Mechanism of Acetylcholinesterase Inhibition by Fasciculin:  A 5-ns Molecular Dynamics Simulation

Abstract

Our previous molecular dynamics simulation (10 ns) of mouse acetylcholinesterase (EC 3.1.1.7) revealed complex fluctuation of the enzyme active site gorge. Now we report a 5-ns simulation of acetylcholinesterase complexed with fasciculin 2. Fasciculin 2 binds to the gorge entrance of acetylcholinesterase with excellent complementarity and many polar and hydrophobic interactions. In this simulation of the protein-protein complex, where fasciculin 2 appears to sterically block access of ligands to the gorge, again we observe a two-peaked probability distribution of the gorge width. When fasciculin is present, the gorge width distribution is altered such that the gorge is more likely to be narrow. Moreover, there are large increases in the opening of alternative passages, namely, the side door (near Thr 75) and the back door (near Tyr 449). Finally, the catalytic triad arrangement in the acetylcholinesterase active site is disrupted with fasciculin bound. These data support that, in addition to the steric obstruction seen in the crystal structure, fasciculin may inhibit acetylcholinesterase by combined allosteric and dynamical means. Additional data from these simulations can be found at http://mccammon.ucsd.edu/.

Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism

“…Previous studies (11,14,19) have shown that FAS2 inhibits AChE by sterically blocking the main gorge entrance and allosterically disrupting the catalytic triad based near the bottom of the 20-Å deep and narrow gorge. As demonstrated above, lowering the energy barrier for conformational conversions of FAS2 when it is bound to AChE is another example of the dynamic flexibility of the enzyme, particularly the long omega loop.…”

“…It is of interest to point out that the 20-ns MD trajectory of FAS2a͞AChE was initiated from a model structure that has FAS2a bound to AChE with a closed back-door passage [formed by AChE:W86, AChE:Y448, AChE:G449, and AChE:V451, an alternative channel leading to the active site of AChE (10,19,23)]. To detect the openings of this passage, a probe with the same radius as a water molecule was rolled around the surface of these residues; the back door is judged to be open if the solvent-accessible surface is continuous from the active site marked by AChE:E202 or S203 to the enzyme surface at this back-door passage (Fig.…”

Nucleotide-Mediated Conformational Changes of Monomeric Actin and Arp3 Studied by Molecular Dynamics Simulations

“…33 "Porcupine" plots of the first eigenvector for the Arp3 simulations show that the main dynamic mode of Arp3 is rotation of each domain about axes pointing out of the page and centered either in subdomain 2 or in subdomain 4 ( Fig. 6d).…”

Differential binding of bispyridinium oxime drugs with acetylcholinesterase

“…Because of excellent PAS complementarity, this situation can have serious implications. The drug molecule would then, instead of reactivating the OP-conjugated enzyme, clog the gorge entrance, inhibiting both entry and exit to the activesite, like other PAS inhibitors [8,15] . On the other hand, the Ortho-7 molecule is centrosymmetric and because of its relatively poor binding compatibility at the PAS is free from such a situation.…”

“…This fourth domain is over 20 Å away from the active site, located at the rim of the active gorge and has been called the peripheral anionic site (PAS) [6][7][8] and comprises aromatic residues Tyr 72, Tyr 124, Trp 286, and Tyr 341 and an acidic residue Asp 74. The four domains of the enzyme act together to produce the complex reaction dynamics [9][10][11][12][13][14][15][16][17] responsible for effective binding with ligands and eventual access to the catalytic triad domain.…”