Synchronized motion of interface residues for evaluating protein–RNA complex binding affinity: Application to aptamer‐mediated inhibition of TDP‐43 aggregates

FIGURE 1. Schematical representations of all the steps involved in the procedure to obtain a reliable reproduction of a biological complex composed by the TAR DNA‐binding protein 43 (TDP‐43) protein and RNA aptamers. (I) We generate a 3D structure of the RNA aptamer using SimRNA webserver. (II) We explore the RNA conformational space by molecular dynamics (MD) simulation of the RNA aptamer in water. (III) The conformational space is splitted into two parts, separating the elongated and close configurations. (IV) We carry out a principal components analysis (PCA), projecting the atomic coordinates obtained during the whole trajectory onto the two principal components. (V) The structures of the k cluster centroids of the elongated populations are finally processed through the web server HDOCK. (VI) Simulation of the protein–RNA complex, which are used to define two descriptors based on the dynamic behavior of the studied molecular system.

FIGURE 2. Analysis of the molecular dynamics of the protein–RNA molecular system. (a) Cartoon representation of the protein–RNA complex as obtained from the Nuclear magnetic resonance (NMR) experiment (PDB code: 4bs2). In particular, the RNA‐binding region is depicted in green, and the RNA molecule is represented in light red. (b) The gyration radius descriptor as a function of time is reported for both the RNA‐1 system (on the left) and the RNA‐6 system (on the right). (c) The root mean square deviation (RMSD) with respect to the initial configuration as a function of time is reported for both the RNA‐1 system (on the left) and the RNA‐6 system (on the right). The RMSD analysis is reported for the entire system (gray curve), protein‐binding site (green curve), and the RNA aptamer (light red curve). (d) The root mean square fluctuations (RMSF) descriptor for each residue is reported for both the RNA‐1 system (on the left) and the RNA‐6 system (on the right).

FIGURE 3. Analysis of the descriptor based on interface atom distance. (a) The Pearson correlation value was computed with variations in the distance threshold that defined the binding region. (b) A scatterplot shows the relationship between the theoretical descriptor D (distance) and the experimental K d value, which is associated with the distance threshold that yielded the highest Pearson correlation. The line on the plot represents the linear fit between the data points.

FIGURE 4. Analysis of the descriptor based on correlated motion of residues within the binding region. (a) We calculated the Pearson correlation value as the distance threshold defining the binding site varied. (b) A scatterplot was generated between the descriptor based on the covariance of residues within the binding site and the experimental K d value associated with the distance threshold producing the highest Pearson correlation. The line on the plot represents the linear fit between the data points.

FIGURE 5. Analysis of the synergistic motion between interface residues mediated for each residue. (a) Distribution of the average covariance values for each residue within the binding site of all protein–RNA systems. The gray area represents the region under the curve corresponding to positive covariance values (AUC = 0.68). (b) Average covariance for each residue, which was obtained by averaging the average covariance for each system across the six protein–RNA systems. Only the residues belonging to the binding site of all protein–RNA systems were selected. (c) Colormap of the average covariances for each residue within each protein–RNA complex. For each residue and each complex, the average covariance is displayed, obtained by averaging the covariance of each residue pair in which the residue is involved. The values have been normalized, ranging from a minimum of −1 to a maximum of +1.