Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase

A 10-ns molecular dynamics simulation of mouse acetylcholinesterase was ana lyzed, with special attention paid to the fluctuation in the width of the g orge and opening events of the back door. The trajectory was first verified to ensure its stability. We defined the gorge proper radius as the measure for the extent of gorge opening. We developed an expression of an inter-at om distance representative of the gorge proper radius in terms of projectio ns on the principal components. This revealed the fact that collective moti ons of many scales contribute to the opening behavior of the gorge. Covaria nce and correlation results identified the motions of the protein backbone as the gorge opens. In the back-door region, side-chain dihedral angles tha t define the opening were identified.