Dynamics of the acetylcholinesterase tetramer

¹ University of California, San Diego
² University of California - San Diego

^* To whom correspondence should be addressed. E-mail: abebe{at}mccammon.ucsd.edu.

Submitted on July 20, 2007
Revised on July 31, 2007
Accepted on 14 September 2007

	Abstract

Acetylcholinesterase rapidly hydrolyzes the neurotransmitter acetylcholine in cholinergic synapses, including the neuromuscular junction. The tetramer is the most important functional form of the enzyme. Two low-resolution crystal structures have been solved. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. These structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). A complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer. Normal mode analysis suggested that AChEt could exist in multiple conformations with subunits fluctuating relative to one another. Here, a multiscale simulation involving all-atom molecular dynamics and C-based coarse-grained Brownian dynamics simulations was carried out to investigate the large scale inter-subunit dynamics in AChEt. We sampled the ns-µs time scale motions and found that the tetramer indeed constitutes a dynamic assembly of monomers. The inter-subunit fluctuation is correlated with the occlusion of the PAS. Such motions of the subunits "gate" ligand-protein association. The gates are open more than 80% of the time on average, which suggests a small reduction of ligand-protein binding. Despite the limitations in the starting model and approximations inherent in coarse graining, these results are consistent with experiments which suggest that binding of a substrate to the PAS is only somewhat hindered by the association of the subunits.

Key Words: Active site occlusion, Coarse-grained Brownian dynamics, Molecular dynamics, inter-subunit fluctuation, multiscale simulation