCL RBDs (Fig 6A ). However,
our docking studies predict the RNP motifs of RBD3-4 are predominantly
involved in miRNA interactions (see docking results, Fig 4-6). The
aromatic and basic residues of RNP1 (K217, Y219, F221) of RBD3, RNP1
(K304, F306, F308) and RNP2 (F269) of RBD4 were the most frequently
predicted RBD residues at the RNA-protein interface (Fig 6B ).
Additionally, the linker region connecting RBD3 to RBD4 contains several
residues frequently predicted to be involved in NCL-miRNA interactions
(R255, N259, R261, Q263; not shown in the figure).
These results are corroborated by a predictive analysis based solely on
primary structure using the Catrapid algorithm that similarly suggests
RBD3, RBD4, and the linker region between RBD3-4 have the highest RNA
binding propensity for all tested miRNA molecules (Supporting
Figure S1 ). Additionally, we performed a control docking of NCL RBD1-4
with miR-155, a microRNA reported to be not affected by NCL [41].
Interestingly, this docking yields noisy and inconsistent results with
no clear selectivity for any particular RBD (Supporting Figure
S2 ), supporting the quality of our in silico prediction.
Similarly, results of the docking experiments with mutant RBD3-4 models
revealed that RNP motifs on RBD3 and 4 lose the specific recognition of
miRNA interactions observed in wild type NCL.