ABSTRACT The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable
feature of this enzyme. Here, we analyze conformational flexibility of the side chains of the 14 conserved aromatic
residues in the active-site gorge of Torpedo californica AChE based on the 47 three-dimensional crystal structures available for
the native enzyme, and for its complexes and conjugates, and on a 20-ns molecular dynamics (MD) trajectory of the native
enzyme. The degree of flexibility of these 14 aromatic side chains is diverse. Although the side-chain conformations of F330
and W279 are both very flexible, the side-chain conformations of F120, W233, W432, Y70, Y121, F288, F290 and F331 appear
to be fixed. Residues located on, or adjacent to, the V-loop (C67–C94), namely W84, Y130, Y442, and Y334, display different
flexibilities in the MD simulations and in the crystal structures. An important outcome of our study is that the majority of the sidechain
conformations observed in the 47 Torpedo californica AChE crystal structures are faithfully reproduced by the MD
simulation on the native enzyme. Thus, the protein can assume these conformations even in the absence of the ligand that
permitted their experimental detection. These observations are pertinent to structure-based drug design.