Intrinsically disordered regions facilitate Mlp1–Nab2 recognition in mRNA quality control

Figures

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  Figure 1.. Representative binding orientations for Mlp1-C:Nab2-N complex. The five docking solutions shown are those consistent with experimental evidence indicating a critical role for Phe73 in the interaction. Mlp1-C is shown in blue.

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  Figure 6.. Proposed regulatory role of Phe73 in mediating interactions between helix4 and helix5 of Nab2-N. Mlp1-C is shown in surface representation (transparent cyan) and Nab2-N is shown in yellow with key residues highlighted in pink. Only the two helices of Nab2-N that engage with Mlp1-C in the simulations are displayed. Panels (b) and (c) illustrate representative configurations of these helices prior to and following association with Mlp1-C.

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  Figure 2.. Interaction energies between Mlp1-C and Nab2-N for the five selected docking orientations after 10 ns of MD simulation following equilibration. Among the samples configurations, solution 1 exhibits a consistently stronger interaction energy relative to the other orientations.

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  Figure 3.. Interaction energy between Mlp1-C and Nab2-N during MD simulations following equilibration. The complex corresponding to docking solution 1 was simulated in wild-type and mutant forms (Nab2-Phe73 mutated to Ala). Each complex (wild-type/mutant) was simulated for 20 ns, with three independent repeats. Solid lines show the mean interaction energy across replicates, and shaded regions indicate variability. The wild-type complex exhibits approximately threefold stronger interaction energy than the mutant, supporting a substantial role of Nab2-Phe73 in this interaction.

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  Figure 4.. Interaction energy between Mlp1-C and Nab2-N in wild-type (upper) and mutant (lower) simulations during equilibration. Comparison of the two plots indicates that the wild-type complex undergoes a gradual energetic stabilization that is not observed in the mutant, resulting in a stronger interaction.

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  Figure 7.. Schematics of a plausible stepwise mechanism for the interaction between Nab2-N and Mlp1-C inferred from docking and MD simulations. a) Nab2-N approaches Mlp1-C as mRNA begins to export through the nuclear pore. b) Nab2-Phe73 forms hydrophobic contacts with residues on helix5 of Nab2-N, c) this interactions reduces the separation between the two helices of Nab2-N that engage with Mlp1-C, facilitating closer association with the flexible, intrinsically disordered region Mlp1-C, d) the coil at the end of Nab2-N can then reposition to form additional electrostatic contacts with Mlp1-C. Only the predicted disordered region of Mlp1-C is shown.

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  Figure 5.. Nab2-N (yellow) consists of five helices, two of which engage with Mlp1-C (cyan) in the simulations. Phe73 of Nab2 is located in the middle of helix4 and forms hydrophobic contacts with the residues on helix5, contributing to stabilization of the helix–helix interface.