Investigation of flap flexibility of β-secretase using molecular dynamic simulations

Flap motif and its dynamics were extensively reported in aspartate proteases, e.g. HIV proteases and plasmepsins. Herein, we report the first account of flap dynamics amongst different conformations of β-secretase using molecular dynamics simulation. Various parameters were proposed and a selected few were picked which could appropriately describe the flap motion. Three systems were studied, namely Free (BACE_Free) and two ligand-bound conformations, which belonged to space groups P6₁22 (BACE_Bound1) and C222₁ (BACE_Bound2), respectively and four parameters (distance between the flaps tip residue, Thr72 and Ser325, d₁; dihedral angle, ϕ (Thr72-Asp32-Asp228-Ser325); TriCα angles, θ₁ (Thr72-Asp32-Ser325), and θ₂ (Thr72-Asp228-Ser325)) were proposed to understand the change in dynamics of flap domain and the extent of flap opening and closing. Analysis of, θ₂, d₁, θ₁ and ϕ confirmed that the BACE_Free adopted semi-open, open and closed conformations with slight twisting during flap opening. However, BACE_Bound1 (P6122) showed an adaptation to open conformation due to lack of hydrogen bond interaction between the ligand and flap tip residue. A slight flap twisting, ϕ (lateral twisting) was observed for BACE_Bound1 during flap opening which correlates with the opening of BACE_Free. Contradictory to the BACE_Bound1, the BACE_Bound2 locked the flap in a closed conformation throughout the simulation due to formation of a stable hydrogen bond interaction between the flap tip residue and ligand. Analyses of all three systems highlight that d₁, θ₂ and ϕ can be precisely used to describe the extent of flap opening and closing concurrently with snapshots along the molecular dynamics trajectory across several conformations of β-secretase.