Unraveling the Bivalent and Rapid Interactions Between a Multivalent RNA Recognition Motif and RNA: A Kinetic Approach

Abstract

The kinetics of the interaction between Musashi-1 (MSI1) and RNA have been characterized using surface plasmon resonance biosensor analysis. Truncated variants of human MSI1 encompassing the two homologous RNA recognition motifs (RRM1 and RRM2) in tandem (aa 1-200), and the two RRMs in isolation (aa 1-103 and aa 104-200, respectively) were produced. The proteins were injected over sensor surfaces with immobilized RNA, varying in sequence and length, and with one or two RRM binding motifs. The interactions of the individual RRMs with all RNA variants were well described by a 1:1 interaction model. The interaction between the MSI1 variant encompassing both RRM motifs was bivalent and rapid for all RNA variants. Due to difficulties in fitting this complex data using standard procedures, we devised a new method to quantify the interactions. It revealed that two RRMs in tandem resulted in a significantly longer residence time than a single RRM. It also showed that RNA with double UAG binding motifs and potential hairpin structures forms less stable bivalent complexes with MSI1 than the single UAG motif containing linear RNA. Substituting the UAG binding motif with a CAG sequence resulted in a reduction of the affinity of the individual RRMs, but for MSI1, this reduction was strongly enhanced, demonstrating the importance of bivalency for specificity. This study has provided new insights into the interaction between MSI1 and RNA and an understanding of how individual domains contribute to the overall interaction. It provides an explanation for why many RNA-binding proteins contain dual RRMs.

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Figure 1

Representative sensorgrams (red) for RRM1 and RRM2 interactions with four different RNA strands. Sensorgrams from regression analysis using the 1:1 model (Scheme 1) are shown in black. The concentration ranges for the interaction pairs were: RRM1-RNA-L1 1.9 to 500 nM; RRM2-RNA-L1 7.8 to 500 nM; RRM1 and RRM2 to RNA-L1a 15.65 to 500 nM; RRM1-RNA-HP2a 3.9 to 62.5 nM; RRM1-RNA-HP2b 7.8, 15.65, 31.25, and 62.5 nM; and RRM2 to RNA-HP2a and HP2b 1.9 to 125 nM. The interaction maps (IM) for RRM1-RNA-L1 and RRM2-RNA-L1 interactions are shown.

Figure 2

Typical sensorgrams (red) for an interaction between MSI1 (7.8 nM to 250 nM) and RNA-L1 immobilized to 82 RU. Black lines represent curves obtained after regression analysis of experimental data with (a) a 1:1 model (Scheme 1), (b) 1:1 induced fit model (Scheme 4), (c) bivalent analyte model (Scheme 3), and (d) heterogeneous ligand (1:2) model (Scheme 2). (e) InteractionMap analysis of the sensorgrams.

Figure 3

Sensorgrams depicting MSI1 interacting with RNA-L1 immobilized to different levels, representing different sensor surface densities, (a) 39 RUs, (b) 82 RUs, and (c) 245 RUs.

Figure 4

Sensorgram of the MSI1 interaction with RNA-L1 at 62.5 nM (dark gray), and results from applying heterogeneous ligand (1:2) model fit (in dotted orange line) depicting the rapid dissociating, monovalent, interaction (red), and slow dissociating interaction corresponding to bivalently bound MSI1 (blue).

Figure 5

Representative sensorgrams (red) for MSI1 interactions with four different RNA strands: (a) RNA-L1 (b) RNA-L1a, (c) RNA-HP2a, and (d) RNA-HP2b. For extracting information on the bivalent interaction process using the new method, all sensorgrams were fitted with a heterogeneous ligand (1:2) model (black). The concentration ranges for the following interactions were: MSI1 to RNA-L1 7.8 to 500 nM; MSI1 to RNA-HP2a and HP2b 1.9 to 500 nM; and MSI1-RNA-L1a 1.9 nM to 1 μM.