Figure 2
Salt concentration and poly-PR length affect the poly-PR–Kapβ binding behavior. (a) Normalized time-average number of contacts \({C}_{t}\), and binding probability \({P}_{\mathrm{b}}\) for the interaction between poly-PR with 7, 20, 35 and 50 repeat units and Kapβs at monovalent salt concentrations of \({C}_{\mathrm{salt}}=200\) mM (left panel) and \({C}_{\mathrm{salt}}=100\) mM (right panel). A linear correlation can be seen between the normalized \({C}_{t}\) and the negative NCPR of Kapβs for poly-PR with number of repeat units \(\ge\) 20. The dashed lines show linear fits for different lengths of poly-PR. The error bars are half of the standard deviation. The data for PR50 interaction with KAP120 and KAP114 were taken from39. (b) Sample snapshots showing the binding of PR7 and PR50 to Impβ1. In each snapshot poly-PR is depicted in red and Impβ1 is depicted in light grey. (c) (Top panels) The structure of Impβ1 shown from a top view (left) along the superhelical axis and a side view (right). A- and B-helices of Impβ1 are highlighted with light blue and yellow tubes, respectively, using the Bendix plugin in VMD. The linkers that connect the A- and B-helices are shown in light grey. A-helices constitute the inner surface and B-helices constitute the other surface of Impβ1. See Table S4 for snapshots of the other Kapβs used in this study. (Bottom panels) The number of residues in each region of Impβ1 that make contact with poly-PR (\({N}_{\mathrm{contact}}\)) at \({C}_{\mathrm{salt}}=100\) plotted for PR7, PR20, PR35 and PR50 (for details see Sect. 2 of the SI). The results for other Kapβs are shown in Fig. S5. Poly-PR tend to make more contacts with the inner surface of Impβ1, i.e. B-helices. The electrostatic potential of Impβ1 shows negatively-charged regions (shown with an arrow) on the inner surface of Impβ1. The electrostatic surface potentials are obtained using PDB2PQR50 and plotted using the Surf representation in VMD on a red-white-blue map. Positive and negative surface potentials are denoted by blue and red, respectively. For better visualization, part of the electrostatic potential surface is depicted using a transparent surface. Electrostatic potentials for the other Kapβs are presented in Table S4.
