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

<p>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<sub>Free</sub>) and two ligand-bound conformations, which belonged to space groups P6<sub>1</sub>22 (BACE<sub>Bound1</sub>) and C222<sub>1</sub> (BACE<sub>Bound2</sub>), respectively and four parameters (distance between the flaps tip residue, Thr72 and Ser325, <i>d</i><sub>1</sub>; dihedral angle, <i>ϕ</i> (Thr72-Asp32-Asp228-Ser325); TriCα angles, <i>θ</i><sub>1</sub> (Thr72-Asp32-Ser325), and <i>θ</i><sub>2</sub> (Thr72-Asp228-Ser325)) were proposed to understand the change in dynamics of flap domain and the extent of flap opening and closing. Analysis of, <i>θ</i><sub>2</sub>, <i>d</i><sub>1</sub>, <i>θ</i><sub>1</sub> and <i>ϕ</i> confirmed that the BACE<sub>Free</sub> adopted semi-open, open and closed conformations with slight twisting during flap opening. However, BACE<sub>Bound1</sub> (P6122) showed an adaptation to open conformation due to lack of hydrogen bond interaction between the ligand and flap tip residue. A slight flap <i>twisting, ϕ</i> (<i>lateral twisting</i>) was observed for BACE<sub>Bound1</sub> during flap opening which correlates with the opening of BACE<sub>Free</sub>. Contradictory to the BACE<sub>Bound1</sub>, the BACE<sub>Bound2</sub> 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 <i>d</i><sub>1</sub>, <i>θ</i><sub>2</sub> and <i>ϕ</i> 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.</p>