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. 2017 Aug 1;8(8):5576-5584.
doi: 10.1039/c7sc00980a. Epub 2017 Jun 5.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach

Rodrigo Aguayo-Ortiz  1 , Cecilia Chávez-García  1 , John E Straub  2 , Laura Dominguez  1
Affiliations

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach

Rodrigo Aguayo-Ortiz et al. Chem Sci. .

Abstract

γ-Secretase is an intramembrane-cleaving aspartyl protease that plays an essential role in the processing of a variety of integral membrane proteins. Its role in the ultimate cleavage step in the processing of amyloid precursor protein to form amyloid-β (Aβ) peptide makes it an important therapeutic target in Alzheimer's disease research. Significant recent advances have been made in structural studies of this critical membrane protein complex. However, details of the mechanism of activation of the enzyme complex remain unclear. Using a multiscale computational modeling approach, combining multiple coarse-grained microsecond dynamic trajectories with all-atom models, the structure and two conformational states of the γ-secretase complex were evaluated. The transition between enzymatic state 1 and state 2 is shown to critically depend on the protonation states of the key catalytic residues Asp257 and Asp385 in the active site domain. The active site formation, related to our γ-secretase state 2, is observed to involve a concerted movement of four transmembrane helices from the catalytic subunit, resulting in the required localization of the catalytic residues. Global analysis of the structural ensemble of the enzyme complex was used to identify collective fluctuations important to the mechanism of substrate recognition and demonstrate that the corresponding fluctuations observed were uncorrelated with structural changes associated with enzyme activation. Overall, this computational study provides essential insight into the role of structure and dynamics in the activation and function of γ-secretase.

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Figures

Fig. 1
Fig. 1. (A) Depiction of the all atom model of γ-secretase, derived from the 5FN2 PDB structure, colored by its subunits: PS1, NCT, PEN-2, and APH-1A in green, blue, yellow, and orange, respectively. (B) Fluctuation analysis of 5FN2-derived atomistic model of γ-secretase in POPC bilayer (gray) color-coded by the normalized per-residue root mean square fluctuation (RMSF) from more flexible (red) to less flexible (blue). The analysis was performed during the last 500 ns of the simulation.
Fig. 2
Fig. 2. (A) Distribution of tilt angles of the PS1 TMs calculated for simulations of ; 5FN2 (color coded by TM helix number) and ; 5FN3 (in gray shade) and compared with TMs tilt angle ranges obtained from available experimental structures of γ-secretase (PDB IDs: ; 5A63, ; 4UIS, ; 5FN2, ; 5FN3, ; 5FN4 and ; 5FN5) (black bars). (B) Depiction of the 3D structure of γ-secretase (color coding PS1 TMs as (A)).
Fig. 3
Fig. 3. Simulated distributions of 5FN2 derived CG model in POPC bilayer projected onto (1) the distance between the catalytic residues (Asp257 and Asp385) and (2) the calculated TM2, TM6, TM7 and TM9 tilt angles in the (A) unprotonated and (B) Asp385 protonated states. The black triangles depict the values of ddAsp and T TM angles obtained from the experimental structures of γ-secretase (PDB IDs: ; 5A63, ; 4UIS, ; 5FN2, ; 5FN3, ; 5FN4 and ; 5FN5).
Fig. 4
Fig. 4. (A) Most representative structures of the state 1 (inactive) and state-2 (active) conformations of the PS1 subunit of γ-secretase obtained from all-atom MD simulations. The dotted red line represents the distance between the gamma carbons of Asp257 and Asp385. (B) Simulated distribution of both conformational state models projected onto the distance between the catalytic aspartic acid residues and the PS1 tilt angles of TM6 and TM7. The black triangles depict ddAsp distances and T TM angles obtained from the experimental structures of γ-secretase (PDB IDs: ; 5A63, ; 4UIS, ; 5FN2, ; 5FN3, ; 5FN4 and ; 5FN5). (C) Time evolution of hydrogen bonds between a coordinated water molecule and both catalytic aspartic residues through the last 50 ns of the state 1 and state 2 simulations.
Fig. 5
Fig. 5. Porcupine representation of the (A) “up/down” movement and (B) “left/right” rotation of the NCT ECD obtained from PCA.
Fig. 6
Fig. 6. Distribution of major axis length and density map representation of the compact, intermediate, and extended conformations of the γ-secretase complex derived from 50 1 μs CG replica simulations of the γ-secretase complex.
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