Fig. 5. Dynamics of the catalytic Asp257–Asp385, large hydrophilic loop 1 (HL1) and PAL motif. Left panel: γ-secretase–C83 complex and right panel: γ-secretase–Notch100 complex. (A) Orientation and Cα–Cα distance between the catalytic aspartates in γ-secretase–C83 compared to the experimental 6IYC. (B) Orientation and Cα–Cα distance between the aspartates in γ-secretase–Notch100 compared to 6IDF (blue: simulation 1, purple: simulation 2 and cyan: simulation 3). (C) Dynamics of the Cα–Cα distance between Asp257 and Asp385 in γ-Secretase–C83. (D) Dynamics of the Cα–Cα distance between Asp257 and Asp385 in γ-secretase–Notch100. The magenta line displays the experimental distance. (E) Minimum distance between the terminal residues of HL1 in γ-secretase–C83. (F) Minimum distance between the terminal residues of HL1 in γ-secretase–Notch100. (G) Minimum distance between the terminal PAL residues (Pro433 and Leu435) in γ-secretase–C83. (H) Minimum distance between Pro433 and Leu435 in γ-secretase–Notch100.