Flexibility of Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase: X-ray vs MD

¹ Weizmann Institute of Science
² University of California, Los Angeles
³ Institute de Biologie Structurale
⁴ Shanghai Institute of Material Medica
⁵ University of Maryland Biotechnology Institute

^* To whom correspondence should be addressed. E-mail: joel.sussman{at}weizmann.ac.il.

Submitted on January 16, 2008
Revised on February 6, 2008
Accepted on 31 March 2008

	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. While those 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 -loop (C67-C94), viz. W84, Y130, Y442, and Y334, display different flexibilities in the MD simulations and in the crystal structures. An important outcome of our study is the fact that the majority of the side-chain conformations observed in the 47 TcAChE crystal structures are faithfully reproduced by the MD simulation of the native enzyme, showing that they can occur even in the absence of the ligand which permitted their experimental detection. These observations are pertinent to structure-based drug design.

Key Words: Acetylcholinesterase, Active-site gorge, Aromatic residues, Crystal structures, Molecular dynamics simulations, Side-chain conformation flexibility