The Dynamic Basis for Signal Propagation in Human Pin1-WW Simon Olsson, Dean Strotz, Beat Vögeli, Roland Riek, Andrea Cavalli  Structure  Volume 24, Issue 9, Pages 1464-1475 (September 2016) DOI: 10.1016/j.str.2016.06.013 Copyright © 2016 Elsevier Ltd Terms and Conditions

Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 Schematic Illustration of Human Pin1 The binding loop (loop 1) of Pin1-WW is highlighted in magenta sticks, loop 2 in cyan sticks, and the conserved prolines are colored orange. The residues important for catalysis and binding in the PPIase domain are highlighted with green sticks and the WW domain interaction surface is highlighted with gray sticks. The flexible interdomain linker is red. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Summary of Generated Ensembles at 278 K and 303 K Free-energy landscapes at (A) 278 K and (B) 303 K and cluster populations as a function of temperature in the REs (E). Cluster centroids are shown with upward pointing red triangles for clusters that have a higher population in the RE compared with the CE, and a downward pointing triangle for the clusters having a lower population. The native and near-native clusters are red triangles annotated with N and NN, respectively. The unfolded clusters are black triangles annotated with U. Renderings of conformational changes in loop 1 (residues 17–20) (C) and the topological reorientation of the N and C termini (D) are shown for ten random conformations from each cluster. The native cluster is purple and the near-native cluster is teal. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 ϕ,ψ Torsion Angle Distributions of Loop 1 in the Near-Native and Native States Scatter points of ϕ,ψ torsion pairs in native (black) and near-native (cyan) states identified by cluster analysis. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Linearly Correlated Motions in Pin1-WW, S18N/W34F Native (A) and near-native (B) conformational states at 278 K identified using cluster analysis. Correlation maps were computed using THESEUS (Theobald and Wuttke, 2006). Secondary structure is shown on residue axes: black lines are loop, turn, and coil regions, and blue blocks are β strands. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 5 Residue-Wise eNOE Violations of Different Models of Pin1-WW, S18N/W34F Violations (root-mean-square deviation [RMSD] from the experimental value) of bidirectional (A and B) and unidirectional (C and D) eNOEs at 278 K and 303 K, respectively. Comparison of violations in canonical and reweighed ensembles (CE and RE, respectively) and the two major conformational clusters identified (native and near native). CE and RE include all clusters (native, near native, and unfolded). Secondary structure is shown on the residue axes: black lines are loop, turn, and coil regions, and blue blocks are β strands. RMSD violations of 0.1–0.2 s−1 translate into distance errors of approximately 0.3–0.4 Å. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 6 Chemical Shift Variability in WT and S18N/W34F Simulations of Pin1-WW Comparison 15N chemical shift differences (|ΔωN,NN| in ppm) back computed using the S18N/W34F simulation (black) and chemical shift variances (|ΦN-NN| in ppm2) back computed using WT simulation (blue) at 278 K. Experimental value for Arg17, 2.5 ± 0.2 ppm (Peng et al., 2007). Chemical shifts back computed using CamShift (Kohlhoff et al., 2009; Fu et al., 2014). Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 7 Changes in Backbone Dihedral Angles upon Ligand Binding in Pin1-WW Histograms of representative backbone dihedral angles in the bound and unbound ensembles generated using WT simulation and previously published data (Wintjens et al., 2001). (A) ϕ angle of residue 17, (B) ψ angle of residue 18, both located in the binding loop. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 8 Comparison of Two Classes of Pin1 Binding Motifs (A and B) Logo plots of (A) binding motifs in Pin1 ligands with only one binding motif and (B) binding motifs in ligands with at least one binding motif. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 9 A Model of Differential Interdomain Contact Propensity in Pin1 with the WW Domain in the Native and Near-Native States The PPIase domain is red while the WW domain is purple in the native state and teal in the near-native state. The double harpoon represents a slow exchange between the two topologies of the WW domain. Fluctuations in the interdomain distance are represented by multiple states of WW domain, with their transparency as qualitative representation of state probability. The exchange rate between these states is fast compared with the interconversion of the near-native and native topologies. The average shortest distance between the interaction sites of the WW and PPIase domains r¯ (±SD) are shown for both states. Structure 2016 24, 1464-1475DOI: (10.1016/j.str.2016.06.013) Copyright © 2016 Elsevier Ltd Terms and Conditions